From 028d7d02f9da9b5b507b447e0f4415a4d6c10a85 Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Tue, 17 Sep 2024 14:48:02 -0400 Subject: [PATCH 01/38] Refactor GFF3 parser to avoid returning internal _linehash variable (#4569) --- .../__snapshots__/Gff3Adapter.test.ts.snap | 20 +- .../Gff3TabixAdapter.test.ts.snap | 24 +- plugins/gff3/src/featureData.ts | 86 +- yarn.lock | 1141 +++++++++-------- 4 files changed, 642 insertions(+), 629 deletions(-) diff --git a/plugins/gff3/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap b/plugins/gff3/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap index 9cf0cfdb27..058f21e430 100644 --- a/plugins/gff3/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap +++ b/plugins/gff3/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap @@ -3,26 +3,20 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = ` [ { - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 6079, "name": "ctgB", "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 0, "strand": undefined, + "subfeatures": [], "type": "contig", "uniqueId": "test-ctgB-0", }, { - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 1984, "name": "f07", @@ -30,17 +24,14 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 1658, "strand": 1, + "subfeatures": [], "type": "remark", "uniqueId": "test-ctgB-1", }, { - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 6130, "name": "f06", @@ -48,17 +39,14 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 3013, "strand": 1, + "subfeatures": [], "type": "remark", "uniqueId": "test-ctgB-2", }, { - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 5968, "name": "f05", @@ -66,10 +54,10 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 4714, "strand": -1, + "subfeatures": [], "type": "remark", "uniqueId": "test-ctgB-3", }, diff --git a/plugins/gff3/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap b/plugins/gff3/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap index 0fde584e19..90e9017181 100644 --- a/plugins/gff3/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap +++ b/plugins/gff3/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap @@ -3,28 +3,20 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = ` [ { - "_linehash": "794328", - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 6079, "name": "ctgB", "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 0, "strand": undefined, + "subfeatures": [], "type": "contig", "uniqueId": "test-offset-794328", }, { - "_linehash": "794371", - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 1984, "name": "f07", @@ -32,18 +24,14 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 1658, "strand": 1, + "subfeatures": [], "type": "remark", "uniqueId": "test-offset-794371", }, { - "_linehash": "794440", - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 6130, "name": "f06", @@ -51,18 +39,14 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 3013, "strand": 1, + "subfeatures": [], "type": "remark", "uniqueId": "test-offset-794440", }, { - "_linehash": "794514", - "attributes": undefined, - "child_features": undefined, - "data": undefined, "derived_features": [], "end": 5968, "name": "f05", @@ -70,10 +54,10 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla "phase": undefined, "refName": "ctgB", "score": undefined, - "seq_id": undefined, "source": "example", "start": 4714, "strand": -1, + "subfeatures": [], "type": "remark", "uniqueId": "test-offset-794514", }, diff --git a/plugins/gff3/src/featureData.ts b/plugins/gff3/src/featureData.ts index 20f4a3772f..e2b0f95470 100644 --- a/plugins/gff3/src/featureData.ts +++ b/plugins/gff3/src/featureData.ts @@ -1,21 +1,41 @@ import { GFF3FeatureLineWithRefs } from 'gff-nostream' -export function featureData(data: GFF3FeatureLineWithRefs) { - const f: Record = { ...data } - ;(f.start as number) -= 1 // convert to interbase - if (data.strand === '+') { - f.strand = 1 - } else if (data.strand === '-') { - f.strand = -1 - } else if (data.strand === '.') { - f.strand = 0 - } else { - f.strand = undefined - } - f.phase = data.phase === null ? undefined : Number(data.phase) - f.refName = data.seq_id - if (data.score === null) { - f.score = undefined +interface GFF3Feature { + start: number + end: number + strand?: number + type: string | null + source: string | null + refName: string + derived_features: unknown[] | null + phase?: number + score?: number + subfeatures: GFF3Feature[] | undefined + [key: string]: unknown +} + +export function featureData(data: GFF3FeatureLineWithRefs): GFF3Feature { + const { + end, + start, + child_features, + derived_features, + attributes, + type, + source, + phase, + seq_id, + score, + strand, + } = data + + let strand2: number | undefined + if (strand === '+') { + strand2 = 1 + } else if (strand === '-') { + strand2 = -1 + } else if (strand === '.') { + strand2 = 0 } const defaultFields = new Set([ @@ -28,7 +48,8 @@ export function featureData(data: GFF3FeatureLineWithRefs) { 'phase', 'strand', ]) - const dataAttributes = data.attributes || {} + const dataAttributes = attributes || {} + const resultAttributes = {} as Record for (const a of Object.keys(dataAttributes)) { let b = a.toLowerCase() if (defaultFields.has(b)) { @@ -36,29 +57,28 @@ export function featureData(data: GFF3FeatureLineWithRefs) { // reproduces behavior of NCList b += '2' } - if (dataAttributes[a]) { + if (dataAttributes[a] && a !== '_lineHash') { let attr: string | string[] | undefined = dataAttributes[a] if (Array.isArray(attr) && attr.length === 1) { ;[attr] = attr } - f[b] = attr + resultAttributes[b] = attr } } - f.refName = f.seq_id - // the SimpleFeature constructor takes care of recursively inflating - // subfeatures - // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition - if (data.child_features && data.child_features.length > 0) { - f.subfeatures = data.child_features.flatMap(childLocs => + return { + ...resultAttributes, + start: start! - 1, + end: end!, + strand: strand2, + type, + source, + refName: seq_id!, + derived_features, + phase: phase === null ? undefined : Number(phase), + score: score === null ? undefined : score, + subfeatures: child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)), - ) + ), } - - f.child_features = undefined - f.data = undefined - // delete f.derived_features - f.attributes = undefined - f.seq_id = undefined - return f } diff --git a/yarn.lock b/yarn.lock index 7ce63e62cb..94f1355b24 100644 --- a/yarn.lock +++ b/yarn.lock @@ -89,16 +89,16 @@ tslib "^2.6.2" "@aws-sdk/client-cloudfront@^3.645.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-cloudfront/-/client-cloudfront-3.650.0.tgz#cf0c982234b9450b8ed860a96adffeb8d8b7b016" - integrity sha512-gamewK+ZWCFp3RBtkPosLaN9+ktWYooZo9JMMllsdfiFS0U+NC/pVc/D4uNhQ7gDPaBJI5OkNGv63yL9b7w9WQ== + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-cloudfront/-/client-cloudfront-3.651.1.tgz#50f1efd0b2988e795b35c9c46005be79b5e1667c" + integrity sha512-M/sNmxm/rLvC+5qKiJhz6lI46tzwUz4m8yK23YoLsrKWNxJP2GPbY72DU3PUDfnti3HzsKxK37drYgIJI9Yc6Q== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/client-sso-oidc" "3.650.0" - "@aws-sdk/client-sts" "3.650.0" - "@aws-sdk/core" "3.649.0" - "@aws-sdk/credential-provider-node" "3.650.0" + "@aws-sdk/client-sso-oidc" "3.651.1" + "@aws-sdk/client-sts" "3.651.1" + "@aws-sdk/core" "3.651.1" + "@aws-sdk/credential-provider-node" "3.651.1" "@aws-sdk/middleware-host-header" "3.649.0" "@aws-sdk/middleware-logger" "3.649.0" "@aws-sdk/middleware-recursion-detection" "3.649.0" @@ -138,30 +138,30 @@ "@smithy/util-waiter" "^3.1.3" tslib "^2.6.2" -"@aws-sdk/client-s3@^3.645.0": - version "3.651.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.651.0.tgz#289c92c7f7c31733503eeb857c6a5f951e0d9335" - integrity sha512-37+kxxjnlOAUCb1aHpoLakW4XRG23HrkX8X3cEjxaFLQxorPUiMvfAYQEQQkYD5yggaG+5aM5GAhxkTUTqA5xw== +"@aws-sdk/client-s3@^3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-s3/-/client-s3-3.651.1.tgz#d90f0560ccbf1b1a39973820d79c245d54bbbdae" + integrity sha512-xNm+ixNRcotyrHgjUGGEyara6kCKgDdW2EVjHBZa5T+tbmtyqezwH3UzbSDZ6MlNoLhJMfR7ozuwYTIOARoBfA== dependencies: "@aws-crypto/sha1-browser" "5.2.0" "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/client-sso-oidc" "3.650.0" - "@aws-sdk/client-sts" "3.650.0" - "@aws-sdk/core" "3.649.0" - "@aws-sdk/credential-provider-node" "3.650.0" + "@aws-sdk/client-sso-oidc" "3.651.1" + "@aws-sdk/client-sts" "3.651.1" + "@aws-sdk/core" "3.651.1" + "@aws-sdk/credential-provider-node" "3.651.1" "@aws-sdk/middleware-bucket-endpoint" "3.649.0" "@aws-sdk/middleware-expect-continue" "3.649.0" - "@aws-sdk/middleware-flexible-checksums" "3.651.0" + "@aws-sdk/middleware-flexible-checksums" "3.651.1" "@aws-sdk/middleware-host-header" "3.649.0" "@aws-sdk/middleware-location-constraint" "3.649.0" "@aws-sdk/middleware-logger" "3.649.0" "@aws-sdk/middleware-recursion-detection" "3.649.0" - "@aws-sdk/middleware-sdk-s3" "3.649.0" + "@aws-sdk/middleware-sdk-s3" "3.651.1" "@aws-sdk/middleware-ssec" "3.649.0" "@aws-sdk/middleware-user-agent" "3.649.0" "@aws-sdk/region-config-resolver" "3.649.0" - "@aws-sdk/signature-v4-multi-region" "3.649.0" + "@aws-sdk/signature-v4-multi-region" "3.651.1" "@aws-sdk/types" "3.649.0" "@aws-sdk/util-endpoints" "3.649.0" "@aws-sdk/util-user-agent-browser" "3.649.0" @@ -202,15 +202,15 @@ "@smithy/util-waiter" "^3.1.3" tslib "^2.6.2" -"@aws-sdk/client-sso-oidc@3.650.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso-oidc/-/client-sso-oidc-3.650.0.tgz#7516b8a2f00ba3b1bdd59aafbbda0ddb66d0ab3f" - integrity sha512-6J7IS0f8ovhvbIAZaynOYP+jPX8344UlTjwHxjaXHgFvI8axu3+NslKtEEV5oHLhgzDvrKbinsu5lgE2n4Sqng== +"@aws-sdk/client-sso-oidc@3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso-oidc/-/client-sso-oidc-3.651.1.tgz#eade611662a4527b2f92cb2740fd0bac5815c195" + integrity sha512-PKwAyTJW8pgaPIXm708haIZWBAwNycs25yNcD7OQ3NLcmgGxvrx6bSlhPEGcvwdTYwQMJsdx8ls+khlYbLqTvQ== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/core" "3.649.0" - "@aws-sdk/credential-provider-node" "3.650.0" + "@aws-sdk/core" "3.651.1" + "@aws-sdk/credential-provider-node" "3.651.1" "@aws-sdk/middleware-host-header" "3.649.0" "@aws-sdk/middleware-logger" "3.649.0" "@aws-sdk/middleware-recursion-detection" "3.649.0" @@ -247,14 +247,14 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@aws-sdk/client-sso@3.650.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso/-/client-sso-3.650.0.tgz#03a02256bef9fa79ebd2791eb24cf950d7d268ea" - integrity sha512-YKm14gCMChD/jlCisFlsVqB8HJujR41bl4Fup2crHwNJxhD/9LTnzwMiVVlBqlXr41Sfa6fSxczX2AMP8NM14A== +"@aws-sdk/client-sso@3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-sso/-/client-sso-3.651.1.tgz#8477ff1126a2816ae84ad27350df7b389597be4b" + integrity sha512-Fm8PoMgiBKmmKrY6QQUGj/WW6eIiQqC1I0AiVXfO+Sqkmxcg3qex+CZBAYrTuIDnvnc/89f9N4mdL8V9DRn03Q== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/core" "3.649.0" + "@aws-sdk/core" "3.651.1" "@aws-sdk/middleware-host-header" "3.649.0" "@aws-sdk/middleware-logger" "3.649.0" "@aws-sdk/middleware-recursion-detection" "3.649.0" @@ -291,16 +291,16 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@aws-sdk/client-sts@3.650.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/client-sts/-/client-sts-3.650.0.tgz#b4e5aeb0c6b516cc4db6db587f5daa72ec4c4b33" - integrity sha512-ISK0ZQYA7O5/WYgslpWy956lUBudGC9d7eL0FFbiL0j50N80Gx3RUv22ezvZgxJWE0W3DqNr4CE19sPYn4Lw8g== +"@aws-sdk/client-sts@3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/client-sts/-/client-sts-3.651.1.tgz#c581e43a222f395004a111d566609b366ea4db43" + integrity sha512-4X2RqLqeDuVLk+Omt4X+h+Fa978Wn+zek/AM4HSPi4C5XzRBEFLRRtOQUvkETvIjbEwTYQhm0LdgzcBH4bUqIg== dependencies: "@aws-crypto/sha256-browser" "5.2.0" "@aws-crypto/sha256-js" "5.2.0" - "@aws-sdk/client-sso-oidc" "3.650.0" - "@aws-sdk/core" "3.649.0" - "@aws-sdk/credential-provider-node" "3.650.0" + "@aws-sdk/client-sso-oidc" "3.651.1" + "@aws-sdk/core" "3.651.1" + "@aws-sdk/credential-provider-node" "3.651.1" "@aws-sdk/middleware-host-header" "3.649.0" "@aws-sdk/middleware-logger" "3.649.0" "@aws-sdk/middleware-recursion-detection" "3.649.0" @@ -337,10 +337,10 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@aws-sdk/core@3.649.0": - version "3.649.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/core/-/core-3.649.0.tgz#8c2a375e3c2e937e2f699f38cbbe031882ce99de" - integrity sha512-dheG/X2y25RHE7K+TlS32kcy7TgDg1OpWV44BQRoE0OBPAWmFR1D1qjjTZ7WWrdqRPKzcnDj1qED8ncyncOX8g== +"@aws-sdk/core@3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/core/-/core-3.651.1.tgz#75208b46b4b450a58ae48812fef9279a038246ef" + integrity sha512-eqOq3W39K+5QTP5GAXtmP2s9B7hhM2pVz8OPe5tqob8o1xQgkwdgHerf3FoshO9bs0LDxassU/fUSz1wlwqfqg== dependencies: "@smithy/core" "^2.4.1" "@smithy/node-config-provider" "^3.1.5" @@ -378,15 +378,15 @@ "@smithy/util-stream" "^3.1.4" tslib "^2.6.2" -"@aws-sdk/credential-provider-ini@3.650.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-ini/-/credential-provider-ini-3.650.0.tgz#4fc98d0caf9c8427a3e6691344cdbe90db0b8fd2" - integrity sha512-x2M9buZxIsKuUbuDgkGHhAKYBpn0/rYdKlwuFuOhXyyAcnhvPj0lgNF2KE4ld/GF1mKr7FF/uV3G9lM6PFaYmA== +"@aws-sdk/credential-provider-ini@3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-ini/-/credential-provider-ini-3.651.1.tgz#09ee9abfd06c43ead021a1c051ef980292a796cc" + integrity sha512-yOzPC3GbwLZ8IYzke4fy70ievmunnBUni/MOXFE8c9kAIV+/RMC7IWx14nAAZm0gAcY+UtCXvBVZprFqmctfzA== dependencies: "@aws-sdk/credential-provider-env" "3.649.0" "@aws-sdk/credential-provider-http" "3.649.0" "@aws-sdk/credential-provider-process" "3.649.0" - "@aws-sdk/credential-provider-sso" "3.650.0" + "@aws-sdk/credential-provider-sso" "3.651.1" "@aws-sdk/credential-provider-web-identity" "3.649.0" "@aws-sdk/types" "3.649.0" "@smithy/credential-provider-imds" "^3.2.1" @@ -395,16 +395,16 @@ "@smithy/types" "^3.4.0" tslib "^2.6.2" -"@aws-sdk/credential-provider-node@3.650.0": - version "3.650.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-node/-/credential-provider-node-3.650.0.tgz#6a4d0793997976b9892600f130770913ae089cf0" - integrity sha512-uBra5YjzS/gWSekAogfqJfY6c+oKQkkou7Cjc4d/cpMNvQtF1IBdekJ7NaE1RfsDEz3uH1+Myd07YWZAJo/2Qw== +"@aws-sdk/credential-provider-node@3.651.1": + version "3.651.1" + resolved "https://registry.yarnpkg.com/@aws-sdk/credential-provider-node/-/credential-provider-node-3.651.1.tgz#bb45097e9f46d7a1251189611547e0a67ec600b6" + integrity sha512-QKA74Qs83FTUz3jS39kBuNbLAnm6cgDqomm7XS/BkYgtUq+1lI9WL97astNIuoYvumGIS58kuIa+I3ycOA4wgw== dependencies: "@aws-sdk/credential-provider-env" "3.649.0" "@aws-sdk/credential-provider-http" "3.649.0" - 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version "8.4.45" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.45.tgz#538d13d89a16ef71edbf75d895284ae06b79e603" - integrity sha512-7KTLTdzdZZYscUc65XmjFiB73vBhBfbPztCYdUNvlaso9PrzjzcmjqBPR0lNGkcVlcO4BjiO5rK/qNz+XAen1Q== + version "8.4.47" + resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.47.tgz#5bf6c9a010f3e724c503bf03ef7947dcb0fea365" + integrity sha512-56rxCq7G/XfB4EkXq9Egn5GCqugWvDFjafDOThIdMBsI15iqPqR5r15TfSr1YPYeEI19YeaXMCbY6u88Y76GLQ== dependencies: nanoid "^3.3.7" - picocolors "^1.0.1" - source-map-js "^1.2.0" + picocolors "^1.1.0" + source-map-js "^1.2.1" prelude-ls@^1.2.1: version "1.2.1" @@ -14761,7 +14782,7 @@ source-list-map@^2.0.1: resolved "https://registry.yarnpkg.com/source-list-map/-/source-list-map-2.0.1.tgz#3993bd873bfc48479cca9ea3a547835c7c154b34" integrity sha512-qnQ7gVMxGNxsiL4lEuJwe/To8UnK7fAnmbGEEH8RpLouuKbeEm0lhbQVFIrNSuB+G7tVrAlVsZgETT5nljf+Iw== -source-map-js@^1.0.1, source-map-js@^1.0.2, source-map-js@^1.2.0: +source-map-js@^1.0.1, source-map-js@^1.0.2, source-map-js@^1.2.1: version "1.2.1" resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.2.1.tgz#1ce5650fddd87abc099eda37dcff024c2667ae46" integrity sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA== @@ -14942,11 +14963,11 @@ statuses@2.0.1: integrity sha512-OpZ3zP+jT1PI7I8nemJX4AKmAX070ZkYPVWV/AaKTJl+tXCTGyVdC1a4SL8RUQYEwk/f34ZX8UTykN68FwrqAA== storybook@^8.0.0: - version "8.3.0" - resolved "https://registry.yarnpkg.com/storybook/-/storybook-8.3.0.tgz#172a5d5e415b83bcb08a3a670a2e6f34383dfea1" - integrity sha512-XKU+nem9OKX/juvJPwka1Q7DTpSbOe0IMp8ZyLQWorhFKpquJdUjryl7Z9GiFZyyTykCqH4ItQ7h8PaOmqVMOw== + version "8.3.1" + resolved "https://registry.yarnpkg.com/storybook/-/storybook-8.3.1.tgz#4f52975bb0b7895eb4ad8125b37c0b3bba33b555" + integrity sha512-CYqt5KOpaTgb8OczNo2+EtMi8YNDPi4vNVebVlLDOroWxyulb8I7MIOH9gALczcIOb+TZUArPztjoa8rkXTaDQ== dependencies: - "@storybook/core" "8.3.0" + "@storybook/core" "8.3.1" string-length@^4.0.1: version "4.0.2" @@ -15311,9 +15332,9 @@ terser-webpack-plugin@^5.2.5, terser-webpack-plugin@^5.3.1, terser-webpack-plugi terser "^5.26.0" terser@^5.10.0, terser@^5.26.0: - version "5.32.0" - resolved "https://registry.yarnpkg.com/terser/-/terser-5.32.0.tgz#ee811c0d2d6b741c1cc34a2bc5bcbfc1b5b1f96c" - integrity sha512-v3Gtw3IzpBJ0ugkxEX8U0W6+TnPKRRCWGh1jC/iM/e3Ki5+qvO1L1EAZ56bZasc64aXHwRHNIQEzm6//i5cemQ== + version "5.33.0" + resolved "https://registry.yarnpkg.com/terser/-/terser-5.33.0.tgz#8f9149538c7468ffcb1246cfec603c16720d2db1" + integrity sha512-JuPVaB7s1gdFKPKTelwUyRq5Sid2A3Gko2S0PncwdBq7kN9Ti9HPWDQ06MPsEDGsZeVESjKEnyGy68quBk1w6g== dependencies: "@jridgewell/source-map" "^0.3.3" acorn "^8.8.2" @@ -15681,13 +15702,13 @@ typedarray@^0.0.6: integrity sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA== typescript-eslint@^8.0.1: - version "8.5.0" - resolved "https://registry.yarnpkg.com/typescript-eslint/-/typescript-eslint-8.5.0.tgz#041f6c302d0e9a8e116a33d60b0bb19f34036dd7" - integrity sha512-uD+XxEoSIvqtm4KE97etm32Tn5MfaZWgWfMMREStLxR6JzvHkc2Tkj7zhTEK5XmtpTmKHNnG8Sot6qDfhHtR1Q== + version "8.6.0" + resolved "https://registry.yarnpkg.com/typescript-eslint/-/typescript-eslint-8.6.0.tgz#5f0b5e23b34385ef146e447616c1a0d6bd14bedb" + integrity sha512-eEhhlxCEpCd4helh3AO1hk0UP2MvbRi9CtIAJTVPQjuSXOOO2jsEacNi4UdcJzZJbeuVg1gMhtZ8UYb+NFYPrA== dependencies: - "@typescript-eslint/eslint-plugin" "8.5.0" - "@typescript-eslint/parser" "8.5.0" - "@typescript-eslint/utils" "8.5.0" + "@typescript-eslint/eslint-plugin" "8.6.0" + "@typescript-eslint/parser" "8.6.0" + "@typescript-eslint/utils" "8.6.0" "typescript@>=3 < 6", typescript@^5.1.3, typescript@^5.4.3, typescript@^5.5.0: version "5.6.2" From ba8fd4d8373a46c4dd4b5f8e9a2877e17ac88425 Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Wed, 18 Sep 2024 14:26:43 -0400 Subject: [PATCH 02/38] [skip ci] Add pif.gz option to synteny import form (#4573) --- .../ImportForm/ImportCustomTrack.tsx | 361 +++++++++-------- .../ImportForm/ImportCustomTrack.tsx | 363 ++++++++++-------- .../__snapshots__/jbrowseModel.test.ts.snap | 51 +++ test_data/volvox/config.json | 22 ++ test_data/volvox/volvox_ins.pif.gz | Bin 0 -> 192 bytes test_data/volvox/volvox_ins.pif.gz.tbi | Bin 0 -> 131 bytes yarn.lock | 203 +++++----- 7 files changed, 584 insertions(+), 416 deletions(-) create mode 100644 test_data/volvox/volvox_ins.pif.gz create mode 100644 test_data/volvox/volvox_ins.pif.gz.tbi diff --git a/plugins/dotplot-view/src/DotplotView/components/ImportForm/ImportCustomTrack.tsx b/plugins/dotplot-view/src/DotplotView/components/ImportForm/ImportCustomTrack.tsx index 814e075bfb..41e9f816c5 100644 --- a/plugins/dotplot-view/src/DotplotView/components/ImportForm/ImportCustomTrack.tsx +++ b/plugins/dotplot-view/src/DotplotView/components/ImportForm/ImportCustomTrack.tsx @@ -19,6 +19,7 @@ function getAdapter({ assembly1, assembly2, fileLocation, + indexFileLocation, bed1Location, bed2Location, }: { @@ -26,6 +27,7 @@ function getAdapter({ assembly1: string assembly2: string fileLocation?: FileLocation + indexFileLocation?: FileLocation bed1Location?: FileLocation bed2Location?: FileLocation }) { @@ -73,6 +75,13 @@ function getAdapter({ bed2Location, assemblyNames: [assembly1, assembly2], } + } else if (radioOption === '.pif.gz') { + return { + type: 'PairwiseIndexedPAFAdapter', + pifGzLocation: fileLocation, + index: { location: indexFileLocation }, + assemblyNames: [assembly1, assembly2], + } } else { throw new Error( `Unknown to detect type ${radioOption} from filename (select radio button to clarify)`, @@ -82,174 +91,206 @@ function getAdapter({ type Conf = SnapshotIn -const OpenTrack = observer( - ({ - assembly1, - assembly2, - setSessionTrackData, - }: { - sessionTrackData: Conf - assembly1: string - assembly2: string - setSessionTrackData: (arg: Conf) => void - }) => { - const [bed2Location, setBed2Location] = useState() - const [bed1Location, setBed1Location] = useState() - const [fileLocation, setFileLocation] = useState() - const [value, setValue] = useState('') - const [error, setError] = useState() - const fileName = getName(fileLocation) +const ImportCustomTrack = observer(function ({ + assembly1, + assembly2, + setSessionTrackData, +}: { + sessionTrackData: Conf + assembly1: string + assembly2: string + setSessionTrackData: (arg: Conf) => void +}) { + const [bed2Location, setBed2Location] = useState() + const [bed1Location, setBed1Location] = useState() + const [fileLocation, setFileLocation] = useState() + const [indexFileLocation, setIndexFileLocation] = useState() + const [value, setValue] = useState('') + const [error, setError] = useState() + const fileName = getName(fileLocation) - const radioOption = value || (fileName ? extName(stripGz(fileName)) : '') + const radioOption = value || (fileName ? extName(stripGz(fileName)) : '') - useEffect(() => { - try { - if (fileLocation) { - const fn = fileName ? basename(fileName) : 'MyTrack' - const trackId = `${fn}-${Date.now()}` - setError(undefined) + useEffect(() => { + try { + if (fileLocation) { + const fn = fileName ? basename(fileName) : 'MyTrack' + const trackId = `${fn}-${Date.now()}` + setError(undefined) - setSessionTrackData({ - trackId, - name: fn, - assemblyNames: [assembly2, assembly1], - type: 'SyntenyTrack', - adapter: getAdapter({ - radioOption, - assembly1, - assembly2, - fileLocation, - bed1Location, - bed2Location, - }), - }) - } - } catch (e) { - console.error(e) - setError(e) + setSessionTrackData({ + trackId, + name: fn, + assemblyNames: [assembly2, assembly1], + type: 'SyntenyTrack', + adapter: getAdapter({ + radioOption, + assembly1, + assembly2, + fileLocation, + indexFileLocation, + bed1Location, + bed2Location, + }), + }) } - }, [ - fileName, - assembly1, - assembly2, - bed1Location, - bed2Location, - fileLocation, - radioOption, - setSessionTrackData, - ]) - return ( - - {error ? : null} - - Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or - .anchors.simple (MCScan) file to view in the dotplot. These file types - can also be gzipped. The first assembly should be the query sequence - (e.g. left column of the PAF) and the second assembly should be the - target sequence (e.g. right column of the PAF) - - { - setValue(event.target.value) - }} - > - - - } label=".paf" /> - - - } label=".out" /> - - - } - label=".delta" - /> - - - } - label=".chain" - /> - - - } - label=".anchors" - /> - - - } - label=".anchors.simple" - /> - - - + } catch (e) { + console.error(e) + setError(e) + } + }, [ + fileName, + assembly1, + assembly2, + bed1Location, + bed2Location, + fileLocation, + indexFileLocation, + radioOption, + setSessionTrackData, + ]) + return ( + + {error ? : null} + + Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or + .anchors.simple (MCScan) file to view. These file types can also be + gzipped. The first assembly should be the query sequence (e.g. left + column of the PAF) and the second assembly should be the target sequence + (e.g. right column of the PAF) + + { + setValue(event.target.value) + }} + > - {value === '.anchors' || value === '.anchors.simple' ? ( -
-
- Open the {value} and .bed files for both genome assemblies - from the MCScan (Python version) pipeline{' '} - - (more info) - + } label=".paf" /> + + + } label=".out" /> + + + + } + label=".delta" + /> + + + } + label=".chain" + /> + + + } + label=".anchors" + /> + + + } + label=".anchors.simple" + /> + + + } + label=".pif.gz" + /> + + + + + + {value === '.anchors' || value === '.anchors.simple' ? ( +
+
+ Open the {value} and .bed files for both genome assemblies from + the MCScan (Python version) pipeline{' '} + + (more info) + +
+
+
+ { + setFileLocation(loc) + }} + />
-
-
- { - setFileLocation(loc) - }} - /> -
-
- { - setBed1Location(loc) - }} - /> -
-
- { - setBed2Location(loc) - }} - /> -
+
+ { + setBed1Location(loc) + }} + /> +
+
+ { + setBed2Location(loc) + }} + />
- ) : ( - { - setFileLocation(loc) - }} - /> - )} - +
+ ) : value === '.pif.gz' ? ( +
+
+ { + setFileLocation(loc) + }} + /> +
+
+ { + setIndexFileLocation(loc) + }} + /> +
+
+ ) : ( + { + setFileLocation(loc) + }} + /> + )} - - ) - }, -) + + + ) +}) -export default OpenTrack +export default ImportCustomTrack diff --git a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx index a17f83d529..41e9f816c5 100644 --- a/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx +++ b/plugins/linear-comparative-view/src/LinearSyntenyView/components/ImportForm/ImportCustomTrack.tsx @@ -12,13 +12,14 @@ import { ErrorMessage, FileSelector } from '@jbrowse/core/ui' import { FileLocation } from '@jbrowse/core/util/types' import { observer } from 'mobx-react' import { AnyConfigurationModel } from '@jbrowse/core/configuration' -import { extName, getName, stripGz, basename } from './util' +import { basename, extName, getName, stripGz } from './util' function getAdapter({ radioOption, assembly1, assembly2, fileLocation, + indexFileLocation, bed1Location, bed2Location, }: { @@ -26,6 +27,7 @@ function getAdapter({ assembly1: string assembly2: string fileLocation?: FileLocation + indexFileLocation?: FileLocation bed1Location?: FileLocation bed2Location?: FileLocation }) { @@ -73,6 +75,13 @@ function getAdapter({ bed2Location, assemblyNames: [assembly1, assembly2], } + } else if (radioOption === '.pif.gz') { + return { + type: 'PairwiseIndexedPAFAdapter', + pifGzLocation: fileLocation, + index: { location: indexFileLocation }, + assemblyNames: [assembly1, assembly2], + } } else { throw new Error( `Unknown to detect type ${radioOption} from filename (select radio button to clarify)`, @@ -82,174 +91,206 @@ function getAdapter({ type Conf = SnapshotIn -const OpenTrack = observer( - ({ - assembly1, - assembly2, - setSessionTrackData, - }: { - sessionTrackData: Conf - assembly1: string - assembly2: string - setSessionTrackData: (arg: Conf) => void - }) => { - const [bed2Location, setBed2Location] = useState() - const [bed1Location, setBed1Location] = useState() - const [fileLocation, setFileLocation] = useState() - const [value, setValue] = useState('') - const [error, setError] = useState() - const fileName = getName(fileLocation) +const ImportCustomTrack = observer(function ({ + assembly1, + assembly2, + setSessionTrackData, +}: { + sessionTrackData: Conf + assembly1: string + assembly2: string + setSessionTrackData: (arg: Conf) => void +}) { + const [bed2Location, setBed2Location] = useState() + const [bed1Location, setBed1Location] = useState() + const [fileLocation, setFileLocation] = useState() + const [indexFileLocation, setIndexFileLocation] = useState() + const [value, setValue] = useState('') + const [error, setError] = useState() + const fileName = getName(fileLocation) - const radioOption = value || (fileName ? extName(stripGz(fileName)) : '') + const radioOption = value || (fileName ? extName(stripGz(fileName)) : '') - useEffect(() => { - try { - if (fileLocation) { - const fn = fileName ? basename(fileName) : 'MyTrack' - const trackId = `${fn}-${Date.now()}` - setError(undefined) + useEffect(() => { + try { + if (fileLocation) { + const fn = fileName ? basename(fileName) : 'MyTrack' + const trackId = `${fn}-${Date.now()}` + setError(undefined) - setSessionTrackData({ - trackId, - name: fn, - assemblyNames: [assembly2, assembly1], - type: 'SyntenyTrack', - adapter: getAdapter({ - radioOption, - assembly1, - assembly2, - fileLocation, - bed1Location, - bed2Location, - }), - }) - } - } catch (e) { - console.error(e) - setError(e) + setSessionTrackData({ + trackId, + name: fn, + assemblyNames: [assembly2, assembly1], + type: 'SyntenyTrack', + adapter: getAdapter({ + radioOption, + assembly1, + assembly2, + fileLocation, + indexFileLocation, + bed1Location, + bed2Location, + }), + }) } - }, [ - fileName, - assembly1, - assembly2, - bed1Location, - bed2Location, - fileLocation, - radioOption, - setSessionTrackData, - ]) - return ( - - {error ? : null} - - Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or - .anchors.simple (MCScan) file to view in the dotplot. These file types - can also be gzipped. The first assembly should be the query sequence - (e.g. left column of the PAF) and the second assembly should be the - target sequence (e.g. right column of the PAF) - - { - setValue(event.target.value) - }} - > - - - } label=".paf" /> - - - } label=".out" /> - - - } - label=".delta" - /> - - - } - label=".chain" - /> - - - } - label=".anchors" - /> - - - } - label=".anchors.simple" - /> - - - + } catch (e) { + console.error(e) + setError(e) + } + }, [ + fileName, + assembly1, + assembly2, + bed1Location, + bed2Location, + fileLocation, + indexFileLocation, + radioOption, + setSessionTrackData, + ]) + return ( + + {error ? : null} + + Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or + .anchors.simple (MCScan) file to view. These file types can also be + gzipped. The first assembly should be the query sequence (e.g. left + column of the PAF) and the second assembly should be the target sequence + (e.g. right column of the PAF) + + { + setValue(event.target.value) + }} + > - {value === '.anchors' || value === '.anchors.simple' ? ( -
-
- Open the {value} and .bed files for both genome assemblies - from the MCScan (Python version) pipeline{' '} - - (more info) - + } label=".paf" /> + + + } label=".out" /> + + + + } + label=".delta" + /> + + + } + label=".chain" + /> + + + } + label=".anchors" + /> + + + } + label=".anchors.simple" + /> + + + } + label=".pif.gz" + /> + + + + + + {value === '.anchors' || value === '.anchors.simple' ? ( +
+
+ Open the {value} and .bed files for both genome assemblies from + the MCScan (Python version) pipeline{' '} + + (more info) + +
+
+
+ { + setFileLocation(loc) + }} + />
-
-
- { - setFileLocation(loc) - }} - /> -
-
- { - setBed1Location(loc) - }} - /> -
-
- { - setBed2Location(loc) - }} - /> -
+
+ { + setBed1Location(loc) + }} + /> +
+
+ { + setBed2Location(loc) + }} + />
- ) : ( - { - setFileLocation(loc) - }} - /> - )} - +
+ ) : value === '.pif.gz' ? ( +
+
+ { + setFileLocation(loc) + }} + /> +
+
+ { + setIndexFileLocation(loc) + }} + /> +
+
+ ) : ( + { + setFileLocation(loc) + }} + /> + )} - - ) - }, -) + + + ) +}) -export default OpenTrack +export default ImportCustomTrack diff --git a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap index 0f62f7bfdd..571ef18387 100644 --- a/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap +++ b/products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap @@ -4262,6 +4262,57 @@ exports[`JBrowse model creates with non-empty snapshot 1`] = ` "trackId": "volvox_bedpe", "type": "VariantTrack", }, + { + "adapter": { + "assemblyNames": [ + "volvox_ins", + "volvox", + ], + "index": { + "location": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox_ins.pif.gz.tbi", + }, + }, + "pifGzLocation": { + "internetAccountId": undefined, + "internetAccountPreAuthorization": undefined, + "locationType": "UriLocation", + "uri": "volvox_ins.pif.gz", + }, + "type": "PairwiseIndexedPAFAdapter", + }, + "assemblyNames": [ + "volvox_ins", + "volvox", + ], + "category": [ + "Synteny", + ], + "displays": [ + { + "displayId": "volvox_ins.pif-DotplotDisplay", + "type": "DotplotDisplay", + }, + { + "displayId": "volvox_ins.pif-LinearComparativeDisplay", + "type": "LinearComparativeDisplay", + }, + { + "displayId": "volvox_ins.pif-LinearSyntenyDisplay", + "type": "LinearSyntenyDisplay", + }, + { + "displayId": "volvox_ins.pif-LGVSyntenyDisplay", + "type": "LGVSyntenyDisplay", + }, + ], + "name": "volvox_ins.pif", + "trackId": "volvox_ins.pif", + "type": "SyntenyTrack", + }, ], } `; diff --git a/test_data/volvox/config.json b/test_data/volvox/config.json index 54074a496f..950f6b6c49 100644 --- a/test_data/volvox/config.json +++ b/test_data/volvox/config.json @@ -2180,6 +2180,28 @@ "displayId": "volvox_bedpe-LinearPairedArcDisplay" } ] + }, + { + "type": "SyntenyTrack", + "trackId": "volvox_ins.pif", + "name": "volvox_ins.pif", + "category": ["Synteny"], + "adapter": { + "type": "PairwiseIndexedPAFAdapter", + "pifGzLocation": { + "uri": "volvox_ins.pif.gz", + "locationType": "UriLocation" + }, + "index": { + "location": { + "uri": "volvox_ins.pif.gz.tbi", + "locationType": "UriLocation" + }, + "indexType": "TBI" + }, + "assemblyNames": ["volvox_ins", "volvox"] + }, + "assemblyNames": ["volvox_ins", "volvox"] } ], "plugins": [ diff --git a/test_data/volvox/volvox_ins.pif.gz b/test_data/volvox/volvox_ins.pif.gz new file mode 100644 index 0000000000000000000000000000000000000000..cb54fe8046c04326e70bc4bf7fbd3ef723ea53cf GIT binary patch literal 192 zcmb2|=3rp}f&Xj_PR>jWiy4mk@8)7M6j*aSUNGhQlRYWB8+u(`Hf-*#;<&d^?SH?g zo>A{6eXP&GbM|6bFCLI;aKHRq9d(q@M0>@^|+`8?0!Eq<+cf89q zgPp26CNm$3;F=|>G<~NJ@1tGY=I9rRMm_!7a(%B?;)KZ>Y1uWF8&i`#e!BijeEsqh&kyQb^&UuaG&j$mY9kVkW)Gy^l($shs%b>2>O literal 0 HcmV?d00001 diff --git a/test_data/volvox/volvox_ins.pif.gz.tbi b/test_data/volvox/volvox_ins.pif.gz.tbi new file mode 100644 index 0000000000000000000000000000000000000000..dbc7323ae1d4e6f9fb02312fed6ae4de7da0f33f GIT binary patch literal 131 zcmb2|=3rp}f&Xj_PR>jWX$;(jpHfni7#Q6YQW6r_lEf6k(i#}#6!d)bJj+uw7$+-i zo#(@ou+?A#n^(1OQbNKZrM@-O7_;mY8*=17.1.2 < 20": - version "19.7.3" - resolved "https://registry.yarnpkg.com/@nx/devkit/-/devkit-19.7.3.tgz#a5c37b13309dbe3490bab16197dcfdd1ddd4ce02" - integrity sha512-dIavuzfcMLCTa5uhd4R7HsxcFO0w9fHwG4wDg76wyBAbPGJlrR+9zg359hZ/SkXdguO6bMVmmQg/EXIvo6g69A== +"@nx/devkit@19.7.4", "@nx/devkit@>=17.1.2 < 20": + version "19.7.4" + resolved "https://registry.yarnpkg.com/@nx/devkit/-/devkit-19.7.4.tgz#49ed45f57696ecda3a420933cd8d77b7ce39ae89" + integrity sha512-n+iFVq6Jp1dyV3JAJp2xY2yo4fzC6ImO32qHJZ+2Aqbh3Ks+yYsfuGpdj6f0/2HfkFylPygJnxphWSu1UDXMug== dependencies: - "@nrwl/devkit" "19.7.3" + "@nrwl/devkit" "19.7.4" ejs "^3.1.7" enquirer "~2.3.6" ignore "^5.0.4" @@ -3187,55 +3200,55 @@ tslib "^2.3.0" yargs-parser "21.1.1" -"@nx/nx-darwin-arm64@19.7.3": - version "19.7.3" - 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"@jsonjoy.com/json-pack" "^1.0.3" "@jsonjoy.com/util" "^1.3.0" @@ -12507,13 +12520,13 @@ nwsapi@^2.2.12, nwsapi@^2.2.2: resolved "https://registry.yarnpkg.com/nwsapi/-/nwsapi-2.2.12.tgz#fb6af5c0ec35b27b4581eb3bbad34ec9e5c696f8" integrity sha512-qXDmcVlZV4XRtKFzddidpfVP4oMSGhga+xdMc25mv8kaLUHtgzCDhUxkrN8exkGdTlLNaXj7CV3GtON7zuGZ+w== -nx@19.7.3, "nx@>=17.1.2 < 20": - version "19.7.3" - resolved "https://registry.yarnpkg.com/nx/-/nx-19.7.3.tgz#ca76e9b9fcca9a61a1a65179daef1a3914121b0e" - integrity sha512-8F4CzKavSuOFv+uKVwXHc00Px0q40CWAYCW6NC5IgU3AMaJVumyHzgB8Sn+yfkaVgfVnZVqznOsyrbZUWuj/VA== +nx@19.7.4, "nx@>=17.1.2 < 20": + version "19.7.4" + resolved "https://registry.yarnpkg.com/nx/-/nx-19.7.4.tgz#5067c18ee0ba87d06f5ccc99bad45430600323ee" + integrity sha512-xvOUQp+jZHtXr7MYF8RdtY2fAz7vzPK58l3o73Wo4LpfFFULIPVF+f33TT1jyAQCez/tsDc9fBOSycr86df+5w== dependencies: "@napi-rs/wasm-runtime" "0.2.4" - "@nrwl/tao" "19.7.3" + "@nrwl/tao" "19.7.4" "@yarnpkg/lockfile" "^1.1.0" "@yarnpkg/parsers" "3.0.0-rc.46" "@zkochan/js-yaml" "0.0.7" @@ -12548,16 +12561,16 @@ nx@19.7.3, "nx@>=17.1.2 < 20": yargs "^17.6.2" yargs-parser "21.1.1" optionalDependencies: - "@nx/nx-darwin-arm64" "19.7.3" - "@nx/nx-darwin-x64" "19.7.3" - "@nx/nx-freebsd-x64" "19.7.3" - "@nx/nx-linux-arm-gnueabihf" "19.7.3" - "@nx/nx-linux-arm64-gnu" "19.7.3" - "@nx/nx-linux-arm64-musl" "19.7.3" - "@nx/nx-linux-x64-gnu" "19.7.3" - "@nx/nx-linux-x64-musl" "19.7.3" - "@nx/nx-win32-arm64-msvc" "19.7.3" - "@nx/nx-win32-x64-msvc" "19.7.3" + "@nx/nx-darwin-arm64" "19.7.4" + "@nx/nx-darwin-x64" "19.7.4" + "@nx/nx-freebsd-x64" "19.7.4" + "@nx/nx-linux-arm-gnueabihf" "19.7.4" + "@nx/nx-linux-arm64-gnu" "19.7.4" + "@nx/nx-linux-arm64-musl" "19.7.4" + "@nx/nx-linux-x64-gnu" "19.7.4" + "@nx/nx-linux-x64-musl" "19.7.4" + "@nx/nx-win32-arm64-msvc" "19.7.4" + "@nx/nx-win32-x64-msvc" "19.7.4" object-assign@^4, object-assign@^4.0.1, object-assign@^4.1.1: version "4.1.1" From 172ccebc81f6a661cd2ac2a53b0784ca9b15c53d Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Wed, 18 Sep 2024 14:28:20 -0400 Subject: [PATCH 03/38] Fix name indexing on desktop (#4572) --- .../TextIndexRpcMethod/TextIndexRpcMethod.ts | 21 +-- .../jbrowse-desktop/src/indexJobsModel.ts | 166 +++++++++++++++--- 2 files changed, 144 insertions(+), 43 deletions(-) diff --git a/plugins/text-indexing/src/TextIndexRpcMethod/TextIndexRpcMethod.ts b/plugins/text-indexing/src/TextIndexRpcMethod/TextIndexRpcMethod.ts index 37a389aebe..7577ccaa6e 100644 --- a/plugins/text-indexing/src/TextIndexRpcMethod/TextIndexRpcMethod.ts +++ b/plugins/text-indexing/src/TextIndexRpcMethod/TextIndexRpcMethod.ts @@ -20,10 +20,6 @@ export class TextIndexRpcMethod extends RpcMethodType { }, rpcDriverClassName: string, ) { - const deserializedArgs = await this.deserializeArguments( - args, - rpcDriverClassName, - ) const { tracks, outLocation, @@ -33,21 +29,18 @@ export class TextIndexRpcMethod extends RpcMethodType { indexType, signal, statusCallback, - } = deserializedArgs + } = await this.deserializeArguments(args, rpcDriverClassName) checkAbortSignal(signal) - const indexingParams = { - outLocation, + await indexTracks({ + outDir: outLocation, tracks, - exclude, - attributes, - assemblies, + featureTypesToExclude: exclude, + attributesToIndex: attributes, + assemblyNames: assemblies, indexType, statusCallback, signal, - } - await indexTracks(indexingParams) - statusCallback('Indexing Complete.') - return [] + }) } } diff --git a/products/jbrowse-desktop/src/indexJobsModel.ts b/products/jbrowse-desktop/src/indexJobsModel.ts index 2a4c7fba2a..eb3c7b0f0c 100644 --- a/products/jbrowse-desktop/src/indexJobsModel.ts +++ b/products/jbrowse-desktop/src/indexJobsModel.ts @@ -13,6 +13,11 @@ import { } from '@jbrowse/text-indexing' import { isAbortException, isSessionModelWithWidgets } from '@jbrowse/core/util' import path from 'path' +import fs from 'fs' + +const { ipcRenderer } = window.require('electron') + +const ONE_HOUR = 60 * 60 * 1000 type Track = Record @@ -40,35 +45,71 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { return types .model('JobsManager', {}) .volatile(() => ({ + /** + * #volatile + */ running: false, + /** + * #volatile + */ statusMessage: '', + /** + * #volatile + */ progressPct: 0, + /** + * #volatile + */ jobName: '', + /** + * #volatile + */ controller: new AbortController(), - jobsQueue: observable.array([] as TextJobsEntry[]), - finishedJobs: observable.array([] as TextJobsEntry[]), + /** + * #volatile + */ + jobsQueue: observable.array([]), + /** + * #volatile + */ + finishedJobs: observable.array([]), })) .views(self => ({ + /** + * #getter + */ get rpcManager() { return getParent(self).jbrowse.rpcManager }, + /** + * #getter + */ get tracks() { return getParent(self).jbrowse.tracks }, + /** + * #getter + */ get sessionPath() { return getParent(self).sessionPath }, + /** + * #getter + */ get session() { return getParent(self).session }, + /** + * #getter + */ get aggregateTextSearchAdapters() { return getParent(self).jbrowse.aggregateTextSearchAdapters }, - get location() { - return path.dirname(getParent(self).sessionPath) - }, })) .actions(self => ({ + /** + * #method + */ getJobStatusWidget() { const { session } = self const { widgets } = session @@ -80,12 +121,21 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { }, })) .actions(self => ({ + /** + * #action + */ setRunning(running: boolean) { self.running = running }, + /** + * #action + */ setJobName(name: string) { self.jobName = name }, + /** + * #action + */ setProgressPct(arg: string) { const progress = +arg if (Number.isNaN(progress)) { @@ -98,35 +148,58 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { } this.setWidgetStatus() }, + /** + * #action + */ setWidgetStatus() { const jobStatusWidget = self.getJobStatusWidget() jobStatusWidget.updateJobStatusMessage(self.jobName, self.statusMessage) jobStatusWidget.updateJobProgressPct(self.jobName, self.progressPct) }, + /** + * #action + */ setStatusMessage(arg: string) { self.statusMessage = arg }, + /** + * #action + */ abortJob() { self.controller.abort() }, + /** + * #action + */ addFinishedJob(entry: TextJobsEntry) { self.finishedJobs.push(entry) }, + /** + * #action + */ queueJob(props: TextJobsEntry) { const { session } = self if (isSessionModelWithWidgets(session)) { const jobStatusWidget = self.getJobStatusWidget() session.showWidget(jobStatusWidget) - const { name, statusMessage, progressPct, cancelCallback } = props + const { + name, + statusMessage = '', + progressPct = 0, + cancelCallback, + } = props jobStatusWidget.addQueuedJob({ name, - statusMessage: statusMessage || '', - progressPct: progressPct || 0, + statusMessage, + progressPct, cancelCallback, }) } self.jobsQueue.push(props) }, + /** + * #action + */ dequeueJob() { const { session } = self if (isSessionModelWithWidgets(session)) { @@ -135,6 +208,9 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { } return self.jobsQueue.splice(0, 1)[0] }, + /** + * #action + */ clear() { this.setRunning(false) this.setStatusMessage('') @@ -142,6 +218,9 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { self.progressPct = 0 self.controller = new AbortController() }, + /** + * #action + */ async runIndexingJob(entry: TextJobsEntry) { const { session } = self const { @@ -160,30 +239,37 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { this.setRunning(true) this.setJobName(entry.name) const { signal } = self.controller + + const userData = await ipcRenderer.invoke('userData') + const outLocation = path.join( + userData, + 'nameIndices', + `trix-${+Date.now()}`, + ) + fs.mkdirSync(outLocation, { recursive: true }) await rpcManager.call('indexTracksSessionId', 'TextIndexRpcMethod', { tracks: trackConfigs, attributes, exclude, assemblies, indexType, - outLocation: self.sessionPath, + outLocation, sessionId: 'indexTracksSessionId', statusCallback: (message: string) => { this.setProgressPct(message) }, - signal: signal, - timeout: 1000 * 60 * 60 * 1000, // 1000 hours, avoid user ever running into this + signal, + timeout: 1000 * ONE_HOUR, }) - // await result if (indexType === 'perTrack') { - // should update the single track conf trackIds.forEach(trackId => { - this.addTrackTextSearchConf( + this.addTrackTextSearchConf({ trackId, assemblies, attributes, exclude, - ) + outLocation, + }) self.session?.notify( `Successfully indexed track with trackId: ${trackId} `, 'success', @@ -198,7 +284,11 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { : true, ) .map(trackConf => trackConf.trackId) - this.addAggregateTextSearchConf(indexedTrackIds, assemblyName) + this.addAggregateTextSearchConf({ + trackIds: indexedTrackIds, + assemblyName, + outLocation, + }) self.session?.notify( `Successfully indexed assembly: ${assemblyName} `, 'success', @@ -264,14 +354,24 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { await this.runIndexingJob(firstIndexingJob) } }, - addTrackTextSearchConf( - trackId: string, - assemblies: string[], - attributes: string[], - exclude: string[], - ) { - const currentTrackIdx = (self.session?.tracks as Track[]).findIndex( - t => trackId === t.trackId, + /** + * #action + */ + addTrackTextSearchConf({ + trackId, + assemblies, + attributes, + exclude, + outLocation, + }: { + trackId: string + assemblies: string[] + attributes: string[] + exclude: string[] + outLocation: string + }) { + const currentTrackIdx = self.session.tracks.findIndex( + (t: Track) => trackId === t.trackId, ) // name of index const id = `${trackId}-index` @@ -279,7 +379,7 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { id, [trackId], assemblies, - self.location, + outLocation, ) self.session?.tracks[currentTrackIdx].textSearching.setSubschema( 'textSearchAdapter', @@ -292,17 +392,25 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { currentTrackIdx ].textSearching.indexingFeatureTypesToExclude.set(exclude) }, - addAggregateTextSearchConf(trackIds: string[], asm: string) { + addAggregateTextSearchConf({ + trackIds, + assemblyName, + outLocation, + }: { + trackIds: string[] + assemblyName: string + outLocation: string + }) { // name of index - const id = `${asm}-index` + const id = `${assemblyName}-index` const foundIdx = self.aggregateTextSearchAdapters.findIndex( (x: any) => x.textSearchAdapterId === id, ) const trixConf = createTextSearchConf( id, trackIds, - [asm], - self.location, + [assemblyName], + outLocation, ) if (foundIdx === -1) { self.aggregateTextSearchAdapters.push(trixConf) From 47a6d09dc439e8393d8594d00b0ad1a9fa6addb5 Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Wed, 18 Sep 2024 14:44:43 -0400 Subject: [PATCH 04/38] Fix code signing on the windows for jbrowse desktop (#4571) --- .github/workflows/release.yml | 18 ++++++++-- eslint.config.mjs | 1 + products/jbrowse-desktop/package.json | 4 +++ products/jbrowse-desktop/sign.js | 48 +++++++++++++++++++++++++++ 4 files changed, 69 insertions(+), 2 deletions(-) create mode 100644 products/jbrowse-desktop/sign.js diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index db4dd1a497..c99b89a61a 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -65,15 +65,29 @@ jobs: - name: Install build deps run: | apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev + # We are just cloning the esigner repo instead of calling their github + # action directly https://github.com/SSLcom/esigner-codesign + - name: Get ssl.com esigner zip file and unzip + run: | + mkdir products/jbrowse-desktop/code_signer + cd products/jbrowse-desktop/code_signer + wget https://www.ssl.com/download/codesigntool-for-linux-and-macos -O out.zip + unzip out.zip + chmod +x CodeSignTool.sh + cd ../../../ + - name: Build app env: - WIN_CSC_LINK: ${{ secrets.WIN_CSC_LINK }} - WIN_CSC_KEY_PASSWORD: ${{ secrets.WIN_CSC_KEY_PASSWORD }} + WINDOWS_SIGN_USER_NAME: ${{ secrets.WINDOWS_SIGN_USER_NAME }} + WINDOWS_SIGN_USER_PASSWORD: ${{ secrets.WINDOWS_SIGN_USER_PASSWORD }} + WINDOWS_SIGN_CREDENTIAL_ID: ${{ secrets.WINDOWS_SIGN_CREDENTIAL_ID }} + WINDOWS_SIGN_USER_TOTP: ${{ secrets.WINDOWS_SIGN_USER_TOTP }} GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: | chown --recursive root:root /github/home yarn build-electron:win --publish always working-directory: products/jbrowse-desktop + buildmac: needs: createrelease name: Build Mac desktop app diff --git a/eslint.config.mjs b/eslint.config.mjs index e981a8e948..93dbaca312 100644 --- a/eslint.config.mjs +++ b/eslint.config.mjs @@ -169,6 +169,7 @@ export default tseslint.config( 'products/jbrowse-img/**/*', 'products/jbrowse-web/scripts/*', 'products/jbrowse-desktop/scripts/*', + 'products/jbrowse-desktop/sign.js', 'products/jbrowse-desktop/linux-sandbox-fix.js', 'products/jbrowse-aws-lambda-functions/**/*.js', 'plugins/data-management/scripts/*.js', diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 306ae93671..b3e2b13fd3 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -117,6 +117,10 @@ "productName": "JBrowse 2", "copyright": "Copyright © 2019", "win": { + "sign": "./sign.js", + "signingHashAlgorithms": [ + "sha256" + ], "publish": [ "github" ], diff --git a/products/jbrowse-desktop/sign.js b/products/jbrowse-desktop/sign.js new file mode 100644 index 0000000000..ed056bb0ee --- /dev/null +++ b/products/jbrowse-desktop/sign.js @@ -0,0 +1,48 @@ +// this script adapted from +// https://github.com/electron-userland/electron-builder/issues/6158#issuecomment-899798533 +const path = require('path') +const fs = require('fs') +const childProcess = require('child_process') + +const TEMP_DIR = path.join(__dirname, 'release', 'temp') + +if (!fs.existsSync(TEMP_DIR)) { + fs.mkdirSync(TEMP_DIR, { recursive: true }) +} + +function sign(configuration) { + console.log(`Signing ${configuration.path}`) + // we move signed files to a file named tmp.exe because our product name + // contains a space, meaning our .exe contains a space, which CodeSignTool + // balks at even with attempted backslash escaping, so we rename to tmp.exe + const tmpExe = `tmp-${Math.random()}.exe` + + // note: CodeSignTool can't sign in place without verifying the overwrite + // with a y/m interaction so we are creating a new file in a temp directory + // and then replacing the original file with the signed file. + const signFile = [ + // code_signer is directory containing the CodeSignTool script in + // products/jbrowse-desktop that is created by .github/workflows/release.sh + // on windows + 'CODE_SIGN_TOOL_PATH=code_signer bash code_signer/CodeSignTool.sh sign', + `-input_file_path='${tmpExe}'`, + `-output_dir_path='${TEMP_DIR}'`, + `-credential_id='${process.env.WINDOWS_SIGN_CREDENTIAL_ID}'`, + `-username='${process.env.WINDOWS_SIGN_USER_NAME}'`, + `-password='${process.env.WINDOWS_SIGN_USER_PASSWORD}'`, + `-totp_secret='${process.env.WINDOWS_SIGN_USER_TOTP}'`, + ].join(' ') + const preMoveFile = `cp "${configuration.path}" "${tmpExe}"` + const postMoveFile = `cp "${path.join(TEMP_DIR, tmpExe)}" "${configuration.path}"` + childProcess.execSync(preMoveFile, { + stdio: 'inherit', + }) + childProcess.execSync(signFile, { + stdio: 'inherit', + }) + childProcess.execSync(postMoveFile, { + stdio: 'inherit', + }) +} + +exports.default = sign From 7d3c8dc22943b7a130bd32a9f24c5d4656ef60d4 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 18:02:35 -0400 Subject: [PATCH 05/38] [skip ci] v2.15.2 release announcement draft --- website/release_announcement_drafts/v2.15.2.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 website/release_announcement_drafts/v2.15.2.md diff --git a/website/release_announcement_drafts/v2.15.2.md b/website/release_announcement_drafts/v2.15.2.md new file mode 100644 index 0000000000..9c14878c2d --- /dev/null +++ b/website/release_announcement_drafts/v2.15.2.md @@ -0,0 +1,2 @@ +This release (hopefully) fixes the SSL code signing on the Windows version of +the jbrowse desktop app. This should help auto-updates work better on Windows From 687253e3e867e96a37b02f5d47b2b36bdd29c6ac Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 22:21:40 +0000 Subject: [PATCH 06/38] Prepare for v2.15.2 release --- CHANGELOG.md | 26 +++++++++++++ website/blog/2024-09-18-v2.15.2-release.md | 43 ++++++++++++++++++++++ website/docusaurus.config.json | 2 +- 3 files changed, 70 insertions(+), 1 deletion(-) create mode 100644 website/blog/2024-09-18-v2.15.2-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d70861d40..693c9e323e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,29 @@ +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 + +## 2.15.2 (2024-09-18) + +#### :rocket: Enhancement + +- [#4573](https://github.com/GMOD/jbrowse-components/pull/4573) Add pif.gz + option to synteny import form ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- [#4571](https://github.com/GMOD/jbrowse-components/pull/4571) Fix code signing + on the windows for jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) +- [#4566](https://github.com/GMOD/jbrowse-components/pull/4566) Fix handling of + "." in VCF ALT field ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- [#4569](https://github.com/GMOD/jbrowse-components/pull/4569) Refactor GFF3 + parser to avoid returning internal \_linehash variable + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. + yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.1 ## 2.15.1 (2024-09-12) diff --git a/website/blog/2024-09-18-v2.15.2-release.md b/website/blog/2024-09-18-v2.15.2-release.md new file mode 100644 index 0000000000..567d21968a --- /dev/null +++ b/website/blog/2024-09-18-v2.15.2-release.md @@ -0,0 +1,43 @@ +--- +title: v2.15.2 Release +date: 2024-09-18 22:21:09 +tags: ['release', 'jbrowse 2'] +--- + +This release (hopefully) fixes the SSL code signing on the Windows version of +the jbrowse desktop app. This should help auto-updates work better on Windows + +## Downloads + +- [v2.15.2](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.2) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 + +## 2.15.2 (2024-09-18) + +#### :rocket: Enhancement + +- [#4573](https://github.com/GMOD/jbrowse-components/pull/4573) Add pif.gz + option to synteny import form ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- [#4571](https://github.com/GMOD/jbrowse-components/pull/4571) Fix code signing + on the windows for jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) +- [#4566](https://github.com/GMOD/jbrowse-components/pull/4566) Fix handling of + "." in VCF ALT field ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- [#4569](https://github.com/GMOD/jbrowse-components/pull/4569) Refactor GFF3 + parser to avoid returning internal \_linehash variable + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index ede8278997..d5b831fccc 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.1" + "currentVersion": "v2.15.2" } } From 8a58cefbfe39af4c97bcb6ead354d72c9fef9224 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 22:23:09 +0000 Subject: [PATCH 07/38] [update docs] v2.15.2 --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 6 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 202 insertions(+), 202 deletions(-) diff --git a/lerna.json b/lerna.json index c797e38c7d..33a5bc6f06 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.1", + "version": "2.15.2", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 40deb110dc..2f19f94458 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.1", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index bd9687c4b9..3f3a1a1e14 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index 86e394b394..e44c0bf3a9 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", + "@jbrowse/core": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index 61a6ea2507..c8c55671d5 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.1", + "version": "2.15.2", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.1", + "@jbrowse/core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index f69d4be7c6..37cf06068c 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,9 +41,9 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { + "@jbrowse/plugin-linear-genome-view": "^2.15.2", "@mui/icons-material": "^6.0.0", - "@mui/material": "^6.0.0", - "@jbrowse/plugin-linear-genome-view": "^2.0.0" + "@mui/material": "^6.0.0" }, "peerDependencies": { "mobx": "^6.0.0", diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index 149121b4dc..c6fe0fee33 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.1", + "@jbrowse/core": "^2.15.2", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index c05bf51656..ba205d628e 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 1509e92047..70dc07abbf 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.1", + "@jbrowse/sv-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index c459df82b1..386fe6329e 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index a2402d3e4a..b1842551ea 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index aa3b913d8c..2151f8025c 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index d1ca9451f1..e68ddd2658 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index c0d5785b87..fb1fbff94e 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 4a5862c9a4..62f3d33834 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 93e1f7ea88..4b3f6b76f6 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index a84a88a2c2..8a11b633be 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 72fc820c40..1cbe8a5b4c 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index c4aeca1568..f1b941d5f3 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index e4145a24b0..bc6e76500f 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index 88d8205330..b4387cd1e1 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index c18accafdc..f178cd5fff 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index 6d5f1071c9..b081564d0b 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index f3bedcc34b..eec648125c 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.1", + "@jbrowse/text-indexing": "^2.15.2", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index 7746cebb4f..571b6a25f6 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 315260672f..906e9d85c4 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index fea1588cb9..1311fd3a8e 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 8b57de14f2..3fc07dc93a 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 15b1a319fb..253763701d 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index c59681183c..60dafce7eb 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index 0145018f39..bb09950164 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index 42718ecff0..cfe6c64364 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.1", + "@jbrowse/plugin-variants": "^2.15.2", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index c4db87927e..ddc5f452ee 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 0a612f41cf..16657acace 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index b4ac3cda47..fccb38f34b 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.1" + "@jbrowse/text-indexing": "^2.15.2" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index 2eba562137..c1249166ac 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index e845a0cb5e..fc0d3ff852 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.1", + "@jbrowse/sv-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index 658195e0a4..77aa24d8f9 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index aa38c69cef..ba2f154d4c 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.1/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index da79490d58..0df3346391 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.1", + "version": "2.15.2", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index b3e2b13fd3..027cfc8b91 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.1", - "@jbrowse/core": "^2.15.1", - "@jbrowse/plugin-alignments": "^2.15.1", - "@jbrowse/plugin-arc": "^2.15.1", - "@jbrowse/plugin-authentication": "^2.15.1", - "@jbrowse/plugin-bed": "^2.15.1", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.1", - "@jbrowse/plugin-circular-view": "^2.15.1", - "@jbrowse/plugin-comparative-adapters": "^2.15.1", - "@jbrowse/plugin-config": "^2.15.1", - "@jbrowse/plugin-data-management": "^2.15.1", - "@jbrowse/plugin-dotplot-view": "^2.15.1", - "@jbrowse/plugin-gccontent": "^2.15.1", - "@jbrowse/plugin-gff3": "^2.15.1", - "@jbrowse/plugin-grid-bookmark": "^2.15.1", - "@jbrowse/plugin-gtf": "^2.15.1", - "@jbrowse/plugin-hic": "^2.15.1", - "@jbrowse/plugin-jobs-management": "^2.15.1", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.1", - "@jbrowse/plugin-linear-comparative-view": "^2.15.1", - "@jbrowse/plugin-linear-genome-view": "^2.15.1", - "@jbrowse/plugin-lollipop": "^2.15.1", - "@jbrowse/plugin-menus": "^2.15.1", - "@jbrowse/plugin-rdf": "^2.15.1", - "@jbrowse/plugin-sequence": "^2.15.1", - "@jbrowse/plugin-spreadsheet-view": "^2.15.1", - "@jbrowse/plugin-sv-inspector": "^2.15.1", - "@jbrowse/plugin-svg": "^2.15.1", - "@jbrowse/plugin-text-indexing": "^2.15.1", - "@jbrowse/plugin-trix": "^2.15.1", - "@jbrowse/plugin-variants": "^2.15.1", - "@jbrowse/plugin-wiggle": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", - "@jbrowse/text-indexing": "^2.15.1", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-jobs-management": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-text-indexing": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/text-indexing": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index 8307c1fd6f..d91d7d798d 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.1", + "version": "2.15.2", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.1", - "@jbrowse/react-linear-genome-view": "^2.15.1", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/react-linear-genome-view": "^2.15.2", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 99549d44f8..1c1bf4dad4 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.1", + "version": "2.15.2", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index 0678a67bfa..744cad66db 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.1", - "@jbrowse/core": "^2.15.1", - "@jbrowse/plugin-alignments": "^2.15.1", - "@jbrowse/plugin-arc": "^2.15.1", - "@jbrowse/plugin-authentication": "^2.15.1", - "@jbrowse/plugin-bed": "^2.15.1", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.1", - "@jbrowse/plugin-circular-view": "^2.15.1", - "@jbrowse/plugin-comparative-adapters": "^2.15.1", - "@jbrowse/plugin-config": "^2.15.1", - "@jbrowse/plugin-data-management": "^2.15.1", - "@jbrowse/plugin-dotplot-view": "^2.15.1", - "@jbrowse/plugin-gccontent": "^2.15.1", - "@jbrowse/plugin-gff3": "^2.15.1", - "@jbrowse/plugin-grid-bookmark": "^2.15.1", - "@jbrowse/plugin-gtf": "^2.15.1", - "@jbrowse/plugin-hic": "^2.15.1", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.1", - "@jbrowse/plugin-linear-comparative-view": "^2.15.1", - "@jbrowse/plugin-linear-genome-view": "^2.15.1", - "@jbrowse/plugin-lollipop": "^2.15.1", - "@jbrowse/plugin-menus": "^2.15.1", - "@jbrowse/plugin-rdf": "^2.15.1", - "@jbrowse/plugin-sequence": "^2.15.1", - "@jbrowse/plugin-spreadsheet-view": "^2.15.1", - "@jbrowse/plugin-sv-inspector": "^2.15.1", - "@jbrowse/plugin-svg": "^2.15.1", - "@jbrowse/plugin-trix": "^2.15.1", - "@jbrowse/plugin-variants": "^2.15.1", - "@jbrowse/plugin-wiggle": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", - "@jbrowse/web-core": "^2.15.1", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/web-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index 1a5f29bcd6..f3146b7e6b 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.1", - "@jbrowse/embedded-core": "^2.15.1", - "@jbrowse/plugin-authentication": "^2.15.1", - "@jbrowse/plugin-circular-view": "^2.15.1", - "@jbrowse/plugin-config": "^2.15.1", - "@jbrowse/plugin-data-management": "^2.15.1", - "@jbrowse/plugin-linear-genome-view": "^2.15.1", - "@jbrowse/plugin-sequence": "^2.15.1", - "@jbrowse/plugin-variants": "^2.15.1", - "@jbrowse/plugin-wiggle": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", + "@jbrowse/core": "^2.15.2", + "@jbrowse/embedded-core": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index ce140ba2db..b4e621629b 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.1", + "version": "2.15.2", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.1", - "@jbrowse/embedded-core": "^2.15.1", - "@jbrowse/plugin-alignments": "^2.15.1", - "@jbrowse/plugin-arc": "^2.15.1", - "@jbrowse/plugin-authentication": "^2.15.1", - "@jbrowse/plugin-bed": "^2.15.1", - "@jbrowse/plugin-circular-view": "^2.15.1", - "@jbrowse/plugin-config": "^2.15.1", - "@jbrowse/plugin-data-management": "^2.15.1", - "@jbrowse/plugin-gccontent": "^2.15.1", - "@jbrowse/plugin-gff3": "^2.15.1", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.1", - "@jbrowse/plugin-linear-genome-view": "^2.15.1", - "@jbrowse/plugin-sequence": "^2.15.1", - "@jbrowse/plugin-svg": "^2.15.1", - "@jbrowse/plugin-trix": "^2.15.1", - "@jbrowse/plugin-variants": "^2.15.1", - "@jbrowse/plugin-wiggle": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", + "@jbrowse/core": "^2.15.2", + "@jbrowse/embedded-core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index be64c5aa63..fa3b78f627 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.1", + "version": "2.15.2", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.1", - "@jbrowse/core": "^2.15.1", - "@jbrowse/plugin-alignments": "^2.15.1", - "@jbrowse/plugin-arc": "^2.15.1", - "@jbrowse/plugin-authentication": "^2.15.1", - "@jbrowse/plugin-bed": "^2.15.1", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.1", - "@jbrowse/plugin-circular-view": "^2.15.1", - "@jbrowse/plugin-comparative-adapters": "^2.15.1", - "@jbrowse/plugin-config": "^2.15.1", - "@jbrowse/plugin-data-management": "^2.15.1", - "@jbrowse/plugin-dotplot-view": "^2.15.1", - "@jbrowse/plugin-gccontent": "^2.15.1", - "@jbrowse/plugin-gff3": "^2.15.1", - "@jbrowse/plugin-grid-bookmark": "^2.15.1", - "@jbrowse/plugin-gtf": "^2.15.1", - "@jbrowse/plugin-hic": "^2.15.1", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.1", - "@jbrowse/plugin-linear-comparative-view": "^2.15.1", - "@jbrowse/plugin-linear-genome-view": "^2.15.1", - "@jbrowse/plugin-lollipop": "^2.15.1", - "@jbrowse/plugin-menus": "^2.15.1", - "@jbrowse/plugin-rdf": "^2.15.1", - "@jbrowse/plugin-sequence": "^2.15.1", - "@jbrowse/plugin-spreadsheet-view": "^2.15.1", - "@jbrowse/plugin-sv-inspector": "^2.15.1", - "@jbrowse/plugin-svg": "^2.15.1", - "@jbrowse/plugin-trix": "^2.15.1", - "@jbrowse/plugin-variants": "^2.15.1", - "@jbrowse/plugin-wiggle": "^2.15.1", - "@jbrowse/product-core": "^2.15.1", - "@jbrowse/web-core": "^2.15.1", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/web-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", From d76f50b34d5e0015eeb0fea818c799bc472f3918 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 22:35:18 +0000 Subject: [PATCH 08/38] [skip ci] Bump version.js --- products/jbrowse-react-circular-genome-view/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-circular-genome-view/src/version.js b/products/jbrowse-react-circular-genome-view/src/version.js index d4947967e5..1a820b8f83 100644 --- a/products/jbrowse-react-circular-genome-view/src/version.js +++ b/products/jbrowse-react-circular-genome-view/src/version.js @@ -1 +1 @@ -export const version = '2.15.1' +export const version = '2.15.2' From 6469727c3379e56f89af8bf36d8cabdc0ac5a494 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 22:35:18 +0000 Subject: [PATCH 09/38] [skip ci] Bump version.js --- products/jbrowse-react-linear-genome-view/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-linear-genome-view/src/version.js b/products/jbrowse-react-linear-genome-view/src/version.js index d4947967e5..1a820b8f83 100644 --- a/products/jbrowse-react-linear-genome-view/src/version.js +++ b/products/jbrowse-react-linear-genome-view/src/version.js @@ -1 +1 @@ -export const version = '2.15.1' +export const version = '2.15.2' From 4d98a3b1c084033d4801878344e8f22a6530cd79 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 22:41:02 +0000 Subject: [PATCH 10/38] [skip ci] Bump version.js --- products/jbrowse-react-app/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-app/src/version.js b/products/jbrowse-react-app/src/version.js index d4947967e5..1a820b8f83 100644 --- a/products/jbrowse-react-app/src/version.js +++ b/products/jbrowse-react-app/src/version.js @@ -1 +1 @@ -export const version = '2.15.1' +export const version = '2.15.2' From 3845ef2f1192462c92d0c241d7234e54e5209965 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:06:00 -0400 Subject: [PATCH 11/38] [skip ci] Add java to windows github action --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index c99b89a61a..3397375c2d 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -64,7 +64,7 @@ jobs: apt install --yes wine wine32 wine64 libwine libwine:i386 fonts-wine - name: Install build deps run: | - apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev + apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev openjdk-21-jdk-headless # We are just cloning the esigner repo instead of calling their github # action directly https://github.com/SSLcom/esigner-codesign - name: Get ssl.com esigner zip file and unzip From b9a52508f4ddc31a5248ec634aabe961ee63eb17 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:06:33 -0400 Subject: [PATCH 12/38] [skip ci] Change in @jbrowse/core to force version bump --- packages/core/util/index.ts | 3 +-- website/release_announcement_drafts/v2.15.3.md | 1 + 2 files changed, 2 insertions(+), 2 deletions(-) create mode 100644 website/release_announcement_drafts/v2.15.3.md diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index 46151a9f06..8cf71d60f9 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -1426,8 +1426,7 @@ export function gatherOverlaps(regions: BasicFeature[], w = 5000) { } export function stripAlpha(str: string) { - const c = colord(str) - return c.alpha(1).toHex() + return colord(str).alpha(1).toHex() } export function getStrokeProps(str: string) { diff --git a/website/release_announcement_drafts/v2.15.3.md b/website/release_announcement_drafts/v2.15.3.md new file mode 100644 index 0000000000..2cdc935d40 --- /dev/null +++ b/website/release_announcement_drafts/v2.15.3.md @@ -0,0 +1 @@ +Re-publish From 61103cc02b443d8cd708479545fda2b9e7f86867 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 23:13:05 +0000 Subject: [PATCH 13/38] Prepare for v2.15.3 release --- CHANGELOG.md | 4 ++++ website/blog/2024-09-18-v2.15.3-release.md | 20 ++++++++++++++++++++ website/docusaurus.config.json | 2 +- 3 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 website/blog/2024-09-18-v2.15.3-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 693c9e323e..22b109be05 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 + +Done in 0.53s. + yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 ## 2.15.2 (2024-09-18) diff --git a/website/blog/2024-09-18-v2.15.3-release.md b/website/blog/2024-09-18-v2.15.3-release.md new file mode 100644 index 0000000000..bf87589c71 --- /dev/null +++ b/website/blog/2024-09-18-v2.15.3-release.md @@ -0,0 +1,20 @@ +--- +title: v2.15.3 Release +date: 2024-09-18 23:12:34 +tags: ['release', 'jbrowse 2'] +--- + +Re-publish + +## Downloads + +- [v2.15.3](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.3) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 + +Done in 0.53s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index d5b831fccc..e6a814856f 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.2" + "currentVersion": "v2.15.3" } } From 74eef530dd30ec58a63d97b1dffe5f4d218d9cff Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 23:14:27 +0000 Subject: [PATCH 14/38] [update docs] v2.15.3 --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 4 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 201 insertions(+), 201 deletions(-) diff --git a/lerna.json b/lerna.json index 33a5bc6f06..41bdf3d775 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.2", + "version": "2.15.3", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 2f19f94458..9424e6c846 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index 3f3a1a1e14..acf48565ae 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index e44c0bf3a9..a578a19767 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index c8c55671d5..f1e636503c 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.2", + "version": "2.15.3", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", + "@jbrowse/core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index 37cf06068c..e6914bdad5 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index c6fe0fee33..f2885e5f10 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", + "@jbrowse/core": "^2.15.3", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index ba205d628e..190c0bf5ce 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 70dc07abbf..9d61dc6ab9 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.2", + "@jbrowse/sv-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index 386fe6329e..df5e78e4f5 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index b1842551ea..8d2389fe31 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 2151f8025c..82859b3759 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index e68ddd2658..205f71e445 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index fb1fbff94e..526ccd84de 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 62f3d33834..8ace6e37b9 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 4b3f6b76f6..4bf197f8cd 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 8a11b633be..530385f2c3 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 1cbe8a5b4c..020c353870 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index f1b941d5f3..a9f567a86d 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index bc6e76500f..a9a0068554 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index b4387cd1e1..d604c6357d 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index f178cd5fff..345bdc7315 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index b081564d0b..2b5e0b25f9 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index eec648125c..43bc82b21d 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.2", + "@jbrowse/text-indexing": "^2.15.3", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index 571b6a25f6..bf19fd4f01 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 906e9d85c4..d7b778ee65 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index 1311fd3a8e..e61561e631 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 3fc07dc93a..40cff9244a 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 253763701d..12681b6d91 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 60dafce7eb..9beff555ed 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index bb09950164..f0e53718f6 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index cfe6c64364..72d45b1209 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.3", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index ddc5f452ee..c87438e6b2 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 16657acace..1b60f1186b 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index fccb38f34b..acf031cfec 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.2" + "@jbrowse/text-indexing": "^2.15.3" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index c1249166ac..d8fbc008cc 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index fc0d3ff852..6e1042b688 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.2", + "@jbrowse/sv-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index 77aa24d8f9..f9e0e2fce0 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index ba2f154d4c..3252df5292 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 0df3346391..68ab6bcdd3 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.2", + "version": "2.15.3", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 027cfc8b91..0b842a4dc3 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-jobs-management": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-text-indexing": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/text-indexing": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-jobs-management": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-text-indexing": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/text-indexing": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index d91d7d798d..295255df9e 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.2", + "version": "2.15.3", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/react-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/react-linear-genome-view": "^2.15.3", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 1c1bf4dad4..99397cfb21 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.2", + "version": "2.15.3", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index 744cad66db..b03ea4b796 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/web-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/web-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index f3146b7e6b..7b6b472b95 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.2", - "@jbrowse/embedded-core": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/embedded-core": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index b4e621629b..e03b6966bd 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.2", - "@jbrowse/embedded-core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/embedded-core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index fa3b78f627..b0c998ee10 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.2", + "version": "2.15.3", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/web-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/web-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", From e057e67f874d697ec9be05dc8e13a769c55c2148 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:22:30 -0400 Subject: [PATCH 15/38] [skip ci] Revert "[update docs] v2.15.3" This reverts commit 74eef530dd30ec58a63d97b1dffe5f4d218d9cff. Revert "Prepare for v2.15.3 release" This reverts commit 61103cc02b443d8cd708479545fda2b9e7f86867. --- CHANGELOG.md | 4 -- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 4 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- website/blog/2024-09-18-v2.15.3-release.md | 20 ------ website/docusaurus.config.json | 2 +- 50 files changed, 202 insertions(+), 226 deletions(-) delete mode 100644 website/blog/2024-09-18-v2.15.3-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 22b109be05..693c9e323e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,3 @@ -yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 - -Done in 0.53s. - yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 ## 2.15.2 (2024-09-18) diff --git a/lerna.json b/lerna.json index 41bdf3d775..33a5bc6f06 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.3", + "version": "2.15.2", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 9424e6c846..2f19f94458 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index acf48565ae..3f3a1a1e14 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index a578a19767..e44c0bf3a9 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index f1e636503c..c8c55671d5 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.3", + "version": "2.15.2", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", + "@jbrowse/core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index e6914bdad5..37cf06068c 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index f2885e5f10..c6fe0fee33 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", + "@jbrowse/core": "^2.15.2", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index 190c0bf5ce..ba205d628e 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 9d61dc6ab9..70dc07abbf 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.3", + "@jbrowse/sv-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index df5e78e4f5..386fe6329e 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index 8d2389fe31..b1842551ea 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 82859b3759..2151f8025c 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index 205f71e445..e68ddd2658 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index 526ccd84de..fb1fbff94e 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 8ace6e37b9..62f3d33834 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 4bf197f8cd..4b3f6b76f6 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 530385f2c3..8a11b633be 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 020c353870..1cbe8a5b4c 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index a9f567a86d..f1b941d5f3 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index a9a0068554..bc6e76500f 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index d604c6357d..b4387cd1e1 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index 345bdc7315..f178cd5fff 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index 2b5e0b25f9..b081564d0b 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index 43bc82b21d..eec648125c 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.3", + "@jbrowse/text-indexing": "^2.15.2", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index bf19fd4f01..571b6a25f6 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index d7b778ee65..906e9d85c4 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index e61561e631..1311fd3a8e 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 40cff9244a..3fc07dc93a 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 12681b6d91..253763701d 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 9beff555ed..60dafce7eb 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index f0e53718f6..bb09950164 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index 72d45b1209..cfe6c64364 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.2", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index c87438e6b2..ddc5f452ee 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 1b60f1186b..16657acace 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index acf031cfec..fccb38f34b 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.3" + "@jbrowse/text-indexing": "^2.15.2" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index d8fbc008cc..c1249166ac 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index 6e1042b688..fc0d3ff852 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.3", + "@jbrowse/sv-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index f9e0e2fce0..77aa24d8f9 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index 3252df5292..ba2f154d4c 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 68ab6bcdd3..0df3346391 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.3", + "version": "2.15.2", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 0b842a4dc3..027cfc8b91 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-jobs-management": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-text-indexing": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/text-indexing": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-jobs-management": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-text-indexing": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/text-indexing": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index 295255df9e..d91d7d798d 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.3", + "version": "2.15.2", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/react-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/react-linear-genome-view": "^2.15.2", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 99397cfb21..1c1bf4dad4 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.3", + "version": "2.15.2", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index b03ea4b796..744cad66db 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/web-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/web-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index 7b6b472b95..f3146b7e6b 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.3", - "@jbrowse/embedded-core": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.2", + "@jbrowse/embedded-core": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index e03b6966bd..b4e621629b 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.3", - "@jbrowse/embedded-core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.2", + "@jbrowse/embedded-core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index b0c998ee10..fa3b78f627 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.3", + "version": "2.15.2", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/web-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/web-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/website/blog/2024-09-18-v2.15.3-release.md b/website/blog/2024-09-18-v2.15.3-release.md deleted file mode 100644 index bf87589c71..0000000000 --- a/website/blog/2024-09-18-v2.15.3-release.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: v2.15.3 Release -date: 2024-09-18 23:12:34 -tags: ['release', 'jbrowse 2'] ---- - -Re-publish - -## Downloads - -- [v2.15.3](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.3) - -To install JBrowse 2 for the web, you can download the link above, or you can -use the JBrowse CLI to automatically download the latest version. See the -[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more -details. - -yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 - -Done in 0.53s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index e6a814856f..d5b831fccc 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.3" + "currentVersion": "v2.15.2" } } From 9d6e38135b04160b020566da38b7bb20684afd54 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:23:11 -0400 Subject: [PATCH 16/38] [skip ci] Get java with github action for CodeSignTool on windows desktop build --- .github/workflows/release.yml | 6 ++++++ packages/core/util/index.ts | 3 ++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 3397375c2d..2c762b53aa 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -56,6 +56,12 @@ jobs: - uses: actions/checkout@v4 - name: Install deps (with cache) uses: bahmutov/npm-install@v1 + - name: Setup java + uses: actions/setup-java@v4 + with: + # eclipse 'temurin' openjdk https://github.com/actions/setup-java/blob/main/docs/advanced-usage.md#Selecting-a-Java-distribution + distribution: 'temurin' + java-version: '21' - name: Install wine # https://wiki.debian.org/Wine run: | diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index 8cf71d60f9..46151a9f06 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -1426,7 +1426,8 @@ export function gatherOverlaps(regions: BasicFeature[], w = 5000) { } export function stripAlpha(str: string) { - return colord(str).alpha(1).toHex() + const c = colord(str) + return c.alpha(1).toHex() } export function getStrokeProps(str: string) { From dbac40e980057e5d45a4db466bcc344d08d4ad63 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 23:30:12 +0000 Subject: [PATCH 17/38] Prepare for v2.15.3 release --- CHANGELOG.md | 4 ++++ website/blog/2024-09-18-v2.15.3-release.md | 20 ++++++++++++++++++++ website/docusaurus.config.json | 2 +- 3 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 website/blog/2024-09-18-v2.15.3-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 693c9e323e..841521f50a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 + +Done in 0.55s. + yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 ## 2.15.2 (2024-09-18) diff --git a/website/blog/2024-09-18-v2.15.3-release.md b/website/blog/2024-09-18-v2.15.3-release.md new file mode 100644 index 0000000000..c95632da98 --- /dev/null +++ b/website/blog/2024-09-18-v2.15.3-release.md @@ -0,0 +1,20 @@ +--- +title: v2.15.3 Release +date: 2024-09-18 23:29:41 +tags: ['release', 'jbrowse 2'] +--- + +Re-publish + +## Downloads + +- [v2.15.3](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.3) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 + +Done in 0.55s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index d5b831fccc..e6a814856f 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.2" + "currentVersion": "v2.15.3" } } From fc404ba2938558fded1a8b1e58a943d0f47c6e76 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 23:34:22 +0000 Subject: [PATCH 18/38] [update docs] v2.15.3 --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 4 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 201 insertions(+), 201 deletions(-) diff --git a/lerna.json b/lerna.json index 33a5bc6f06..41bdf3d775 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.2", + "version": "2.15.3", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 2f19f94458..9424e6c846 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index 3f3a1a1e14..acf48565ae 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index e44c0bf3a9..a578a19767 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index c8c55671d5..f1e636503c 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.2", + "version": "2.15.3", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", + "@jbrowse/core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index 37cf06068c..e6914bdad5 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index c6fe0fee33..f2885e5f10 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", + "@jbrowse/core": "^2.15.3", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index ba205d628e..190c0bf5ce 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 70dc07abbf..9d61dc6ab9 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.2", + "@jbrowse/sv-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index 386fe6329e..df5e78e4f5 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index b1842551ea..8d2389fe31 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 2151f8025c..82859b3759 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index e68ddd2658..205f71e445 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index fb1fbff94e..526ccd84de 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 62f3d33834..8ace6e37b9 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 4b3f6b76f6..4bf197f8cd 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 8a11b633be..530385f2c3 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 1cbe8a5b4c..020c353870 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index f1b941d5f3..a9f567a86d 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index bc6e76500f..a9a0068554 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index b4387cd1e1..d604c6357d 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index f178cd5fff..345bdc7315 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index b081564d0b..2b5e0b25f9 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index eec648125c..43bc82b21d 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.2", + "@jbrowse/text-indexing": "^2.15.3", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index 571b6a25f6..bf19fd4f01 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 906e9d85c4..d7b778ee65 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index 1311fd3a8e..e61561e631 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 3fc07dc93a..40cff9244a 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 253763701d..12681b6d91 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 60dafce7eb..9beff555ed 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index bb09950164..f0e53718f6 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index cfe6c64364..72d45b1209 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.3", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index ddc5f452ee..c87438e6b2 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 16657acace..1b60f1186b 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index fccb38f34b..acf031cfec 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.2" + "@jbrowse/text-indexing": "^2.15.3" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index c1249166ac..d8fbc008cc 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index fc0d3ff852..6e1042b688 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.2", + "@jbrowse/sv-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index 77aa24d8f9..f9e0e2fce0 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index ba2f154d4c..3252df5292 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 0df3346391..68ab6bcdd3 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.2", + "version": "2.15.3", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 027cfc8b91..0b842a4dc3 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-jobs-management": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-text-indexing": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/text-indexing": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-jobs-management": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-text-indexing": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/text-indexing": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index d91d7d798d..295255df9e 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.2", + "version": "2.15.3", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/react-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/react-linear-genome-view": "^2.15.3", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 1c1bf4dad4..99397cfb21 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.2", + "version": "2.15.3", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index 744cad66db..b03ea4b796 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/web-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/web-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index f3146b7e6b..7b6b472b95 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.2", - "@jbrowse/embedded-core": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/embedded-core": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index b4e621629b..e03b6966bd 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.2", - "@jbrowse/embedded-core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/embedded-core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index fa3b78f627..b0c998ee10 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.2", + "version": "2.15.3", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/web-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/web-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", From 06061c34e44349b661fc9e94ede36eeeed31cd3d Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:46:44 -0400 Subject: [PATCH 19/38] Revert "[update docs] v2.15.3" This reverts commit fc404ba2938558fded1a8b1e58a943d0f47c6e76. --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 4 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 201 insertions(+), 201 deletions(-) diff --git a/lerna.json b/lerna.json index 41bdf3d775..33a5bc6f06 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.3", + "version": "2.15.2", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 9424e6c846..2f19f94458 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index acf48565ae..3f3a1a1e14 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index a578a19767..e44c0bf3a9 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index f1e636503c..c8c55671d5 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.3", + "version": "2.15.2", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", + "@jbrowse/core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index e6914bdad5..37cf06068c 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index f2885e5f10..c6fe0fee33 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", + "@jbrowse/core": "^2.15.2", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index 190c0bf5ce..ba205d628e 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 9d61dc6ab9..70dc07abbf 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.3", + "@jbrowse/sv-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index df5e78e4f5..386fe6329e 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index 8d2389fe31..b1842551ea 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 82859b3759..2151f8025c 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index 205f71e445..e68ddd2658 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index 526ccd84de..fb1fbff94e 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 8ace6e37b9..62f3d33834 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 4bf197f8cd..4b3f6b76f6 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 530385f2c3..8a11b633be 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 020c353870..1cbe8a5b4c 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index a9f567a86d..f1b941d5f3 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index a9a0068554..bc6e76500f 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index d604c6357d..b4387cd1e1 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index 345bdc7315..f178cd5fff 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index 2b5e0b25f9..b081564d0b 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index 43bc82b21d..eec648125c 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.3", + "@jbrowse/text-indexing": "^2.15.2", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index bf19fd4f01..571b6a25f6 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index d7b778ee65..906e9d85c4 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index e61561e631..1311fd3a8e 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 40cff9244a..3fc07dc93a 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 12681b6d91..253763701d 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 9beff555ed..60dafce7eb 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index f0e53718f6..bb09950164 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index 72d45b1209..cfe6c64364 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.2", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index c87438e6b2..ddc5f452ee 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 1b60f1186b..16657acace 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index acf031cfec..fccb38f34b 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.3" + "@jbrowse/text-indexing": "^2.15.2" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index d8fbc008cc..c1249166ac 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index 6e1042b688..fc0d3ff852 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.3", + "@jbrowse/sv-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index f9e0e2fce0..77aa24d8f9 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index 3252df5292..ba2f154d4c 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 68ab6bcdd3..0df3346391 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.3", + "version": "2.15.2", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 0b842a4dc3..027cfc8b91 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-jobs-management": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-text-indexing": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/text-indexing": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-jobs-management": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-text-indexing": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/text-indexing": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index 295255df9e..d91d7d798d 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.3", + "version": "2.15.2", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/react-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/react-linear-genome-view": "^2.15.2", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 99397cfb21..1c1bf4dad4 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.3", + "version": "2.15.2", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index b03ea4b796..744cad66db 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/web-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/web-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index 7b6b472b95..f3146b7e6b 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.3", - "@jbrowse/embedded-core": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.2", + "@jbrowse/embedded-core": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index e03b6966bd..b4e621629b 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.3", + "version": "2.15.2", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.3", - "@jbrowse/embedded-core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.2", + "@jbrowse/embedded-core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index b0c998ee10..fa3b78f627 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.3", + "version": "2.15.2", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/web-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.2", + "@jbrowse/core": "^2.15.2", + "@jbrowse/plugin-alignments": "^2.15.2", + "@jbrowse/plugin-arc": "^2.15.2", + "@jbrowse/plugin-authentication": "^2.15.2", + "@jbrowse/plugin-bed": "^2.15.2", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", + "@jbrowse/plugin-circular-view": "^2.15.2", + "@jbrowse/plugin-comparative-adapters": "^2.15.2", + "@jbrowse/plugin-config": "^2.15.2", + "@jbrowse/plugin-data-management": "^2.15.2", + "@jbrowse/plugin-dotplot-view": "^2.15.2", + "@jbrowse/plugin-gccontent": "^2.15.2", + "@jbrowse/plugin-gff3": "^2.15.2", + "@jbrowse/plugin-grid-bookmark": "^2.15.2", + "@jbrowse/plugin-gtf": "^2.15.2", + "@jbrowse/plugin-hic": "^2.15.2", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", + "@jbrowse/plugin-linear-comparative-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-lollipop": "^2.15.2", + "@jbrowse/plugin-menus": "^2.15.2", + "@jbrowse/plugin-rdf": "^2.15.2", + "@jbrowse/plugin-sequence": "^2.15.2", + "@jbrowse/plugin-spreadsheet-view": "^2.15.2", + "@jbrowse/plugin-sv-inspector": "^2.15.2", + "@jbrowse/plugin-svg": "^2.15.2", + "@jbrowse/plugin-trix": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-wiggle": "^2.15.2", + "@jbrowse/product-core": "^2.15.2", + "@jbrowse/web-core": "^2.15.2", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", From 10ac720e7225ec61832ba450cddc94f99127dd78 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:46:49 -0400 Subject: [PATCH 20/38] Revert "Prepare for v2.15.3 release" This reverts commit dbac40e980057e5d45a4db466bcc344d08d4ad63. --- CHANGELOG.md | 4 ---- website/blog/2024-09-18-v2.15.3-release.md | 20 -------------------- website/docusaurus.config.json | 2 +- 3 files changed, 1 insertion(+), 25 deletions(-) delete mode 100644 website/blog/2024-09-18-v2.15.3-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 841521f50a..693c9e323e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,3 @@ -yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 - -Done in 0.55s. - yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 ## 2.15.2 (2024-09-18) diff --git a/website/blog/2024-09-18-v2.15.3-release.md b/website/blog/2024-09-18-v2.15.3-release.md deleted file mode 100644 index c95632da98..0000000000 --- a/website/blog/2024-09-18-v2.15.3-release.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: v2.15.3 Release -date: 2024-09-18 23:29:41 -tags: ['release', 'jbrowse 2'] ---- - -Re-publish - -## Downloads - -- [v2.15.3](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.3) - -To install JBrowse 2 for the web, you can download the link above, or you can -use the JBrowse CLI to automatically download the latest version. See the -[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more -details. - -yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 - -Done in 0.55s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index e6a814856f..d5b831fccc 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.3" + "currentVersion": "v2.15.2" } } From ffb6fb31c8f267c7e6945ad6416dc11462993099 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:47:14 -0400 Subject: [PATCH 21/38] [skip ci] misc to bump build --- .github/workflows/release.yml | 2 +- packages/core/util/index.ts | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2c762b53aa..b65e941033 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -70,7 +70,7 @@ jobs: apt install --yes wine wine32 wine64 libwine libwine:i386 fonts-wine - name: Install build deps run: | - apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev openjdk-21-jdk-headless + apt install --yes python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev # We are just cloning the esigner repo instead of calling their github # action directly https://github.com/SSLcom/esigner-codesign - name: Get ssl.com esigner zip file and unzip diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index 46151a9f06..8cf71d60f9 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -1426,8 +1426,7 @@ export function gatherOverlaps(regions: BasicFeature[], w = 5000) { } export function stripAlpha(str: string) { - const c = colord(str) - return c.alpha(1).toHex() + return colord(str).alpha(1).toHex() } export function getStrokeProps(str: string) { From 5b8e66d1faaff438d516a25453f9cb5f6cabb7fa Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 19 Sep 2024 00:01:13 +0000 Subject: [PATCH 22/38] Prepare for v2.15.3 release --- CHANGELOG.md | 4 ++++ website/blog/2024-09-19-v2.15.3-release.md | 20 ++++++++++++++++++++ website/docusaurus.config.json | 2 +- 3 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 website/blog/2024-09-19-v2.15.3-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 693c9e323e..3a2875d51f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 + +Done in 0.57s. + yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 ## 2.15.2 (2024-09-18) diff --git a/website/blog/2024-09-19-v2.15.3-release.md b/website/blog/2024-09-19-v2.15.3-release.md new file mode 100644 index 0000000000..b70f546672 --- /dev/null +++ b/website/blog/2024-09-19-v2.15.3-release.md @@ -0,0 +1,20 @@ +--- +title: v2.15.3 Release +date: 2024-09-19 00:00:42 +tags: ['release', 'jbrowse 2'] +--- + +Re-publish + +## Downloads + +- [v2.15.3](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.3) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 + +Done in 0.57s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index d5b831fccc..e6a814856f 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.2" + "currentVersion": "v2.15.3" } } From c0f82fe7b210622dd462e702641cc6da01109c6e Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 19 Sep 2024 00:02:53 +0000 Subject: [PATCH 23/38] [update docs] v2.15.3 --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 4 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 201 insertions(+), 201 deletions(-) diff --git a/lerna.json b/lerna.json index 33a5bc6f06..41bdf3d775 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.2", + "version": "2.15.3", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 2f19f94458..9424e6c846 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index 3f3a1a1e14..acf48565ae 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index e44c0bf3a9..a578a19767 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index c8c55671d5..f1e636503c 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.2", + "version": "2.15.3", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", + "@jbrowse/core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index 37cf06068c..e6914bdad5 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index c6fe0fee33..f2885e5f10 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.2", + "@jbrowse/core": "^2.15.3", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index ba205d628e..190c0bf5ce 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 70dc07abbf..9d61dc6ab9 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.2", + "@jbrowse/sv-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index 386fe6329e..df5e78e4f5 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index b1842551ea..8d2389fe31 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 2151f8025c..82859b3759 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index e68ddd2658..205f71e445 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index fb1fbff94e..526ccd84de 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 62f3d33834..8ace6e37b9 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 4b3f6b76f6..4bf197f8cd 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 8a11b633be..530385f2c3 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 1cbe8a5b4c..020c353870 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index f1b941d5f3..a9f567a86d 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index bc6e76500f..a9a0068554 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index b4387cd1e1..d604c6357d 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index f178cd5fff..345bdc7315 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index b081564d0b..2b5e0b25f9 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index eec648125c..43bc82b21d 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.2", + "@jbrowse/text-indexing": "^2.15.3", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index 571b6a25f6..bf19fd4f01 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index 906e9d85c4..d7b778ee65 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index 1311fd3a8e..e61561e631 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 3fc07dc93a..40cff9244a 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 253763701d..12681b6d91 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 60dafce7eb..9beff555ed 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index bb09950164..f0e53718f6 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index cfe6c64364..72d45b1209 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.2", + "@jbrowse/plugin-variants": "^2.15.3", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index ddc5f452ee..c87438e6b2 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 16657acace..1b60f1186b 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index fccb38f34b..acf031cfec 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.2" + "@jbrowse/text-indexing": "^2.15.3" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index c1249166ac..d8fbc008cc 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index fc0d3ff852..6e1042b688 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.2", + "@jbrowse/sv-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index 77aa24d8f9..f9e0e2fce0 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index ba2f154d4c..3252df5292 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.2/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 0df3346391..68ab6bcdd3 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.2", + "version": "2.15.3", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 027cfc8b91..0b842a4dc3 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-jobs-management": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-text-indexing": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/text-indexing": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-jobs-management": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-text-indexing": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/text-indexing": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index d91d7d798d..295255df9e 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.2", + "version": "2.15.3", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/react-linear-genome-view": "^2.15.2", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/react-linear-genome-view": "^2.15.3", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 1c1bf4dad4..99397cfb21 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.2", + "version": "2.15.3", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index 744cad66db..b03ea4b796 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/web-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/web-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index f3146b7e6b..7b6b472b95 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.2", - "@jbrowse/embedded-core": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/embedded-core": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index b4e621629b..e03b6966bd 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.2", + "version": "2.15.3", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.2", - "@jbrowse/embedded-core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", + "@jbrowse/core": "^2.15.3", + "@jbrowse/embedded-core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index fa3b78f627..b0c998ee10 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.2", + "version": "2.15.3", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.2", - "@jbrowse/core": "^2.15.2", - "@jbrowse/plugin-alignments": "^2.15.2", - "@jbrowse/plugin-arc": "^2.15.2", - "@jbrowse/plugin-authentication": "^2.15.2", - "@jbrowse/plugin-bed": "^2.15.2", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.2", - "@jbrowse/plugin-circular-view": "^2.15.2", - "@jbrowse/plugin-comparative-adapters": "^2.15.2", - "@jbrowse/plugin-config": "^2.15.2", - "@jbrowse/plugin-data-management": "^2.15.2", - "@jbrowse/plugin-dotplot-view": "^2.15.2", - "@jbrowse/plugin-gccontent": "^2.15.2", - "@jbrowse/plugin-gff3": "^2.15.2", - "@jbrowse/plugin-grid-bookmark": "^2.15.2", - "@jbrowse/plugin-gtf": "^2.15.2", - "@jbrowse/plugin-hic": "^2.15.2", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.2", - "@jbrowse/plugin-linear-comparative-view": "^2.15.2", - "@jbrowse/plugin-linear-genome-view": "^2.15.2", - "@jbrowse/plugin-lollipop": "^2.15.2", - "@jbrowse/plugin-menus": "^2.15.2", - "@jbrowse/plugin-rdf": "^2.15.2", - "@jbrowse/plugin-sequence": "^2.15.2", - "@jbrowse/plugin-spreadsheet-view": "^2.15.2", - "@jbrowse/plugin-sv-inspector": "^2.15.2", - "@jbrowse/plugin-svg": "^2.15.2", - "@jbrowse/plugin-trix": "^2.15.2", - "@jbrowse/plugin-variants": "^2.15.2", - "@jbrowse/plugin-wiggle": "^2.15.2", - "@jbrowse/product-core": "^2.15.2", - "@jbrowse/web-core": "^2.15.2", + "@jbrowse/app-core": "^2.15.3", + "@jbrowse/core": "^2.15.3", + "@jbrowse/plugin-alignments": "^2.15.3", + "@jbrowse/plugin-arc": "^2.15.3", + "@jbrowse/plugin-authentication": "^2.15.3", + "@jbrowse/plugin-bed": "^2.15.3", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", + "@jbrowse/plugin-circular-view": "^2.15.3", + "@jbrowse/plugin-comparative-adapters": "^2.15.3", + "@jbrowse/plugin-config": "^2.15.3", + "@jbrowse/plugin-data-management": "^2.15.3", + "@jbrowse/plugin-dotplot-view": "^2.15.3", + "@jbrowse/plugin-gccontent": "^2.15.3", + "@jbrowse/plugin-gff3": "^2.15.3", + "@jbrowse/plugin-grid-bookmark": "^2.15.3", + "@jbrowse/plugin-gtf": "^2.15.3", + "@jbrowse/plugin-hic": "^2.15.3", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", + "@jbrowse/plugin-linear-comparative-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-lollipop": "^2.15.3", + "@jbrowse/plugin-menus": "^2.15.3", + "@jbrowse/plugin-rdf": "^2.15.3", + "@jbrowse/plugin-sequence": "^2.15.3", + "@jbrowse/plugin-spreadsheet-view": "^2.15.3", + "@jbrowse/plugin-sv-inspector": "^2.15.3", + "@jbrowse/plugin-svg": "^2.15.3", + "@jbrowse/plugin-trix": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-wiggle": "^2.15.3", + "@jbrowse/product-core": "^2.15.3", + "@jbrowse/web-core": "^2.15.3", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", From 096f59a91f13cbe6912ff2a827affeb62faeb40c Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 19 Sep 2024 00:14:50 +0000 Subject: [PATCH 24/38] [skip ci] Bump version.js --- products/jbrowse-react-linear-genome-view/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-linear-genome-view/src/version.js b/products/jbrowse-react-linear-genome-view/src/version.js index 1a820b8f83..626d897e35 100644 --- a/products/jbrowse-react-linear-genome-view/src/version.js +++ b/products/jbrowse-react-linear-genome-view/src/version.js @@ -1 +1 @@ -export const version = '2.15.2' +export const version = '2.15.3' From 0b4c9a04374842184a4999a8fe5e56e8d3e5afa7 Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 19 Sep 2024 00:14:50 +0000 Subject: [PATCH 25/38] [skip ci] Bump version.js --- products/jbrowse-react-circular-genome-view/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-circular-genome-view/src/version.js b/products/jbrowse-react-circular-genome-view/src/version.js index 1a820b8f83..626d897e35 100644 --- a/products/jbrowse-react-circular-genome-view/src/version.js +++ b/products/jbrowse-react-circular-genome-view/src/version.js @@ -1 +1 @@ -export const version = '2.15.2' +export const version = '2.15.3' From 814dee875831cb5bdc21312cdfc5c811f4784992 Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 19 Sep 2024 00:20:37 +0000 Subject: [PATCH 26/38] [skip ci] Bump version.js --- products/jbrowse-react-app/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-app/src/version.js b/products/jbrowse-react-app/src/version.js index 1a820b8f83..626d897e35 100644 --- a/products/jbrowse-react-app/src/version.js +++ b/products/jbrowse-react-app/src/version.js @@ -1 +1 @@ -export const version = '2.15.2' +export const version = '2.15.3' From 37cfb5c0ce04f684eff0f65d08061e99ce80f8f6 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 19:58:00 -0400 Subject: [PATCH 27/38] [update docs] Autogen docs --- website/docs/config/BaseAssembly.md | 3 +- .../docs/config/LinearAlignmentsDisplay.md | 5 +- website/docs/config/LinearGCContentDisplay.md | 4 +- .../config/LinearGCContentTrackDisplay.md | 4 +- website/docs/config/LinearHicDisplay.md | 2 +- website/docs/config/LinearPileupDisplay.md | 5 +- .../docs/config/LinearSNPCoverageDisplay.md | 7 +- .../config/NcbiSequenceReportAliasAdapter.md | 27 + website/docs/config/ReferenceSequenceTrack.md | 20 + website/docs/config/UnindexedFastaAdapter.md | 38 + website/docs/models/Assembly.md | 11 +- website/docs/models/AssemblyManager.md | 8 +- website/docs/models/BaseChordDisplay.md | 2 +- website/docs/models/BaseConnectionModel.md | 6 +- website/docs/models/BaseLinearDisplay.md | 22 +- website/docs/models/BaseRootModel.md | 2 +- website/docs/models/BaseWebSession.md | 2 +- website/docs/models/BreakpointSplitView.md | 32 +- website/docs/models/CircularView.md | 7 - website/docs/models/DotplotDisplay.md | 2 +- website/docs/models/DotplotView.md | 10 - .../docs/models/JBrowseDesktopSessionModel.md | 2 +- ...JBrowseReactCircularGenomeViewRootModel.md | 4 +- ...owseReactCircularGenomeViewSessionModel.md | 2 +- .../JBrowseReactLinearGenomeViewRootModel.md | 4 +- ...BrowseReactLinearGenomeViewSessionModel.md | 2 +- .../docs/models/LinearAlignmentsDisplay.md | 9 +- .../models/LinearAlignmentsDisplayMixin.md | 8 +- website/docs/models/LinearComparativeView.md | 12 +- website/docs/models/LinearGenomeView.md | 21 +- website/docs/models/LinearPileupDisplay.md | 2 +- .../models/LinearReferenceSequenceDisplay.md | 34 + .../docs/models/LinearSNPCoverageDisplay.md | 2 +- website/docs/models/LinearWiggleDisplay.md | 2 +- .../docs/models/MultiLinearWiggleDisplay.md | 2 +- website/docs/models/SnackbarModel.md | 18 +- website/docs/models/SpreadsheetView.md | 7 - website/docs/models/SvInspectorView.md | 9 +- yarn.lock | 914 +++++++++--------- 39 files changed, 696 insertions(+), 577 deletions(-) create mode 100644 website/docs/config/NcbiSequenceReportAliasAdapter.md create mode 100644 website/docs/config/UnindexedFastaAdapter.md diff --git a/website/docs/config/BaseAssembly.md b/website/docs/config/BaseAssembly.md index 720a35ca34..e13fb60d3d 100644 --- a/website/docs/config/BaseAssembly.md +++ b/website/docs/config/BaseAssembly.md @@ -36,7 +36,8 @@ sequence refers to a reference sequence track that has an adapter containing, importantly, a sequence adapter such as IndexedFastaAdapter ```js -sequence: pluginManager.getTrackType('ReferenceSequenceTrack').configSchema +sequence: pluginManager.getTrackType('ReferenceSequenceTrack')! + .configSchema ``` #### slot: refNameColors diff --git a/website/docs/config/LinearAlignmentsDisplay.md b/website/docs/config/LinearAlignmentsDisplay.md index 28a6c6da15..f82c627bfe 100644 --- a/website/docs/config/LinearAlignmentsDisplay.md +++ b/website/docs/config/LinearAlignmentsDisplay.md @@ -18,13 +18,14 @@ quantitative "snpcoverage" sub-display track showing SNP frequencies #### slot: pileupDisplay ```js -pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema +pileupDisplay: pm.getDisplayType('LinearPileupDisplay')!.configSchema ``` #### slot: snpCoverageDisplay ```js -snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay').configSchema +snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')! + .configSchema ``` #### slot: height diff --git a/website/docs/config/LinearGCContentDisplay.md b/website/docs/config/LinearGCContentDisplay.md index 8b864be16c..dfbfd19233 100644 --- a/website/docs/config/LinearGCContentDisplay.md +++ b/website/docs/config/LinearGCContentDisplay.md @@ -15,6 +15,6 @@ extends LinearWiggleDisplay ### LinearGCContentDisplay - Derives from ```js -baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay') - .configSchema +baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')! + .configSchema ``` diff --git a/website/docs/config/LinearGCContentTrackDisplay.md b/website/docs/config/LinearGCContentTrackDisplay.md index 67110a5edc..6352d286c1 100644 --- a/website/docs/config/LinearGCContentTrackDisplay.md +++ b/website/docs/config/LinearGCContentTrackDisplay.md @@ -15,6 +15,6 @@ extends LinearWiggleDisplay, used specifically for GCContentTrack ### LinearGCContentTrackDisplay - Derives from ```js -baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay') - .configSchema +baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')! + .configSchema ``` diff --git a/website/docs/config/LinearHicDisplay.md b/website/docs/config/LinearHicDisplay.md index e7cd1db3b0..1193802de3 100644 --- a/website/docs/config/LinearHicDisplay.md +++ b/website/docs/config/LinearHicDisplay.md @@ -15,7 +15,7 @@ source code. See [Config guide](/docs/config_guide) for more info #### slot: renderer ```js -renderer: pluginManager.getRendererType('HicRenderer').configSchema +renderer: pluginManager.getRendererType('HicRenderer')!.configSchema ``` ### LinearHicDisplay - Derives from diff --git a/website/docs/config/LinearPileupDisplay.md b/website/docs/config/LinearPileupDisplay.md index 6e548bde0c..4585d89905 100644 --- a/website/docs/config/LinearPileupDisplay.md +++ b/website/docs/config/LinearPileupDisplay.md @@ -26,8 +26,9 @@ defaultRendering: { ```js renderers: ConfigurationSchema('RenderersConfiguration', { - PileupRenderer: pluginManager.getRendererType('PileupRenderer').configSchema, -}) + PileupRenderer: + pluginManager.getRendererType('PileupRenderer')!.configSchema, + }) ``` #### slot: maxFeatureScreenDensity diff --git a/website/docs/config/LinearSNPCoverageDisplay.md b/website/docs/config/LinearSNPCoverageDisplay.md index 54913914ff..fa3ba3720d 100644 --- a/website/docs/config/LinearSNPCoverageDisplay.md +++ b/website/docs/config/LinearSNPCoverageDisplay.md @@ -83,9 +83,10 @@ multiTicks: { ```js renderers: ConfigurationSchema('RenderersConfiguration', { - SNPCoverageRenderer: pluginManager.getRendererType('SNPCoverageRenderer') - .configSchema, -}) + SNPCoverageRenderer: pluginManager.getRendererType( + 'SNPCoverageRenderer', + )!.configSchema, + }) ``` ### LinearSNPCoverageDisplay - Derives from diff --git a/website/docs/config/NcbiSequenceReportAliasAdapter.md b/website/docs/config/NcbiSequenceReportAliasAdapter.md new file mode 100644 index 0000000000..ac48a0b654 --- /dev/null +++ b/website/docs/config/NcbiSequenceReportAliasAdapter.md @@ -0,0 +1,27 @@ +--- +id: ncbisequencereportaliasadapter +title: NcbiSequenceReportAliasAdapter +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +### Source file + +[plugins/config/src/NcbiSequenceReportAliasAdapter/configSchema.ts](https://github.com/GMOD/jbrowse-components/blob/main/plugins/config/src/NcbiSequenceReportAliasAdapter/configSchema.ts) + +can read "sequence_report.tsv" type files from NCBI + +### NcbiSequenceReportAliasAdapter - Slots + +#### slot: location + +```js +location: { + type: 'fileLocation', + defaultValue: { + uri: '/path/to/my/sequence_report.tsv', + locationType: 'UriLocation', + }, + } +``` diff --git a/website/docs/config/ReferenceSequenceTrack.md b/website/docs/config/ReferenceSequenceTrack.md index d9ebca549e..2e97174505 100644 --- a/website/docs/config/ReferenceSequenceTrack.md +++ b/website/docs/config/ReferenceSequenceTrack.md @@ -45,6 +45,26 @@ name: { } ``` +#### slot: sequenceType + +```js +sequenceType: { + type: 'string', + description: 'either dna or pep', + defaultValue: 'dna', + } +``` + +#### slot: description + +```js +description: { + description: 'a description of the track', + type: 'string', + defaultValue: '', + } +``` + #### slot: metadata ```js diff --git a/website/docs/config/UnindexedFastaAdapter.md b/website/docs/config/UnindexedFastaAdapter.md new file mode 100644 index 0000000000..d462d0fab0 --- /dev/null +++ b/website/docs/config/UnindexedFastaAdapter.md @@ -0,0 +1,38 @@ +--- +id: unindexedfastaadapter +title: UnindexedFastaAdapter +--- + +Note: this document is automatically generated from configuration objects in our +source code. See [Config guide](/docs/config_guide) for more info + +### Source file + +[plugins/sequence/src/UnindexedFastaAdapter/configSchema.ts](https://github.com/GMOD/jbrowse-components/blob/main/plugins/sequence/src/UnindexedFastaAdapter/configSchema.ts) + +### UnindexedFastaAdapter - Slots + +#### slot: fastaLocation + +```js +fastaLocation: { + type: 'fileLocation', + defaultValue: { + uri: '/path/to/seq.fa', + locationType: 'UriLocation', + }, + } +``` + +#### slot: metadataLocation + +```js +metadataLocation: { + description: 'Optional metadata file', + type: 'fileLocation', + defaultValue: { + uri: '/path/to/fa.metadata.yaml', + locationType: 'UriLocation', + }, + } +``` diff --git a/website/docs/models/Assembly.md b/website/docs/models/Assembly.md index 8bde975ab9..71e8000a48 100644 --- a/website/docs/models/Assembly.md +++ b/website/docs/models/Assembly.md @@ -122,6 +122,13 @@ string[] ### Assembly - Methods +#### method: getConf + +```js +// type signature +getConf: (arg: string) => any +``` + #### method: getCanonicalRefName ```js @@ -174,7 +181,7 @@ getReverseRefNameMapForAdapter: (adapterConf: AdapterConf, opts: BaseOptions) => ```js // type signature -setLoaded: ({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: Loading) => void +setLoaded: ({ regions, refNameAliases, lowerCaseRefNameAliases, cytobands, }: { regions: Region[]; refNameAliases: RefNameAliases; lowerCaseRefNameAliases: RefNameAliases; cytobands: Feature[]; }) => void ``` #### action: setError @@ -195,7 +202,7 @@ setRegions: (regions: Region[]) => void ```js // type signature -setRefNameAliases: (aliases: RefNameAliases, lcAliases: RefNameAliases) => void +setRefNameAliases: (aliases: RefNameAliases, lowerCaseAliases: RefNameAliases) => void ``` #### action: setCytobands diff --git a/website/docs/models/AssemblyManager.md b/website/docs/models/AssemblyManager.md index c9ea4e6ac8..0ac0849609 100644 --- a/website/docs/models/AssemblyManager.md +++ b/website/docs/models/AssemblyManager.md @@ -21,7 +21,7 @@ session.assemblies, session.sessionAssemblies, and session.temporaryAssemblies ```js // type signature -IArrayType>; }, { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undef... +IArrayType>; }, { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 5 m... // code assemblies: types.array(assemblyFactory(conf, pm)) ``` @@ -51,7 +51,7 @@ session.temporaryAssemblies to load from ```js // type signature -get: (asmName: string) => { configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ..... +get: (asmName: string) => { configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 more ... & IS... ``` #### method: waitForAssembly @@ -61,7 +61,7 @@ with regions loaded ```js // type signature -waitForAssembly: (assemblyName: string) => Promise<{ configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | unde... +waitForAssembly: (assemblyName: string) => Promise<{ configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 ... ``` #### method: getRefNameMapForAdapter @@ -95,7 +95,7 @@ directly ```js // type signature -removeAssembly: (asm: { configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 more ... & ... +removeAssembly: (asm: { configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined; } & ... 6 more ... & IStateTreeNode<..... ``` #### action: addAssembly diff --git a/website/docs/models/BaseChordDisplay.md b/website/docs/models/BaseChordDisplay.md index 5613af7605..0c00dfdece 100644 --- a/website/docs/models/BaseChordDisplay.md +++ b/website/docs/models/BaseChordDisplay.md @@ -93,7 +93,7 @@ isCompatibleWithRenderer: (renderer: RendererType) => renderer is CircularChordR ```js // type signature -renderSvg: (opts: ExportSvgOptions & { theme: ThemeOptions; }) => Promise +renderSvg: (opts: ExportSvgOptions & { theme?: ThemeOptions; }) => Promise ``` ### BaseChordDisplay - Actions diff --git a/website/docs/models/BaseConnectionModel.md b/website/docs/models/BaseConnectionModel.md index 3a451cc7a9..3f351167dd 100644 --- a/website/docs/models/BaseConnectionModel.md +++ b/website/docs/models/BaseConnectionModel.md @@ -54,21 +54,21 @@ connect: (_arg: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName ```js // type signature -addTrackConf: (trackConf: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record): Record | ({ [x: string]: any; } & NonEmptyObject & ... & IStateTreeNode<...>); } & IStateTreeNode<...>) => any +addTrackConf: (trackConf: TrackConf) => any ``` #### action: addTrackConfs ```js // type signature -addTrackConfs: (trackConfs: ({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record): Record | ({ [x: string]: any; } & NonEmptyObject & ... & IStateTreeNode<...>); } & IStateTreeNode<...>)[]) => any[] +addTrackConfs: (trackConfs: TrackConf[]) => void ``` #### action: setTrackConfs ```js // type signature -setTrackConfs: (trackConfs: ({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record): Record | ({ [x: string]: any; } & NonEmptyObject & ... & IStateTreeNode<...>); } & IStateTreeNode<...>)[]) => IMSTArray<...> & IStateTreeNode<...> +setTrackConfs: (trackConfs: ({ [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: Record): Record | ({ [x: string]: any; } & NonEmptyObject & ... & IStateTreeNode<...>); } & IStateTreeNode<...>)[]) => void ``` #### action: clear diff --git a/website/docs/models/BaseLinearDisplay.md b/website/docs/models/BaseLinearDisplay.md index 180bd12813..9b9d99dcea 100644 --- a/website/docs/models/BaseLinearDisplay.md +++ b/website/docs/models/BaseLinearDisplay.md @@ -45,6 +45,16 @@ configuration: ConfigurationReference(configSchema) ### BaseLinearDisplay - Getters +#### getter: DisplayMessageComponent + +if a display-level message should be displayed instead of the blocks, make this +return a react component + +```js +// type +any +``` + #### getter: blockType ```js @@ -73,7 +83,7 @@ number ```js // type -React.FC +React.ComponentType ``` #### getter: selectedFeatureId @@ -86,16 +96,6 @@ feature string ``` -#### getter: DisplayMessageComponent - -if a display-level message should be displayed instead of the blocks, make this -return a react component - -```js -// type -any -``` - #### getter: features a CompositeMap of `featureId -> feature obj` that just looks in all the block diff --git a/website/docs/models/BaseRootModel.md b/website/docs/models/BaseRootModel.md index 2e89283900..ece73c32fe 100644 --- a/website/docs/models/BaseRootModel.md +++ b/website/docs/models/BaseRootModel.md @@ -52,7 +52,7 @@ sessionPath: types.optional(types.string, '') ```js // type signature -IOptionalIType>; }, { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases |... +IOptionalIType>; }, { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytob... // code assemblyManager: types.optional( assemblyManagerFactory(assemblyConfigSchema, pluginManager), diff --git a/website/docs/models/BaseWebSession.md b/website/docs/models/BaseWebSession.md index 24e436adab..f0c06ccf2f 100644 --- a/website/docs/models/BaseWebSession.md +++ b/website/docs/models/BaseWebSession.md @@ -117,7 +117,7 @@ TextSearchManager ```js // type -{ assemblies: IMSTArray>; }, { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feat... +{ assemblies: IMSTArray>; }, { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined... ``` #### getter: savedSessions diff --git a/website/docs/models/BreakpointSplitView.md b/website/docs/models/BreakpointSplitView.md index bf99ccaa55..8476933906 100644 --- a/website/docs/models/BreakpointSplitView.md +++ b/website/docs/models/BreakpointSplitView.md @@ -86,7 +86,7 @@ interactToggled: false IArrayType, [undefined]>; displayName: IMaybe>; minimized: IType; } & { ...; }, { ...; } & ... 15 more ... & { ...; }, ModelCreationType<...>, _NotCustomized>> // code views: types.array( - pluginManager.getViewType('LinearGenomeView') + pluginManager.getViewType('LinearGenomeView')! .stateModel as LinearGenomeViewStateModel, ) ``` @@ -95,11 +95,12 @@ views: types.array( #### getter: matchedTracks -Find all track ids that match across multiple views +Find all track ids that match across multiple views, or return just the single +view's track if only a single row is used ```js // type -any[] +(IMSTArray & IStateTreeNode>) | { configuration: { trackId: string; }; }[] ``` ### BreakpointSplitView - Methods @@ -132,6 +133,15 @@ e.g. they are one sided hasTranslocations: (trackConfigId: string) => any ``` +#### method: hasPairedFeatures + +Paired features similar to breakends, but simpler, like BEDPE + +```js +// type signature +hasPairedFeatures: (trackConfigId: string) => any +``` + #### method: getTrackFeatures Get a composite map of featureId-\>feature map for a track across multiple views @@ -152,7 +162,7 @@ getMatchedFeaturesInLayout: (trackConfigId: string, features: Feature[][]) => { ```js // type signature -menuItems: () => ({ label: string; subMenu: MenuItem[]; } | { label: string; type: string; checked: boolean; onClick: () => void; icon?: undefined; } | { label: string; type: string; icon: OverridableComponent> & { ...; }; checked: boolean; onClick: () => void; } | { ...; })[] +menuItems: () => ({ label: string; subMenu: MenuItem[]; } | { label: string; onClick: () => void; type?: undefined; checked?: undefined; icon?: undefined; } | { label: string; type: string; checked: boolean; onClick: () => void; icon?: undefined; } | { ...; } | { ...; })[] ``` ### BreakpointSplitView - Actions @@ -171,13 +181,6 @@ setWidth: (newWidth: number) => void removeView: (view: { id: string; displayName: string; minimized: boolean; type: string; offsetPx: number; bpPerPx: number; displayedRegions: Region[] & IStateTreeNode, [...]>>; ... 11 more ...; showTrackOutlines: boolean; } & ... 18 more ... & IStateTreeNode<...>) => void ``` -#### action: closeView - -```js -// type signature -closeView: () => void -``` - #### action: toggleInteract ```js @@ -205,3 +208,10 @@ toggleLinkViews: () => void // type signature setMatchedTrackFeatures: (obj: Record) => void ``` + +#### action: reverseViewOrder + +```js +// type signature +reverseViewOrder: () => void +``` diff --git a/website/docs/models/CircularView.md b/website/docs/models/CircularView.md index 213c8aa29b..e43b40774a 100644 --- a/website/docs/models/CircularView.md +++ b/website/docs/models/CircularView.md @@ -455,13 +455,6 @@ setBpPerPx: (newVal: number) => void setModelViewWhenAdjust: (secondCondition: boolean) => void ``` -#### action: closeView - -```js -// type signature -closeView: () => void -``` - #### action: setDisplayedRegions ```js diff --git a/website/docs/models/DotplotDisplay.md b/website/docs/models/DotplotDisplay.md index fc4318d37d..51325b140e 100644 --- a/website/docs/models/DotplotDisplay.md +++ b/website/docs/models/DotplotDisplay.md @@ -54,7 +54,7 @@ renderProps: () => any ```js // type signature -renderSvg: (opts: ExportSvgOptions & { theme: ThemeOptions; }) => Promise +renderSvg: (opts: ExportSvgOptions & { theme?: ThemeOptions; }) => Promise ``` ### DotplotDisplay - Actions diff --git a/website/docs/models/DotplotView.md b/website/docs/models/DotplotView.md index d5f34da8f6..507d9ab6fb 100644 --- a/website/docs/models/DotplotView.md +++ b/website/docs/models/DotplotView.md @@ -327,16 +327,6 @@ setHeight: (newHeight: number) => number setError: (e: unknown) => void ``` -#### action: closeView - -removes the view itself from the state tree entirely by calling the parent -removeView - -```js -// type signature -closeView: () => void -``` - #### action: zoomOutButton ```js diff --git a/website/docs/models/JBrowseDesktopSessionModel.md b/website/docs/models/JBrowseDesktopSessionModel.md index b5177574ec..c9e482fbf9 100644 --- a/website/docs/models/JBrowseDesktopSessionModel.md +++ b/website/docs/models/JBrowseDesktopSessionModel.md @@ -76,7 +76,7 @@ Menu[] ```js // type -{ assemblies: IMSTArray>; }, { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feat... +{ assemblies: IMSTArray>; }, { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undefined... ``` #### getter: savedSessionNames diff --git a/website/docs/models/JBrowseReactCircularGenomeViewRootModel.md b/website/docs/models/JBrowseReactCircularGenomeViewRootModel.md index 15f1608287..5e520d3cc1 100644 --- a/website/docs/models/JBrowseReactCircularGenomeViewRootModel.md +++ b/website/docs/models/JBrowseReactCircularGenomeViewRootModel.md @@ -27,7 +27,7 @@ config: createConfigModel(pluginManager, assemblyConfigSchema) ```js // type signature -IModelType<{ id: IOptionalIType, [undefined]>; name: ISimpleType; margin: IType; } & { ...; } & { ...; } & { ...; }, { ...; } & ... 20 more ... & { ...; }, _NotCustomized, _NotCustomized> +IModelType<{ id: IOptionalIType, [undefined]>; name: ISimpleType; margin: IType; } & { ...; } & { ...; } & { ...; }, { ...; } & ... 21 more ... & { ...; }, _NotCustomized, _NotCustomized> // code session: Session ``` @@ -36,7 +36,7 @@ session: Session ```js // type signature -IOptionalIType>; }, { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases |... +IOptionalIType>; }, { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytob... // code assemblyManager: types.optional(assemblyManagerType, {}) ``` diff --git a/website/docs/models/JBrowseReactCircularGenomeViewSessionModel.md b/website/docs/models/JBrowseReactCircularGenomeViewSessionModel.md index 3d2306cb4b..4944090c55 100644 --- a/website/docs/models/JBrowseReactCircularGenomeViewSessionModel.md +++ b/website/docs/models/JBrowseReactCircularGenomeViewSessionModel.md @@ -30,7 +30,7 @@ composed of // type signature IAnyModelType // code -view: pluginManager.getViewType('CircularView').stateModel +view: pluginManager.getViewType('CircularView')!.stateModel ``` ### JBrowseReactCircularGenomeViewSessionModel - Getters diff --git a/website/docs/models/JBrowseReactLinearGenomeViewRootModel.md b/website/docs/models/JBrowseReactLinearGenomeViewRootModel.md index 42b4182eed..a28c26e524 100644 --- a/website/docs/models/JBrowseReactLinearGenomeViewRootModel.md +++ b/website/docs/models/JBrowseReactLinearGenomeViewRootModel.md @@ -27,7 +27,7 @@ config: createConfigModel(pluginManager, assemblyConfig) ```js // type signature -IModelType<{ id: IOptionalIType, [undefined]>; name: ISimpleType; margin: IType; } & { ...; } & { ...; } & { ...; } & { ...; }, { ...; } & ... 21 more ... & { ...; }, _NotCustomized, _NotCustomized> +IModelType<{ id: IOptionalIType, [undefined]>; name: ISimpleType; margin: IType; } & { ...; } & { ...; } & { ...; } & { ...; }, { ...; } & ... 22 more ... & { ...; }, _NotCustomized, _NotCustomized> // code session: Session ``` @@ -36,7 +36,7 @@ session: Session ```js // type signature -IOptionalIType>; }, { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases |... +IOptionalIType>; }, { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytob... // code assemblyManager: types.optional(AssemblyManager, {}) ``` diff --git a/website/docs/models/JBrowseReactLinearGenomeViewSessionModel.md b/website/docs/models/JBrowseReactLinearGenomeViewSessionModel.md index 8b17d27f3e..0913727d83 100644 --- a/website/docs/models/JBrowseReactLinearGenomeViewSessionModel.md +++ b/website/docs/models/JBrowseReactLinearGenomeViewSessionModel.md @@ -31,7 +31,7 @@ composed of // type signature IModelType<{ id: IOptionalIType, [undefined]>; displayName: IMaybe>; minimized: IType; } & { ...; }, { ...; } & ... 15 more ... & { ...; }, ModelCreationType<...>, _NotCustomized> // code -view: pluginManager.getViewType('LinearGenomeView') +view: pluginManager.getViewType('LinearGenomeView')! .stateModel as LinearGenomeViewStateModel ``` diff --git a/website/docs/models/LinearAlignmentsDisplay.md b/website/docs/models/LinearAlignmentsDisplay.md index fc05c9151b..990a696ca8 100644 --- a/website/docs/models/LinearAlignmentsDisplay.md +++ b/website/docs/models/LinearAlignmentsDisplay.md @@ -47,7 +47,7 @@ any any ``` -#### getter: DisplayBlurb +#### getter: alignmentsdisplaymodel ```js // type @@ -135,6 +135,13 @@ setPileupDisplay: (configuration: { [x: string]: any; } & NonEmptyObject & { set setHeight: (n: number) => number ``` +#### action: setFilterBy + +```js +// type signature +setFilterBy: (filter: IFilter) => void +``` + #### action: setLowerPanelType ```js diff --git a/website/docs/models/LinearAlignmentsDisplayMixin.md b/website/docs/models/LinearAlignmentsDisplayMixin.md index cdf514f506..281f8fd0f6 100644 --- a/website/docs/models/LinearAlignmentsDisplayMixin.md +++ b/website/docs/models/LinearAlignmentsDisplayMixin.md @@ -22,7 +22,11 @@ refers to LinearPileupDisplay sub-display model // type signature IMaybe // code -PileupDisplay: types.maybe(types.union(...lowerPanelDisplays)) +PileupDisplay: types.maybe( + types.union( + ...getLowerPanelDisplays(pluginManager).map(f => f.stateModel), + ), + ) ``` #### property: SNPCoverageDisplay @@ -34,7 +38,7 @@ refers to LinearSNPCoverageDisplay sub-display model IMaybe // code SNPCoverageDisplay: types.maybe( - pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel, + pluginManager.getDisplayType('LinearSNPCoverageDisplay')!.stateModel, ) ``` diff --git a/website/docs/models/LinearComparativeView.md b/website/docs/models/LinearComparativeView.md index d69b9b0bc0..2f39860a74 100644 --- a/website/docs/models/LinearComparativeView.md +++ b/website/docs/models/LinearComparativeView.md @@ -92,7 +92,7 @@ currently this is limited to an array of two IArrayType, [undefined]>; displayName: IMaybe>; minimized: IType; } & { ...; }, { ...; } & ... 15 more ... & { ...; }, ModelCreationType<...>, _NotCustomized>> // code views: types.array( - pluginManager.getViewType('LinearGenomeView') + pluginManager.getViewType('LinearGenomeView')! .stateModel as LinearGenomeViewStateModel, ) ``` @@ -190,16 +190,6 @@ setViews: (views: ModelCreationType, [...]>>; ... 11 more ...; showTrackOutlines: boolean; } & ... 18 more ... & IStateTreeNode<...>) => void ``` -#### action: closeView - -removes the view itself from the state tree entirely by calling the parent -removeView - -```js -// type signature -closeView: () => void -``` - #### action: setMiddleComparativeHeight ```js diff --git a/website/docs/models/LinearGenomeView.md b/website/docs/models/LinearGenomeView.md index de5ddc1a26..ef3a61729d 100644 --- a/website/docs/models/LinearGenomeView.md +++ b/website/docs/models/LinearGenomeView.md @@ -191,10 +191,10 @@ highlights on the LGV from the URL parameters ```js // type signature -IOptionalIType, Required, Required>>, [...]> +IOptionalIType>, [undefined]> // code highlight: types.optional( - types.array(types.frozen>()), + types.array(types.frozen()), [], ) ``` @@ -348,7 +348,7 @@ number ```js // type -any +unknown ``` #### getter: maxOffset @@ -656,21 +656,21 @@ setShowGridlines: (b: boolean) => void ```js // type signature -addToHighlights: (highlight: Required) => void +addToHighlights: (highlight: HighlightType) => void ``` #### action: setHighlight ```js // type signature -setHighlight: (highlight: Required[]) => void +setHighlight: (highlight?: HighlightType[]) => void ``` #### action: removeHighlight ```js // type signature -removeHighlight: (highlight: Required) => void +removeHighlight: (highlight: HighlightType) => void ``` #### action: scrollTo @@ -768,13 +768,6 @@ moveTrackToBottom: (id: string) => void moveTrack: (movingId: string, targetId: string) => void ``` -#### action: closeView - -```js -// type signature -closeView: () => void -``` - #### action: toggleTrack ```js @@ -922,7 +915,7 @@ is returned. Will pop up a search dialog if multiple results are returned ```js // type signature -navToSearchString: ({ input, assembly, }: { input: string; assembly: { configuration: any; } & NonEmptyObject & { error: unknown; loaded: boolean; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: ... +navToSearchString: ({ input, assembly, }: { input: string; assembly: { configuration: any; } & NonEmptyObject & { error: unknown; loadingP: Promise | undefined; volatileRegions: BasicRegion[] | undefined; refNameAliases: RefNameAliases | undefined; lowerCaseRefNameAliases: RefNameAliases | undefined; cytobands: Feature[] | undef... ``` #### action: navToLocations diff --git a/website/docs/models/LinearPileupDisplay.md b/website/docs/models/LinearPileupDisplay.md index 7e9844610a..52286d8bb9 100644 --- a/website/docs/models/LinearPileupDisplay.md +++ b/website/docs/models/LinearPileupDisplay.md @@ -114,7 +114,7 @@ renderProps: () => any ```js // type signature -trackMenuItems: () => (MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | { ...; } | { ...; } | { ...; } | { ...; })[] +trackMenuItems: () => readonly [...MenuItem[], { readonly label: "Sort by..."; readonly icon: OverridableComponent> & { muiName: string; }; readonly disabled: boolean; readonly subMenu: readonly [......[]]; }, { ...; }, { ...; }, { ...; }, { ...; }] ``` ### LinearPileupDisplay - Actions diff --git a/website/docs/models/LinearReferenceSequenceDisplay.md b/website/docs/models/LinearReferenceSequenceDisplay.md index f9f7796d84..09f27ffd9c 100644 --- a/website/docs/models/LinearReferenceSequenceDisplay.md +++ b/website/docs/models/LinearReferenceSequenceDisplay.md @@ -72,6 +72,40 @@ rowHeight: 15 ### LinearReferenceSequenceDisplay - Getters +#### getter: sequenceType + +```js +// type +any +``` + +#### getter: showForwardActual + +showReverse setting, it is NOT disabled for non-dna sequences + +```js +// type +boolean +``` + +#### getter: showReverseActual + +showReverse setting, is disabled for non-dna sequences + +```js +// type +boolean +``` + +#### getter: showTranslationActual + +showTranslation setting is disabled for non-dna sequences + +```js +// type +boolean +``` + #### getter: sequenceHeight ```js diff --git a/website/docs/models/LinearSNPCoverageDisplay.md b/website/docs/models/LinearSNPCoverageDisplay.md index f0a73cbc9a..c0446ba0e9 100644 --- a/website/docs/models/LinearSNPCoverageDisplay.md +++ b/website/docs/models/LinearSNPCoverageDisplay.md @@ -127,7 +127,7 @@ boolean ```js // type -(props: { model: { featureUnderMouse: Feature; }; height: number; offsetMouseCoord: Coord; clientMouseCoord: Coord; clientRect?: DOMRect; }) => Element +LazyExoticComponent<(props: { model: { featureUnderMouse?: Feature; }; height: number; offsetMouseCoord: Coord; clientMouseCoord: Coord; clientRect?: DOMRect; }) => Element> ``` #### getter: adapterConfig diff --git a/website/docs/models/LinearWiggleDisplay.md b/website/docs/models/LinearWiggleDisplay.md index 59bb040524..9242cf086c 100644 --- a/website/docs/models/LinearWiggleDisplay.md +++ b/website/docs/models/LinearWiggleDisplay.md @@ -33,7 +33,7 @@ type: types.literal('LinearWiggleDisplay') ```js // type -React.FC +React.ComponentType ``` #### getter: rendererTypeName diff --git a/website/docs/models/MultiLinearWiggleDisplay.md b/website/docs/models/MultiLinearWiggleDisplay.md index 410705545d..e23f5d6f49 100644 --- a/website/docs/models/MultiLinearWiggleDisplay.md +++ b/website/docs/models/MultiLinearWiggleDisplay.md @@ -49,7 +49,7 @@ Feature ```js // type -React.FC +React.ComponentType ``` #### getter: rendererTypeName diff --git a/website/docs/models/SnackbarModel.md b/website/docs/models/SnackbarModel.md index 68ba6690cf..6b40b69e77 100644 --- a/website/docs/models/SnackbarModel.md +++ b/website/docs/models/SnackbarModel.md @@ -12,6 +12,15 @@ info [packages/core/ui/SnackbarModel.tsx](https://github.com/GMOD/jbrowse-components/blob/main/packages/core/ui/SnackbarModel.tsx) +### SnackbarModel - Getters + +#### getter: snackbarMessageSet + +```js +// type +Map +``` + ### SnackbarModel - Actions #### action: notify @@ -21,11 +30,18 @@ info notify: (message: string, level?: NotificationLevel, action?: SnackAction) => void ``` +#### action: notifyError + +```js +// type signature +notifyError: (errorMessage: string, error?: unknown, extra?: unknown) => void +``` + #### action: pushSnackbarMessage ```js // type signature -pushSnackbarMessage: (message: string, level?: NotificationLevel, action?: SnackAction) => number +pushSnackbarMessage: (message: string, level?: NotificationLevel, action?: SnackAction) => void ``` #### action: popSnackbarMessage diff --git a/website/docs/models/SpreadsheetView.md b/website/docs/models/SpreadsheetView.md index 396b58a6b4..e393d108c2 100644 --- a/website/docs/models/SpreadsheetView.md +++ b/website/docs/models/SpreadsheetView.md @@ -210,10 +210,3 @@ setImportMode: () => void // type signature setDisplayMode: () => void ``` - -#### action: closeView - -```js -// type signature -closeView: () => void -``` diff --git a/website/docs/models/SvInspectorView.md b/website/docs/models/SvInspectorView.md index 735d48408f..0ccc184898 100644 --- a/website/docs/models/SvInspectorView.md +++ b/website/docs/models/SvInspectorView.md @@ -124,7 +124,7 @@ circularView: types.optional(CircularModel, () => ```js // type -any +string ``` #### getter: showCircularView @@ -204,13 +204,6 @@ setImportMode: () => void setDisplayMode: () => void ``` -#### action: closeView - -```js -// type signature -closeView: () => void -``` - #### action: setDisplayedRegions ```js diff --git a/yarn.lock b/yarn.lock index c378c0bd16..09b2b11d5d 100644 --- a/yarn.lock +++ b/yarn.lock @@ -89,522 +89,522 @@ tslib "^2.6.2" "@aws-sdk/client-cloudfront@^3.645.0": - 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+"@aws-sdk/util-endpoints@3.654.0": + version "3.654.0" + resolved "https://registry.yarnpkg.com/@aws-sdk/util-endpoints/-/util-endpoints-3.654.0.tgz#ae8ac05c8afe73cf1428942c3a6d0ab8765f3911" + integrity sha512-i902fcBknHs0Irgdpi62+QMvzxE+bczvILXigYrlHL4+PiEnlMVpni5L5W1qCkNZXf8AaMrSBuR1NZAGp6UOUw== dependencies: - "@aws-sdk/types" "3.649.0" - "@smithy/types" "^3.4.0" - "@smithy/util-endpoints" "^2.1.0" + "@aws-sdk/types" "3.654.0" + "@smithy/types" "^3.4.2" + "@smithy/util-endpoints" "^2.1.2" tslib "^2.6.2" "@aws-sdk/util-locate-window@^3.0.0": @@ -631,32 +631,32 @@ dependencies: tslib "^2.6.2" -"@aws-sdk/util-user-agent-browser@3.649.0": - version "3.649.0" - resolved "https://registry.yarnpkg.com/@aws-sdk/util-user-agent-browser/-/util-user-agent-browser-3.649.0.tgz#fa533fe882757f82b7b9f2927dda8111f3601b33" - integrity sha512-IY43r256LhKAvdEVQO/FPdUyVpcZS5EVxh/WHVdNzuN1bNLoUK2rIzuZqVA0EGguvCxoXVmQv9m50GvG7cGktg== +"@aws-sdk/util-user-agent-browser@3.654.0": + version "3.654.0" + 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"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.16.7", "@babel/code-frame@^7.24.7", "@babel/code-frame@^7.8.3": @@ -3603,7 +3603,7 @@ dependencies: tslib "^2.6.2" -"@smithy/config-resolver@^3.0.6", "@smithy/config-resolver@^3.0.8": +"@smithy/config-resolver@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/config-resolver/-/config-resolver-3.0.8.tgz#8717ea934f1d72474a709fc3535d7b8a11de2e33" integrity sha512-Tv1obAC18XOd2OnDAjSWmmthzx6Pdeh63FbLin8MlPiuJ2ATpKkq0NcNOJFr0dO+JmZXnwu8FQxKJ3TKJ3Hulw== @@ -3614,7 +3614,7 @@ "@smithy/util-middleware" "^3.0.6" tslib "^2.6.2" -"@smithy/core@^2.4.1": +"@smithy/core@^2.4.3": version "2.4.3" resolved "https://registry.yarnpkg.com/@smithy/core/-/core-2.4.3.tgz#18344c2ff63f748f625ebc5171755816f3043849" integrity sha512-4LTusLqFMRVQUfC3RNuTg6IzYTeJNpydRdTKq7J5wdEyIRQSu3rGIa3s80mgG2hhe6WOZl9IqTSo1pgbn6EHhA== @@ -3630,7 +3630,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/credential-provider-imds@^3.2.1", "@smithy/credential-provider-imds@^3.2.3": +"@smithy/credential-provider-imds@^3.2.3": version "3.2.3" resolved "https://registry.yarnpkg.com/@smithy/credential-provider-imds/-/credential-provider-imds-3.2.3.tgz#93314e58e4f81f2b641de6efac037c7a3250c050" integrity sha512-VoxMzSzdvkkjMJNE38yQgx4CfnmT+Z+5EUXkg4x7yag93eQkVQgZvN3XBSHC/ylfBbLbAtdu7flTCChX9I+mVg== @@ -3651,7 +3651,7 @@ "@smithy/util-hex-encoding" "^3.0.0" tslib "^2.6.2" -"@smithy/eventstream-serde-browser@^3.0.7": +"@smithy/eventstream-serde-browser@^3.0.9": version "3.0.9" resolved "https://registry.yarnpkg.com/@smithy/eventstream-serde-browser/-/eventstream-serde-browser-3.0.9.tgz#bb71b836a8755dd5d5fed85ac2fa500702f60544" integrity sha512-PiQLo6OQmZAotJweIcObL1H44gkvuJACKMNqpBBe5Rf2Ax1DOcGi/28+feZI7yTe1ERHlQQaGnm8sSkyDUgsMg== @@ -3660,7 +3660,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/eventstream-serde-config-resolver@^3.0.4": +"@smithy/eventstream-serde-config-resolver@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/eventstream-serde-config-resolver/-/eventstream-serde-config-resolver-3.0.6.tgz#538862ef05e549c0ef97b060100a5ffbb5d7adfb" integrity sha512-iew15It+c7WfnVowWkt2a7cdPp533LFJnpjDQgfZQcxv2QiOcyEcea31mnrk5PVbgo0nNH3VbYGq7myw2q/F6A== @@ -3668,7 +3668,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/eventstream-serde-node@^3.0.6": +"@smithy/eventstream-serde-node@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/eventstream-serde-node/-/eventstream-serde-node-3.0.8.tgz#0221c555f2851fd847b041f27a6231945822018f" integrity sha512-6m+wI+fT0na+6oao6UqALVA38fsScCpoG5UO/A8ZSyGLnPM2i4MS1cFUhpuALgvLMxfYoTCh7qSeJa0aG4IWpQ== @@ -3686,7 +3686,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/fetch-http-handler@^3.2.5", "@smithy/fetch-http-handler@^3.2.7": +"@smithy/fetch-http-handler@^3.2.7": version "3.2.7" resolved "https://registry.yarnpkg.com/@smithy/fetch-http-handler/-/fetch-http-handler-3.2.7.tgz#30520ca939fb817d3eb3ab9445ddc0f6c1df2960" integrity sha512-Ra6IPI1spYLO+t62/3jQbodjOwAbto9wlpJdHZwkycm0Kit+GVpzHW/NMmSgY4rK1bjJ4qLAmCnaBzePO5Nkkg== @@ -3697,7 +3697,7 @@ "@smithy/util-base64" "^3.0.0" tslib "^2.6.2" -"@smithy/hash-blob-browser@^3.1.3": +"@smithy/hash-blob-browser@^3.1.5": version "3.1.5" resolved "https://registry.yarnpkg.com/@smithy/hash-blob-browser/-/hash-blob-browser-3.1.5.tgz#db1cf756647f8f39b4214403482750afbb8f2236" integrity sha512-Vi3eoNCmao4iKglS80ktYnBOIqZhjbDDwa1IIbF/VaJ8PsHnZTQ5wSicicPrU7nTI4JPFn92/txzWkh4GlK18Q== @@ -3707,7 +3707,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/hash-node@^3.0.4": +"@smithy/hash-node@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/hash-node/-/hash-node-3.0.6.tgz#7c1a869afcbd411eac04c4777dd193ea7ac4e588" integrity sha512-c/FHEdKK/7DU2z6ZE91L36ahyXWayR3B+FzELjnYq7wH5YqIseM24V+pWCS9kFn1Ln8OFGTf+pyYPiHZuX0s/Q== @@ -3717,7 +3717,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/hash-stream-node@^3.1.3": +"@smithy/hash-stream-node@^3.1.5": version "3.1.5" resolved "https://registry.yarnpkg.com/@smithy/hash-stream-node/-/hash-stream-node-3.1.5.tgz#4c8d290f6e4d55fdb143d65d645031da12af7fc1" integrity sha512-61CyFCzqN3VBfcnGX7mof/rkzLb8oHjm4Lr6ZwBIRpBssBb8d09ChrZAqinP2rUrA915BRNkq9NpJz18N7+3hQ== @@ -3726,7 +3726,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/invalid-dependency@^3.0.4": +"@smithy/invalid-dependency@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/invalid-dependency/-/invalid-dependency-3.0.6.tgz#3b3e30a55b92341412626b412fe919929871eeb1" integrity sha512-czM7Ioq3s8pIXht7oD+vmgy4Wfb4XavU/k/irO8NdXFFOx7YAlsCCcKOh/lJD1mJSYQqiR7NmpZ9JviryD/7AQ== @@ -3748,7 +3748,7 @@ dependencies: tslib "^2.6.2" -"@smithy/md5-js@^3.0.4": +"@smithy/md5-js@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/md5-js/-/md5-js-3.0.6.tgz#cb8881ffef4ffbf68b0daf52d8add30dc57e3a7a" integrity sha512-Ze690T8O3M5SVbb70WormwrKzVf9QQRtIuxtJDgpUQDkmt+PtdYDetBbyCbF9ryupxLw6tgzWKgwffAShhVIXQ== @@ -3757,7 +3757,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/middleware-content-length@^3.0.6": +"@smithy/middleware-content-length@^3.0.8": version "3.0.8" resolved "https://registry.yarnpkg.com/@smithy/middleware-content-length/-/middleware-content-length-3.0.8.tgz#4e1c1631718e4d6dfe9a06f37faa90de92e884ed" integrity sha512-VuyszlSO49WKh3H9/kIO2kf07VUwGV80QRiaDxUfP8P8UKlokz381ETJvwLhwuypBYhLymCYyNhB3fLAGBX2og== @@ -3766,7 +3766,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/middleware-endpoint@^3.1.1", "@smithy/middleware-endpoint@^3.1.3": +"@smithy/middleware-endpoint@^3.1.3": version "3.1.3" resolved "https://registry.yarnpkg.com/@smithy/middleware-endpoint/-/middleware-endpoint-3.1.3.tgz#8c84d40c9d26b77e2bbb99721fd4a3d379828505" integrity sha512-KeM/OrK8MVFUsoJsmCN0MZMVPjKKLudn13xpgwIMpGTYpA8QZB2Xq5tJ+RE6iu3A6NhOI4VajDTwBsm8pwwrhg== @@ -3779,7 +3779,7 @@ "@smithy/util-middleware" "^3.0.6" tslib "^2.6.2" -"@smithy/middleware-retry@^3.0.16", "@smithy/middleware-retry@^3.0.18": +"@smithy/middleware-retry@^3.0.18": version "3.0.18" resolved "https://registry.yarnpkg.com/@smithy/middleware-retry/-/middleware-retry-3.0.18.tgz#58372e264ca0c3a35f0526c531eb433ed8472df0" integrity sha512-YU1o/vYob6vlqZdd97MN8cSXRToknLXhFBL3r+c9CZcnxkO/rgNZ++CfgX2vsmnEKvlqdi26+SRtSzlVp5z6Mg== @@ -3794,7 +3794,7 @@ tslib "^2.6.2" uuid "^9.0.1" -"@smithy/middleware-serde@^3.0.4", "@smithy/middleware-serde@^3.0.6": +"@smithy/middleware-serde@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/middleware-serde/-/middleware-serde-3.0.6.tgz#9f7a9c152989b59c12865ef3a17acbdb7b6a1566" integrity sha512-KKTUSl1MzOM0MAjGbudeaVNtIDo+PpekTBkCNwvfZlKndodrnvRo+00USatiyLOc0ujjO9UydMRu3O9dYML7ag== @@ -3802,7 +3802,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/middleware-stack@^3.0.4", "@smithy/middleware-stack@^3.0.6": +"@smithy/middleware-stack@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/middleware-stack/-/middleware-stack-3.0.6.tgz#e63d09b3e292b7a46ac3b9eb482973701de15a6f" integrity sha512-2c0eSYhTQ8xQqHMcRxLMpadFbTXg6Zla5l0mwNftFCZMQmuhI7EbAJMx6R5eqfuV3YbJ3QGyS3d5uSmrHV8Khg== @@ -3810,7 +3810,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/node-config-provider@^3.1.5", "@smithy/node-config-provider@^3.1.7": +"@smithy/node-config-provider@^3.1.7": version "3.1.7" resolved "https://registry.yarnpkg.com/@smithy/node-config-provider/-/node-config-provider-3.1.7.tgz#6ae71aeff45e8c9792720986f0b1623cf6da671f" integrity sha512-g3mfnC3Oo8pOI0dYuPXLtdW1WGVb3bR2tkV21GNkm0ZvQjLTtamXAwCWt/FCb0HGvKt3gHHmF1XerG0ICfalOg== @@ -3820,7 +3820,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/node-http-handler@^3.2.0", "@smithy/node-http-handler@^3.2.2": +"@smithy/node-http-handler@^3.2.2": version "3.2.2" resolved "https://registry.yarnpkg.com/@smithy/node-http-handler/-/node-http-handler-3.2.2.tgz#1e659d52ba4d27123efc7b8a5c1abe76f97ea915" integrity sha512-42Cy4/oT2O+00aiG1iQ7Kd7rE6q8j7vI0gFfnMlUiATvyo8vefJkhb7O10qZY0jAqo5WZdUzfl9IV6wQ3iMBCg== @@ -3831,7 +3831,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/property-provider@^3.1.4", "@smithy/property-provider@^3.1.6": +"@smithy/property-provider@^3.1.6": version "3.1.6" resolved "https://registry.yarnpkg.com/@smithy/property-provider/-/property-provider-3.1.6.tgz#141a245ad8cac074d29a836ec992ef7dc3363bf7" integrity sha512-NK3y/T7Q/Bw+Z8vsVs9MYIQ5v7gOX7clyrXcwhhIBQhbPgRl6JDrZbusO9qWDhcEus75Tg+VCxtIRfo3H76fpw== @@ -3839,7 +3839,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/protocol-http@^4.1.1", "@smithy/protocol-http@^4.1.3": +"@smithy/protocol-http@^4.1.3": version "4.1.3" resolved "https://registry.yarnpkg.com/@smithy/protocol-http/-/protocol-http-4.1.3.tgz#91d894ec7d82c012c5674cb3e209800852f05abd" integrity sha512-GcbMmOYpH9iRqtC05RbRnc/0FssxSTHlmaNhYBTgSgNCYpdR3Kt88u5GAZTBmouzv+Zlj/VRv92J9ruuDeJuEw== @@ -3871,7 +3871,7 @@ dependencies: "@smithy/types" "^3.4.2" -"@smithy/shared-ini-file-loader@^3.1.5", "@smithy/shared-ini-file-loader@^3.1.7": +"@smithy/shared-ini-file-loader@^3.1.7": version "3.1.7" resolved "https://registry.yarnpkg.com/@smithy/shared-ini-file-loader/-/shared-ini-file-loader-3.1.7.tgz#bdcf3f0213c3c5779c3fbb41580e9a217ad52e8f" integrity sha512-IA4K2qTJYXkF5OfVN4vsY1hfnUZjaslEE8Fsr/gGFza4TAC2A9NfnZuSY2srQIbt9bwtjHiAayrRVgKse4Q7fA== @@ -3879,7 +3879,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/signature-v4@^4.1.1": +"@smithy/signature-v4@^4.1.3": version "4.1.3" resolved "https://registry.yarnpkg.com/@smithy/signature-v4/-/signature-v4-4.1.3.tgz#1a5adc19563b8cf8f28ae1ada4d6cda7d351943d" integrity sha512-YD2KYSCEEeFHcWZ1E3mLdAaHl8T/TANh6XwmocQ6nPcTdBfh4N5fusgnblnWDlnlU1/cUqEq3PiGi22GmT2Lkg== @@ -3893,7 +3893,7 @@ "@smithy/util-utf8" "^3.0.0" tslib "^2.6.2" -"@smithy/smithy-client@^3.3.0", "@smithy/smithy-client@^3.3.2": +"@smithy/smithy-client@^3.3.2": version "3.3.2" resolved "https://registry.yarnpkg.com/@smithy/smithy-client/-/smithy-client-3.3.2.tgz#0c5511525f3e64ac5132d513c38d5d0d4a770719" integrity sha512-RKDfhF2MTwXl7jan5d7QfS9eCC6XJbO3H+EZAvLQN8A5in4ib2Ml4zoeLo57w9QrqFekBPcsoC2hW3Ekw4vQ9Q== @@ -3905,14 +3905,14 @@ "@smithy/util-stream" "^3.1.6" tslib "^2.6.2" -"@smithy/types@^3.4.0", "@smithy/types@^3.4.2": +"@smithy/types@^3.4.2": version "3.4.2" resolved "https://registry.yarnpkg.com/@smithy/types/-/types-3.4.2.tgz#aa2d087922d57205dbad68df8a45c848699c551e" integrity sha512-tHiFcfcVedVBHpmHUEUHOCCih8iZbIAYn9NvPsNzaPm/237I3imdDdZoOC8c87H5HBAVEa06tTgb+OcSWV9g5w== dependencies: tslib "^2.6.2" -"@smithy/url-parser@^3.0.4", "@smithy/url-parser@^3.0.6": +"@smithy/url-parser@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/url-parser/-/url-parser-3.0.6.tgz#98b426f9a492e0c992fcd5dceac35444c2632837" integrity sha512-47Op/NU8Opt49KyGpHtVdnmmJMsp2hEwBdyjuFB9M2V5QVOwA7pBhhxKN5z6ztKGrMw76gd8MlbPuzzvaAncuQ== @@ -3967,7 +3967,7 @@ dependencies: tslib "^2.6.2" -"@smithy/util-defaults-mode-browser@^3.0.16": +"@smithy/util-defaults-mode-browser@^3.0.18": version "3.0.18" resolved "https://registry.yarnpkg.com/@smithy/util-defaults-mode-browser/-/util-defaults-mode-browser-3.0.18.tgz#c3904b71db96c9b99861fc2017fea503fcff12a4" integrity sha512-/eveCzU6Z6Yw8dlYQLA4rcK30XY0E4L3lD3QFHm59mzDaWYelrXE1rlynuT3J6qxv+5yNy3a1JuzhG5hk5hcmw== @@ -3978,7 +3978,7 @@ bowser "^2.11.0" tslib "^2.6.2" -"@smithy/util-defaults-mode-node@^3.0.16": +"@smithy/util-defaults-mode-node@^3.0.18": version "3.0.18" resolved "https://registry.yarnpkg.com/@smithy/util-defaults-mode-node/-/util-defaults-mode-node-3.0.18.tgz#6b46911f2f749bb048cdc287d7237be9d58f4a6b" integrity sha512-9cfzRjArtOFPlTYRREJk00suUxVXTgbrzVncOyMRTUeMKnecG/YentLF3cORa+R6mUOMSrMSnT18jos1PKqK6Q== @@ -3991,7 +3991,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/util-endpoints@^2.1.0": +"@smithy/util-endpoints@^2.1.2": version "2.1.2" resolved "https://registry.yarnpkg.com/@smithy/util-endpoints/-/util-endpoints-2.1.2.tgz#e1d789d598da9ab955b8cf3257ab2f263c35031a" integrity sha512-FEISzffb4H8DLzGq1g4MuDpcv6CIG15fXoQzDH9SjpRJv6h7J++1STFWWinilG0tQh9H1v2UKWG19Jjr2B16zQ== @@ -4007,7 +4007,7 @@ dependencies: tslib "^2.6.2" -"@smithy/util-middleware@^3.0.4", "@smithy/util-middleware@^3.0.6": +"@smithy/util-middleware@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/util-middleware/-/util-middleware-3.0.6.tgz#463c41e74d6e8d758f6cceba4dbed4dc5a4afe50" integrity sha512-BxbX4aBhI1O9p87/xM+zWy0GzT3CEVcXFPBRDoHAM+pV0eSW156pR+PSYEz0DQHDMYDsYAflC2bQNz2uaDBUZQ== @@ -4015,7 +4015,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/util-retry@^3.0.4", "@smithy/util-retry@^3.0.6": +"@smithy/util-retry@^3.0.6": version "3.0.6" resolved "https://registry.yarnpkg.com/@smithy/util-retry/-/util-retry-3.0.6.tgz#297de1cd5a836fb957ab2ad3439041e848815499" integrity sha512-BRZiuF7IwDntAbevqMco67an0Sr9oLQJqqRCsSPZZHYRnehS0LHDAkJk/pSmI7Z8c/1Vet294H7fY2fWUgB+Rg== @@ -4024,7 +4024,7 @@ "@smithy/types" "^3.4.2" tslib "^2.6.2" -"@smithy/util-stream@^3.1.4", "@smithy/util-stream@^3.1.6": +"@smithy/util-stream@^3.1.6": version "3.1.6" resolved "https://registry.yarnpkg.com/@smithy/util-stream/-/util-stream-3.1.6.tgz#424dbb4e321129807e5fb01d961ef902ee7c04f8" integrity sha512-lQEUfTx1ht5CRdvIjdAN/gUL6vQt2wSARGGLaBHNe+iJSkRHlWzY+DOn0mFTmTgyU3jcI5n9DkT5gTzYuSOo6A== @@ -4061,7 +4061,7 @@ "@smithy/util-buffer-from" "^3.0.0" tslib "^2.6.2" -"@smithy/util-waiter@^3.1.3": +"@smithy/util-waiter@^3.1.5": version "3.1.5" resolved "https://registry.yarnpkg.com/@smithy/util-waiter/-/util-waiter-3.1.5.tgz#56b3a0fa6498ed22dfee7f40c64d13a54dd04fcc" integrity sha512-jYOSvM3H6sZe3CHjzD2VQNCjWBJs+4DbtwBMvUp9y5EnnwNa7NQxTeYeQw0CKCAdGGZ3QvVkyJmvbvs5M/B10A== From 03e1d91c1f550d6416e38ed93be48cd83f77db75 Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 18 Sep 2024 20:13:30 -0400 Subject: [PATCH 28/38] [update docs] move v2.15.2->v2.15.3 release notes just for simplicity --- website/blog/2024-09-18-v2.15.2-release.md | 43 ---------------------- website/blog/2024-09-19-v2.15.3-release.md | 29 +++++++++++++-- 2 files changed, 26 insertions(+), 46 deletions(-) delete mode 100644 website/blog/2024-09-18-v2.15.2-release.md diff --git a/website/blog/2024-09-18-v2.15.2-release.md b/website/blog/2024-09-18-v2.15.2-release.md deleted file mode 100644 index 567d21968a..0000000000 --- a/website/blog/2024-09-18-v2.15.2-release.md +++ /dev/null @@ -1,43 +0,0 @@ ---- -title: v2.15.2 Release -date: 2024-09-18 22:21:09 -tags: ['release', 'jbrowse 2'] ---- - -This release (hopefully) fixes the SSL code signing on the Windows version of -the jbrowse desktop app. This should help auto-updates work better on Windows - -## Downloads - -- [v2.15.2](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.2) - -To install JBrowse 2 for the web, you can download the link above, or you can -use the JBrowse CLI to automatically download the latest version. See the -[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more -details. - -yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 - -## 2.15.2 (2024-09-18) - -#### :rocket: Enhancement - -- [#4573](https://github.com/GMOD/jbrowse-components/pull/4573) Add pif.gz - option to synteny import form ([@cmdcolin](https://github.com/cmdcolin)) - -#### :bug: Bug Fix - -- [#4571](https://github.com/GMOD/jbrowse-components/pull/4571) Fix code signing - on the windows for jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) -- [#4566](https://github.com/GMOD/jbrowse-components/pull/4566) Fix handling of - "." in VCF ALT field ([@cmdcolin](https://github.com/cmdcolin)) - -#### :house: Internal - -- [#4569](https://github.com/GMOD/jbrowse-components/pull/4569) Refactor GFF3 - parser to avoid returning internal \_linehash variable - ([@cmdcolin](https://github.com/cmdcolin)) - -#### Committers: 1 - -- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. diff --git a/website/blog/2024-09-19-v2.15.3-release.md b/website/blog/2024-09-19-v2.15.3-release.md index b70f546672..ca6e6874d7 100644 --- a/website/blog/2024-09-19-v2.15.3-release.md +++ b/website/blog/2024-09-19-v2.15.3-release.md @@ -4,7 +4,8 @@ date: 2024-09-19 00:00:42 tags: ['release', 'jbrowse 2'] --- -Re-publish +This release (hopefully) fixes the SSL code signing on the Windows version of +the jbrowse desktop app. This should help auto-updates work better on Windows ## Downloads @@ -15,6 +16,28 @@ use the JBrowse CLI to automatically download the latest version. See the [JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more details. -yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2 -Done in 0.57s. +## 2.15.2 (2024-09-18) + +#### :rocket: Enhancement + +- [#4573](https://github.com/GMOD/jbrowse-components/pull/4573) Add pif.gz + option to synteny import form ([@cmdcolin](https://github.com/cmdcolin)) + +#### :bug: Bug Fix + +- [#4571](https://github.com/GMOD/jbrowse-components/pull/4571) Fix code signing + on the windows for jbrowse desktop ([@cmdcolin](https://github.com/cmdcolin)) +- [#4566](https://github.com/GMOD/jbrowse-components/pull/4566) Fix handling of + "." in VCF ALT field ([@cmdcolin](https://github.com/cmdcolin)) + +#### :house: Internal + +- [#4569](https://github.com/GMOD/jbrowse-components/pull/4569) Refactor GFF3 + parser to avoid returning internal \_linehash variable + ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.30s. From 6a1fc5b4ee556bad6ca8f5135e95dec307d1a263 Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Thu, 19 Sep 2024 15:57:31 -0400 Subject: [PATCH 29/38] Fix indexing plaintext gff/vcf on desktop (#4580) --- packages/text-indexing/src/TextIndexing.ts | 36 +++++++++++++++++-- .../jbrowse-desktop/src/indexJobsModel.ts | 1 + 2 files changed, 34 insertions(+), 3 deletions(-) diff --git a/packages/text-indexing/src/TextIndexing.ts b/packages/text-indexing/src/TextIndexing.ts index b0f3573cc8..25d940ab9c 100644 --- a/packages/text-indexing/src/TextIndexing.ts +++ b/packages/text-indexing/src/TextIndexing.ts @@ -215,7 +215,22 @@ async function* indexFiles({ indexingAttributes: attributesToIndex = idx1, } = textSearching || {} let myTotalBytes: number | undefined - if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') { + if (type === 'Gff3Adapter') { + yield* indexGff3({ + config: track, + attributesToIndex, + inLocation: getLoc('gffLocation', track), + outDir, + featureTypesToExclude, + onStart: totalBytes => { + myTotalBytes = totalBytes + }, + onUpdate: progressBytes => { + statusCallback(`${progressBytes}/${myTotalBytes}`) + }, + }) + } + if (type === 'Gff3TabixAdapter') { yield* indexGff3({ config: track, attributesToIndex, @@ -229,7 +244,20 @@ async function* indexFiles({ statusCallback(`${progressBytes}/${myTotalBytes}`) }, }) - } else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') { + } else if (type === 'VcfAdapter') { + yield* indexVcf({ + config: track, + attributesToIndex, + inLocation: getLoc('vcfLocation', track), + outDir, + onStart: totalBytes => { + myTotalBytes = totalBytes + }, + onUpdate: progressBytes => { + statusCallback(`${progressBytes}/${myTotalBytes}`) + }, + }) + } else if (type === 'VcfTabixAdapter') { yield* indexVcf({ config: track, attributesToIndex, @@ -252,7 +280,9 @@ function getLoc(attr: string, config: Track) { | { uri: string; localPath: string } | undefined if (!elt) { - throw new Error('none') + throw new Error( + `can't get find ${attr} from ${config.adapter} for text indexing`, + ) } return elt.uri || elt.localPath } diff --git a/products/jbrowse-desktop/src/indexJobsModel.ts b/products/jbrowse-desktop/src/indexJobsModel.ts index eb3c7b0f0c..02196dd7a5 100644 --- a/products/jbrowse-desktop/src/indexJobsModel.ts +++ b/products/jbrowse-desktop/src/indexJobsModel.ts @@ -313,6 +313,7 @@ export default function jobsModelFactory(_pluginManager: PluginManager) { } } } catch (e) { + console.error(e) if (isAbortException(e)) { self.session?.notify('Cancelled job', 'info') } else { From 0983007bc6107fa4bd2a4f09cfcc592436085072 Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Fri, 20 Sep 2024 09:15:34 -0400 Subject: [PATCH 30/38] Fix text indexing on Windows (#4582) --- yarn.lock | 352 +++++++++++++++++++++++++++--------------------------- 1 file changed, 176 insertions(+), 176 deletions(-) diff --git a/yarn.lock b/yarn.lock index 09b2b11d5d..b8aabe3511 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2783,28 +2783,28 @@ resolved "https://registry.yarnpkg.com/@microsoft/tsdoc/-/tsdoc-0.15.0.tgz#f29a55df17cb6e87cfbabce33ff6a14a9f85076d" integrity sha512-HZpPoABogPvjeJOdzCOSJsXeL/SMCBgBZMVC3X3d7YYp2gf31MfxhUoYUNwf1ERPJOnQc0wkFn9trqI6ZEdZuA== -"@mui/core-downloads-tracker@^6.1.0": - version "6.1.0" - resolved "https://registry.yarnpkg.com/@mui/core-downloads-tracker/-/core-downloads-tracker-6.1.0.tgz#35e37713a4240c09db92c082502fa0c90f6e37be" - integrity sha512-covEnIn/2er5YdtuukDRA52kmARhKrHjOvPsyTFMQApZdrTBI4h8jbEy2mxZqwMwcAFS9coonQXnEZKL1rUNdQ== +"@mui/core-downloads-tracker@^6.1.1": + version "6.1.1" + resolved "https://registry.yarnpkg.com/@mui/core-downloads-tracker/-/core-downloads-tracker-6.1.1.tgz#2300ea530b31663bdf4eb716b5c7faa762524dee" + integrity sha512-VdQC1tPIIcZAnf62L2M1eQif0x2vlKg3YK4kGYbtijSH4niEgI21GnstykW1vQIs+Bc6L+Hua2GATYVjilJ22A== "@mui/icons-material@^6.0.0": - version "6.1.0" - resolved 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sha512-b+eULldTqtqTCbN++2BtBWCir/1LwEYw+2mIlOt2GiEUh1EBBw4/wIukGKKNt3xrCZqRA80yLLkV6tF61Lq3cA== dependencies: "@babel/runtime" "^7.25.6" - "@mui/core-downloads-tracker" "^6.1.0" - "@mui/system" "^6.1.0" - "@mui/types" "^7.2.16" - "@mui/utils" "^6.1.0" + "@mui/core-downloads-tracker" "^6.1.1" + "@mui/system" "^6.1.1" + "@mui/types" "^7.2.17" + "@mui/utils" "^6.1.1" "@popperjs/core" "^2.11.8" "@types/react-transition-group" "^4.4.11" clsx "^2.1.1" @@ -2813,19 +2813,19 @@ react-is "^18.3.1" react-transition-group "^4.4.5" -"@mui/private-theming@^6.1.0": - version "6.1.0" - resolved "https://registry.yarnpkg.com/@mui/private-theming/-/private-theming-6.1.0.tgz#f55d2dd472028e6deda3a519f6c285ce7171c908" - integrity sha512-+L5qccs4gwsR0r1dgjqhN24QEQRkqIbfOdxILyMbMkuI50x6wNyt9XrV+J3WtjtZTMGJCrUa5VmZBE6OEPGPWA== +"@mui/private-theming@^6.1.1": + version "6.1.1" + resolved "https://registry.yarnpkg.com/@mui/private-theming/-/private-theming-6.1.1.tgz#6e56aa4bd35d701efccaa5125920fc9250754725" + 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"8.3.2" + "@storybook/react" "8.3.2" "@types/node" "^22.0.0" -"@storybook/react@8.3.1", "@storybook/react@^8.0.0": - version "8.3.1" - resolved "https://registry.yarnpkg.com/@storybook/react/-/react-8.3.1.tgz#8873dc4cab4ffa9caa2b444f36ea0fb660e8a446" - integrity sha512-uxr5o5TzUHB1vFMgdayxatDTYUYWJxDse4hcpr+D2E5QMrMCKBk/KRYgJtnPhmEBASoT40lcZvYmEWnP973KWA== +"@storybook/react@8.3.2", "@storybook/react@^8.0.0": + version "8.3.2" + resolved "https://registry.yarnpkg.com/@storybook/react/-/react-8.3.2.tgz#87b390ebdf204fa6661e711e2878ddd7c3d65614" + integrity sha512-GvnqhxvaYC6s8WMiDWr184UlNp5jmRVNMBHasXlUsVDYvs6J1tStJeN+XBZbAJBW/0zkHLuf4REk8lLBi2eKRQ== dependencies: - "@storybook/components" "^8.3.1" + "@storybook/components" "^8.3.2" "@storybook/global" "^5.0.0" - "@storybook/manager-api" "^8.3.1" - "@storybook/preview-api" "^8.3.1" - "@storybook/react-dom-shim" "8.3.1" - "@storybook/theming" "^8.3.1" + "@storybook/manager-api" "^8.3.2" + "@storybook/preview-api" "^8.3.2" + "@storybook/react-dom-shim" "8.3.2" + "@storybook/theming" "^8.3.2" "@types/escodegen" "^0.0.6" "@types/estree" "^0.0.51" "@types/node" "^22.0.0" @@ -4366,10 +4366,10 @@ type-fest "~2.19" util-deprecate "^1.0.2" -"@storybook/theming@^8.3.1": - version "8.3.1" - resolved "https://registry.yarnpkg.com/@storybook/theming/-/theming-8.3.1.tgz#762cf6dd337ccf05adf751d3e7560f8cdae21fd6" - integrity sha512-R6YZnIdN9P9gTauVkZfVmob0/i6/yaAQxnwfMgRLCaFD0TFQ+UQ2pCz40zPAUp3BcNPwMD168GVxmheBb8cGag== +"@storybook/theming@^8.3.2": + version "8.3.2" + resolved "https://registry.yarnpkg.com/@storybook/theming/-/theming-8.3.2.tgz#f3bf95888fe43ec884aad5d5f97ad406561ab83b" + integrity sha512-JXAVc08Tlbu4GTTMGNmwUy69lShqSpJixAJc4bvWTnNAtPTRltiNJCg/KJ0GauEyRFk8ZR2Ha4KhN3DB1felNQ== "@szmarczak/http-timer@^4.0.5": version "4.0.6" @@ -5023,9 +5023,9 @@ "@types/react" "*" "@types/react@*", "@types/react@^16.8.0 || ^17.0.0 || ^18.0.0", "@types/react@^18.0.26": - version "18.3.7" - resolved "https://registry.yarnpkg.com/@types/react/-/react-18.3.7.tgz#6decbfbb01f8d82d56ff5403394121940faa6569" - integrity sha512-KUnDCJF5+AiZd8owLIeVHqmW9yM4sqmDVf2JRJiBMFkGvkoZ4/WyV2lL4zVsoinmRS/W3FeEdZLEWFRofnT2FQ== + version "18.3.8" + resolved "https://registry.yarnpkg.com/@types/react/-/react-18.3.8.tgz#1672ab19993f8aca7c7dc844c07d5d9e467d5a79" + integrity sha512-syBUrW3/XpnW4WJ41Pft+I+aPoDVbrBVQGEnbD7NijDGlVC+8gV/XKRY+7vMDlfPpbwYt0l1vd/Sj8bJGMbs9Q== dependencies: "@types/prop-types" "*" csstype "^3.0.2" @@ -6466,9 +6466,9 @@ caniuse-api@^3.0.0: lodash.uniq "^4.5.0" caniuse-lite@^1.0.0, caniuse-lite@^1.0.30001646: - version "1.0.30001660" - resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001660.tgz#31218de3463fabb44d0b7607b652e56edf2e2355" - integrity sha512-GacvNTTuATm26qC74pt+ad1fW15mlQ/zuTzzY1ZoIzECTP8HURDfF43kNxPgf7H1jmelCBQTTbBNxdSXOA7Bqg== + version "1.0.30001662" + resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001662.tgz#3574b22dfec54a3f3b6787331da1040fe8e763ec" + integrity sha512-sgMUVwLmGseH8ZIrm1d51UbrhqMCH3jvS7gF/M6byuHOnKyLOBL7W8yz5V02OHwgLGA36o/AFhWzzh4uc5aqTA== canvas-sequencer@^3.1.0: version "3.1.0" @@ -10584,9 +10584,9 @@ iterator.prototype@^1.1.2: set-function-name "^2.0.1" ixixx@^2.0.1: - version "2.2.2" - resolved "https://registry.yarnpkg.com/ixixx/-/ixixx-2.2.2.tgz#5118219d4fa53d5bfede893283fd15668c4cd826" - integrity sha512-waSzGJppi42tQ0I17YgfCOR59kkgT6Wgi4htSmfs9xPabOCZ6I1geDP03oztm/5NBDUVyePQRDkBfGa/QghLMg== + version "2.2.3" + resolved "https://registry.yarnpkg.com/ixixx/-/ixixx-2.2.3.tgz#f0b2d744d46b7e272734929e614319de479cd0ae" + integrity sha512-GKyTpatGx74isJQZEWDm/CY6smzN3UnLKiB1I93CHnw88oZnd3gU6bHPmgPG7rU6lwya5OF0DPEaieQSnYQpbQ== dependencies: command-exists "^1.2.9" external-sorting "^1.3.1" @@ -11797,9 +11797,9 @@ memfs@^3.1.2, memfs@^3.4.1, memfs@^3.4.12: fs-monkey "^1.0.4" memfs@^4.6.0: - version "4.11.2" - resolved "https://registry.yarnpkg.com/memfs/-/memfs-4.11.2.tgz#7b036eb53374f6b7bc79920c2ae2033adb1feb9e" - integrity sha512-VcR7lEtgQgv7AxGkrNNeUAimFLT+Ov8uGu1LuOfbe/iF/dKoh/QgpoaMZlhfejvLtMxtXYyeoT7Ar1jEbWdbPA== + version "4.12.0" + resolved "https://registry.yarnpkg.com/memfs/-/memfs-4.12.0.tgz#76570478aee461695fb3336ca3356a7a8cfc26cc" + integrity sha512-74wDsex5tQDSClVkeK1vtxqYCAgCoXxx+K4NSHzgU/muYVYByFqa+0RnrPO9NM6naWm1+G9JmZ0p6QHhXmeYfA== dependencies: "@jsonjoy.com/json-pack" "^1.0.3" "@jsonjoy.com/util" "^1.3.0" @@ -12236,9 +12236,9 @@ nock@^13.5.4: propagate "^2.0.0" node-abi@^3.45.0: - version "3.67.0" - resolved "https://registry.yarnpkg.com/node-abi/-/node-abi-3.67.0.tgz#1d159907f18d18e18809dbbb5df47ed2426a08df" - integrity sha512-bLn/fU/ALVBE9wj+p4Y21ZJWYFjUXLXPi/IewyLZkx3ApxKDNBWCKdReeKOtD8dWpOdDCeMyLh6ZewzcLsG2Nw== + version "3.68.0" + resolved "https://registry.yarnpkg.com/node-abi/-/node-abi-3.68.0.tgz#8f37fb02ecf4f43ebe694090dcb52e0c4cc4ba25" + integrity sha512-7vbj10trelExNjFSBm5kTvZXXa7pZyKWx9RCKIyqe6I9Ev3IzGpQoqBP3a+cOdxY+pWj6VkP28n/2wWysBHD/A== dependencies: semver "^7.3.5" @@ -14976,11 +14976,11 @@ statuses@2.0.1: integrity sha512-OpZ3zP+jT1PI7I8nemJX4AKmAX070ZkYPVWV/AaKTJl+tXCTGyVdC1a4SL8RUQYEwk/f34ZX8UTykN68FwrqAA== storybook@^8.0.0: - version "8.3.1" - resolved "https://registry.yarnpkg.com/storybook/-/storybook-8.3.1.tgz#4f52975bb0b7895eb4ad8125b37c0b3bba33b555" - integrity sha512-CYqt5KOpaTgb8OczNo2+EtMi8YNDPi4vNVebVlLDOroWxyulb8I7MIOH9gALczcIOb+TZUArPztjoa8rkXTaDQ== + version "8.3.2" + resolved "https://registry.yarnpkg.com/storybook/-/storybook-8.3.2.tgz#264315dd2c1df1136a3f55a8a8ad2be6988248c0" + integrity sha512-jfDPtoPTtXcQ4O82u6+VE0V8q05hnj9NdmTVJvUxab796FoEbhk07xFLynOopfd9h9i0D/jc5Sf4C+iMe1bhmA== dependencies: - "@storybook/core" "8.3.1" + "@storybook/core" "8.3.2" string-length@^4.0.1: version "4.0.2" From 08f77f2ecd33364979b9539cf034fd60ff515343 Mon Sep 17 00:00:00 2001 From: Colin Diesh Date: Fri, 20 Sep 2024 10:01:14 -0400 Subject: [PATCH 31/38] Fix Hi-C track regression after removal of buffer polyfill (#4584) --- eslint.config.mjs | 2 + packages/core/util/index.ts | 1 + .../alignments/src/MismatchParser/index.ts | 1 + .../authentication/src/OAuthModel/model.tsx | 1 + .../src/ChainAdapter/ChainAdapter.ts | 3 + .../src/ChainAdapter/util.ts | 1 + .../src/DeltaAdapter/DeltaAdapter.ts | 4 +- .../src/DeltaAdapter/util.ts | 1 + .../src/MashMapAdapter/MashMapAdapter.ts | 1 + .../src/PAFAdapter/PAFAdapter.ts | 1 + plugins/comparative-adapters/src/util.ts | 1 + plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts | 1 + plugins/gtf/src/GtfAdapter/GtfAdapter.ts | 1 + plugins/hic/src/HicAdapter/HicAdapter.ts | 1 + .../src/JBrowse1TextSearchAdapter/HttpMap.ts | 1 + .../importAdapters/BedImport.ts | 1 + .../importAdapters/ImportUtils.ts | 1 + .../importAdapters/STARFusionImport.ts | 1 + .../importAdapters/VcfImport.ts | 1 + plugins/variants/src/VcfAdapter/VcfAdapter.ts | 1 + .../jbrowse-web/src/tests/Loader.test.tsx | 112 ++++++----- .../jbrowse-web/src/tests/Synteny.test.tsx | 1 + products/jbrowse-web/src/tests/util.tsx | 1 + yarn.lock | 186 +++++++++--------- 24 files changed, 175 insertions(+), 151 deletions(-) diff --git a/eslint.config.mjs b/eslint.config.mjs index 93dbaca312..6447d40db5 100644 --- a/eslint.config.mjs +++ b/eslint.config.mjs @@ -61,6 +61,7 @@ export default tseslint.config( }, { rules: { + 'no-restricted-globals': ['error', 'Buffer'], 'no-empty': 'off', 'no-console': [ 'warn', @@ -180,6 +181,7 @@ export default tseslint.config( }, }, rules: { + 'no-restricted-globals': ['off'], '@typescript-eslint/no-require-imports': 'off', 'no-console': 'off', }, diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts index 8cf71d60f9..0046a00143 100644 --- a/packages/core/util/index.ts +++ b/packages/core/util/index.ts @@ -1,6 +1,7 @@ import React, { useEffect, useRef, useState } from 'react' import isObject from 'is-object' import PluginManager from '../PluginManager' +import type { Buffer } from 'buffer' import { addDisposer, getParent, diff --git a/plugins/alignments/src/MismatchParser/index.ts b/plugins/alignments/src/MismatchParser/index.ts index 362b82cf62..cd7d61f405 100644 --- a/plugins/alignments/src/MismatchParser/index.ts +++ b/plugins/alignments/src/MismatchParser/index.ts @@ -1,4 +1,5 @@ import { revcom, Feature } from '@jbrowse/core/util' +import type { Buffer } from 'buffer' import { getTagAlt } from '../util' export interface Mismatch { diff --git a/plugins/authentication/src/OAuthModel/model.tsx b/plugins/authentication/src/OAuthModel/model.tsx index 72323129b0..eecb4f2db6 100644 --- a/plugins/authentication/src/OAuthModel/model.tsx +++ b/plugins/authentication/src/OAuthModel/model.tsx @@ -2,6 +2,7 @@ import { ConfigurationReference, getConf } from '@jbrowse/core/configuration' import { InternetAccount } from '@jbrowse/core/pluggableElementTypes/models' import { isElectron, UriLocation } from '@jbrowse/core/util' import { Instance, types } from 'mobx-state-tree' +import { Buffer } from 'buffer' // locals import { OAuthInternetAccountConfigModel } from './configSchema' diff --git a/plugins/comparative-adapters/src/ChainAdapter/ChainAdapter.ts b/plugins/comparative-adapters/src/ChainAdapter/ChainAdapter.ts index 3990aaa72c..5507c8d1a3 100644 --- a/plugins/comparative-adapters/src/ChainAdapter/ChainAdapter.ts +++ b/plugins/comparative-adapters/src/ChainAdapter/ChainAdapter.ts @@ -2,6 +2,9 @@ import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter' import { openLocation } from '@jbrowse/core/util/io' import { isGzip } from '@jbrowse/core/util' import { unzip } from '@gmod/bgzf-filehandle' +import type { Buffer } from 'buffer' + +// locals import PAFAdapter from '../PAFAdapter/PAFAdapter' import { paf_chain2paf } from './util' diff --git a/plugins/comparative-adapters/src/ChainAdapter/util.ts b/plugins/comparative-adapters/src/ChainAdapter/util.ts index c39c335b7a..24296b1e74 100644 --- a/plugins/comparative-adapters/src/ChainAdapter/util.ts +++ b/plugins/comparative-adapters/src/ChainAdapter/util.ts @@ -1,3 +1,4 @@ +import type { Buffer } from 'buffer' const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined diff --git a/plugins/comparative-adapters/src/DeltaAdapter/DeltaAdapter.ts b/plugins/comparative-adapters/src/DeltaAdapter/DeltaAdapter.ts index 5d7e03ba20..48be78ff5c 100644 --- a/plugins/comparative-adapters/src/DeltaAdapter/DeltaAdapter.ts +++ b/plugins/comparative-adapters/src/DeltaAdapter/DeltaAdapter.ts @@ -1,9 +1,11 @@ import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter' import { openLocation } from '@jbrowse/core/util/io' import { unzip } from '@gmod/bgzf-filehandle' +import { isGzip } from '@jbrowse/core/util' +import type { Buffer } from 'buffer' +// locals import PAFAdapter from '../PAFAdapter/PAFAdapter' import { paf_delta2paf } from './util' -import { isGzip } from '@jbrowse/core/util' export default class DeltaAdapter extends PAFAdapter { async setupPre(opts?: BaseOptions) { diff --git a/plugins/comparative-adapters/src/DeltaAdapter/util.ts b/plugins/comparative-adapters/src/DeltaAdapter/util.ts index 8b2e3e3869..b5f1482ec4 100644 --- a/plugins/comparative-adapters/src/DeltaAdapter/util.ts +++ b/plugins/comparative-adapters/src/DeltaAdapter/util.ts @@ -1,3 +1,4 @@ +import type { Buffer } from 'buffer' const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined diff --git a/plugins/comparative-adapters/src/MashMapAdapter/MashMapAdapter.ts b/plugins/comparative-adapters/src/MashMapAdapter/MashMapAdapter.ts index d0a0797f97..26fef59fb3 100644 --- a/plugins/comparative-adapters/src/MashMapAdapter/MashMapAdapter.ts +++ b/plugins/comparative-adapters/src/MashMapAdapter/MashMapAdapter.ts @@ -2,6 +2,7 @@ import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter' import { openLocation } from '@jbrowse/core/util/io' import { unzip } from '@gmod/bgzf-filehandle' import { isGzip } from '@jbrowse/core/util' +import type { Buffer } from 'buffer' import PAFAdapter from '../PAFAdapter/PAFAdapter' import { parseLineByLine } from '../util' diff --git a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts index 794c163096..b32fc0765c 100644 --- a/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts +++ b/plugins/comparative-adapters/src/PAFAdapter/PAFAdapter.ts @@ -13,6 +13,7 @@ import { } from '@jbrowse/core/configuration' import { unzip } from '@gmod/bgzf-filehandle' import { MismatchParser } from '@jbrowse/plugin-alignments' +import type { Buffer } from 'buffer' // locals import SyntenyFeature from '../SyntenyFeature' diff --git a/plugins/comparative-adapters/src/util.ts b/plugins/comparative-adapters/src/util.ts index b7f6abf91a..a37d906e13 100644 --- a/plugins/comparative-adapters/src/util.ts +++ b/plugins/comparative-adapters/src/util.ts @@ -2,6 +2,7 @@ import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter' import { GenericFilehandle } from 'generic-filehandle' import { unzip } from '@gmod/bgzf-filehandle' import { isGzip } from '@jbrowse/core/util' +import type { Buffer } from 'buffer' import { PAFRecord } from './PAFAdapter/util' diff --git a/plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts b/plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts index 22b60f589c..1f7ae6c5fb 100644 --- a/plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts +++ b/plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts @@ -10,6 +10,7 @@ import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature' import { unzip } from '@gmod/bgzf-filehandle' import { parseStringSync } from 'gff-nostream' import { isGzip, updateStatus } from '@jbrowse/core/util' +import type { Buffer } from 'buffer' import { featureData } from '../featureData' diff --git a/plugins/gtf/src/GtfAdapter/GtfAdapter.ts b/plugins/gtf/src/GtfAdapter/GtfAdapter.ts index 72ccf3aad4..02f7b991d4 100644 --- a/plugins/gtf/src/GtfAdapter/GtfAdapter.ts +++ b/plugins/gtf/src/GtfAdapter/GtfAdapter.ts @@ -14,6 +14,7 @@ import { } from '@jbrowse/core/util' import { unzip } from '@gmod/bgzf-filehandle' import { parseStringSync } from 'gtf-nostream' +import type { Buffer } from 'buffer' // locals import { FeatureLoc, featureData } from '../util' diff --git a/plugins/hic/src/HicAdapter/HicAdapter.ts b/plugins/hic/src/HicAdapter/HicAdapter.ts index b2cb118be6..aea060b40c 100644 --- a/plugins/hic/src/HicAdapter/HicAdapter.ts +++ b/plugins/hic/src/HicAdapter/HicAdapter.ts @@ -10,6 +10,7 @@ import HicStraw from 'hic-straw' import PluginManager from '@jbrowse/core/PluginManager' import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache' import { AnyConfigurationModel } from '@jbrowse/core/configuration' +import { Buffer } from 'buffer' interface ContactRecord { bin1: number diff --git a/plugins/legacy-jbrowse/src/JBrowse1TextSearchAdapter/HttpMap.ts b/plugins/legacy-jbrowse/src/JBrowse1TextSearchAdapter/HttpMap.ts index 2e6cfcff12..b19ed1bd69 100644 --- a/plugins/legacy-jbrowse/src/JBrowse1TextSearchAdapter/HttpMap.ts +++ b/plugins/legacy-jbrowse/src/JBrowse1TextSearchAdapter/HttpMap.ts @@ -3,6 +3,7 @@ * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js */ import crc32 from 'crc/crc32' +import { Buffer } from 'buffer' export default class HttpMap { url: string diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts index 6eec18dcc7..c67b3ac1c9 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/BedImport.ts @@ -1,4 +1,5 @@ import { ParseOptions, parseTsvBuffer } from './ImportUtils' +import type { Buffer } from 'buffer' const browserBytes = 'browser '.split('').map(c => c.charCodeAt(0)) const trackBytes = 'track '.split('').map(c => c.charCodeAt(0)) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts index cef8c22eeb..c9cef1f62b 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/ImportUtils.ts @@ -1,4 +1,5 @@ import { ParsedLocString, parseLocString } from '@jbrowse/core/util' +import type { Buffer } from 'buffer' export function bufferToString(buffer: Buffer) { return new TextDecoder('utf8', { fatal: true }).decode(buffer) diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts index 0a36b29bd3..e5356aab0c 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/STARFusionImport.ts @@ -1,4 +1,5 @@ import { parseTsvBuffer, ParseOptions } from './ImportUtils' +import type { Buffer } from 'buffer' function parseSTARFusionBreakpointString(str: string) { const fields = str.split(':') diff --git a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts index 5e00e37f9c..016524bad5 100644 --- a/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts +++ b/plugins/spreadsheet-view/src/SpreadsheetView/importAdapters/VcfImport.ts @@ -7,6 +7,7 @@ import { Column, ParseOptions, } from './ImportUtils' +import type { Buffer } from 'buffer' const vcfCoreColumns: { name: string; type: string }[] = [ { name: 'CHROM', type: 'Text' }, // 0 diff --git a/plugins/variants/src/VcfAdapter/VcfAdapter.ts b/plugins/variants/src/VcfAdapter/VcfAdapter.ts index 74d639c3ec..0538a95017 100644 --- a/plugins/variants/src/VcfAdapter/VcfAdapter.ts +++ b/plugins/variants/src/VcfAdapter/VcfAdapter.ts @@ -8,6 +8,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs' import IntervalTree from '@flatten-js/interval-tree' import { unzip } from '@gmod/bgzf-filehandle' import VCF from '@gmod/vcf' +import type { Buffer } from 'buffer' // local import VcfFeature from '../VcfFeature' diff --git a/products/jbrowse-web/src/tests/Loader.test.tsx b/products/jbrowse-web/src/tests/Loader.test.tsx index 6ee44bfdae..1894eaa6dc 100644 --- a/products/jbrowse-web/src/tests/Loader.test.tsx +++ b/products/jbrowse-web/src/tests/Loader.test.tsx @@ -1,5 +1,6 @@ import React from 'react' import { render, waitFor } from '@testing-library/react' +import { Buffer } from 'buffer' import { LocalFile } from 'generic-filehandle' import rangeParser from 'range-parser' @@ -25,65 +26,62 @@ jest.mock('../makeWorkerInstance', () => () => {}) const delay = { timeout: 20000 } -jest - .spyOn(global, 'fetch') - - .mockImplementation(async (url: any, args: any) => { - if (/plugin-store/.exec(`${url}`)) { - return new Response( - JSON.stringify({ - plugins: [ - { - url: 'https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js', - }, - ], - }), - ) - } - if (`${url}`.includes('testid')) { - return new Response( - `{"session":"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"}`, - ) - } - if (`${url}`.includes('testcustomcallback')) { - return new Response( - `{"session":"eJzVVm1v2zYQ_isCvzQB7NiK4zTQt9TNVm9p59puUmANAlo6SdwoSiPptwb-7zuSsiw7dhpk2YB9MGAe7-W5e053fCAsIgHRX5fwOfslnJAGETQDFPWFhkRSzXLhaVDagwXNCg6e37ponbZP_YbXDfyLoPvWG3xEs4zKhAkStBskknQO8pZFOiVB5-KsQWYM5ooEvz-4cGzj-974RnO9LEzUayaAyp9B5BncoBHe5HGsQA8WJDhtt9H7pBiANMf2SbuLwZgqOF1CNIQE_bkoEuJPLo1QJ5foRGkqtQUHAhF00ZPfQLUZSAUoiClX0CBUKcgmfFkaz3I-yxdkdYf4JA3_rKUwHOpr-XF0c7PBfslZIjIQWo2NMl6EuYhZMnWZVv6aPBdJUwKNVFPNmhOaNf1zv312cX7WOe-87TQVKIUGay9lhrXgf_XTL1dt6Y-Gu5XbYHjvrFBhwDhMi_U5KH2o3kD9OhmLSO362NZvkBRYkmLxfFP9nZQenjYtofejp5I_gHy7KPeFdX2_WH43zZZPFeRIHvqNpyI0YI5ioHoq4dh7-CY8TwIehFcKTxLQR28UsiiiN8ffxIoY9kUEEhvApOGQD0tRLbGdi1WDjGbJT87rHvU9l6sVGqk0n4_yWPc4KwomkqrlYsY1yHeWmJjTpC9CPo3A9qo5Xy3Ks9_tnBtPo0-DnkmdJrDLaZq__0qv2Kw72eV0j9GG2LMf8rrX_BXJVaIIS___GsO1HPbxtufWEQccQm3Gi5Fa5oh1rXI-dcXybflMaBxsJtbqBbQ-e1Y8q6I1dk-7bdd-6_xIoOUUnMx1t5Os7sygS1kEHzCeqU7ZohvRb-jBzPLqyo7FkS1RLseulCnDMDJMWUg5KVWu6QQ4loYYDJy6T6CEhUmANFmVXg2KOYuQT8tb3d24Hm7T9gc1qq_gwyGVWxvIzmqOuOwy2PA3hoV2fLusH2-uirmriNUxbQkrGL06ye6yAoAbyvx52ZZAGCwrcqlHTlp6XaPZd1eB6u-5NB1J8aObwW3FhEtVgP0W-9jvVIRQXtTBuEV1cCnafnh6aDy5DkV9N1tjzxp7c6ZTb3TjHYV5sTwm29vcgFrvc-wvGtFCbw2AdzS7LIX4xqDZdR5Ws3Aq2QG4J6hp9RV8sUqp1kXQanG05mmudNDBp0bLtMp9RDVtOSct1x4nfygMYLjD2bIwkfizo-KP_ePIhuat58UPHxOvN_T_d2u88cIV8npvpC3TR9X8L98zr_w-eGz_dHYvIsKut3KY9KpBZvr-bvU3l2iNHA"}`, - ) - } - if (`${url}`.includes('nonexist')) { - return new Response('', { - status: 404, - statusText: 'failed to find session', - }) - } - // this is the analytics - if (`${url}`.includes('jb2=true')) { - return new Response('{}') - } - try { - const file = getFile(`${url}`) - const maxRangeRequest = 2000000 // kind of arbitrary, part of the rangeParser - if (args?.headers && 'range' in args.headers) { - const range = rangeParser(maxRangeRequest, args.headers.range) - if (range === -2 || range === -1) { - throw new Error(`Error parsing range "${args.headers.range}"`) - } - const { start, end } = range[0]! - const len = end - start + 1 - const buf = Buffer.alloc(len) - const { bytesRead } = await file.read(buf, 0, len, start) - const stat = await file.stat() - return new Response(buf.subarray(0, bytesRead), { - status: 206, - headers: [['content-range', `${start}-${end}/${stat.size}`]], - }) +jest.spyOn(global, 'fetch').mockImplementation(async (url: any, args: any) => { + if (/plugin-store/.exec(`${url}`)) { + return new Response( + JSON.stringify({ + plugins: [ + { + url: 'https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js', + }, + ], + }), + ) + } + if (`${url}`.includes('testid')) { + return new Response( + `{"session":"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"}`, + ) + } + if (`${url}`.includes('testcustomcallback')) { + return new Response( + `{"session":"eJzVVm1v2zYQ_isCvzQB7NiK4zTQt9TNVm9p59puUmANAlo6SdwoSiPptwb-7zuSsiw7dhpk2YB9MGAe7-W5e053fCAsIgHRX5fwOfslnJAGETQDFPWFhkRSzXLhaVDagwXNCg6e37ponbZP_YbXDfyLoPvWG3xEs4zKhAkStBskknQO8pZFOiVB5-KsQWYM5ooEvz-4cGzj-974RnO9LEzUayaAyp9B5BncoBHe5HGsQA8WJDhtt9H7pBiANMf2SbuLwZgqOF1CNIQE_bkoEuJPLo1QJ5foRGkqtQUHAhF00ZPfQLUZSAUoiClX0CBUKcgmfFkaz3I-yxdkdYf4JA3_rKUwHOpr-XF0c7PBfslZIjIQWo2NMl6EuYhZMnWZVv6aPBdJUwKNVFPNmhOaNf1zv312cX7WOe-87TQVKIUGay9lhrXgf_XTL1dt6Y-Gu5XbYHjvrFBhwDhMi_U5KH2o3kD9OhmLSO362NZvkBRYkmLxfFP9nZQenjYtofejp5I_gHy7KPeFdX2_WH43zZZPFeRIHvqNpyI0YI5ioHoq4dh7-CY8TwIehFcKTxLQR28UsiiiN8ffxIoY9kUEEhvApOGQD0tRLbGdi1WDjGbJT87rHvU9l6sVGqk0n4_yWPc4KwomkqrlYsY1yHeWmJjTpC9CPo3A9qo5Xy3Ks9_tnBtPo0-DnkmdJrDLaZq__0qv2Kw72eV0j9GG2LMf8rrX_BXJVaIIS___GsO1HPbxtufWEQccQm3Gi5Fa5oh1rXI-dcXybflMaBxsJtbqBbQ-e1Y8q6I1dk-7bdd-6_xIoOUUnMx1t5Os7sygS1kEHzCeqU7ZohvRb-jBzPLqyo7FkS1RLseulCnDMDJMWUg5KVWu6QQ4loYYDJy6T6CEhUmANFmVXg2KOYuQT8tb3d24Hm7T9gc1qq_gwyGVWxvIzmqOuOwy2PA3hoV2fLusH2-uirmriNUxbQkrGL06ye6yAoAbyvx52ZZAGCwrcqlHTlp6XaPZd1eB6u-5NB1J8aObwW3FhEtVgP0W-9jvVIRQXtTBuEV1cCnafnh6aDy5DkV9N1tjzxp7c6ZTb3TjHYV5sTwm29vcgFrvc-wvGtFCbw2AdzS7LIX4xqDZdR5Ws3Aq2QG4J6hp9RV8sUqp1kXQanG05mmudNDBp0bLtMp9RDVtOSct1x4nfygMYLjD2bIwkfizo-KP_ePIhuat58UPHxOvN_T_d2u88cIV8npvpC3TR9X8L98zr_w-eGz_dHYvIsKut3KY9KpBZvr-bvU3l2iNHA"}`, + ) + } + if (`${url}`.includes('nonexist')) { + return new Response('', { + status: 404, + statusText: 'failed to find session', + }) + } + // this is the analytics + if (`${url}`.includes('jb2=true')) { + return new Response('{}') + } + try { + const file = getFile(`${url}`) + const maxRangeRequest = 2000000 // kind of arbitrary, part of the rangeParser + if (args?.headers && 'range' in args.headers) { + const range = rangeParser(maxRangeRequest, args.headers.range) + if (range === -2 || range === -1) { + throw new Error(`Error parsing range "${args.headers.range}"`) } - return new Response(await file.readFile(), { status: 200 }) - } catch (e) { - console.error(e) - return new Response(undefined, { status: 404 }) + const { start, end } = range[0]! + const len = end - start + 1 + const buf = Buffer.alloc(len) + const { bytesRead } = await file.read(buf, 0, len, start) + const stat = await file.stat() + return new Response(buf.subarray(0, bytesRead), { + status: 206, + headers: [['content-range', `${start}-${end}/${stat.size}`]], + }) } - }) + return new Response(await file.readFile(), { status: 200 }) + } catch (e) { + console.error(e) + return new Response(undefined, { status: 404 }) + } +}) afterEach(() => { localStorage.clear() diff --git a/products/jbrowse-web/src/tests/Synteny.test.tsx b/products/jbrowse-web/src/tests/Synteny.test.tsx index 22478bc84e..5fda5af09e 100644 --- a/products/jbrowse-web/src/tests/Synteny.test.tsx +++ b/products/jbrowse-web/src/tests/Synteny.test.tsx @@ -3,6 +3,7 @@ import { render } from '@testing-library/react' import { LocalFile } from 'generic-filehandle' import rangeParser from 'range-parser' +import { Buffer } from 'buffer' // local import { App } from './loaderUtil' diff --git a/products/jbrowse-web/src/tests/util.tsx b/products/jbrowse-web/src/tests/util.tsx index 896cf1bb83..145deddd23 100644 --- a/products/jbrowse-web/src/tests/util.tsx +++ b/products/jbrowse-web/src/tests/util.tsx @@ -5,6 +5,7 @@ import { render, waitFor } from '@testing-library/react' import { toMatchImageSnapshot } from 'jest-image-snapshot' import { LocalFile, GenericFilehandle } from 'generic-filehandle' import rangeParser from 'range-parser' +import { Buffer } from 'buffer' import { QueryParamProvider } from 'use-query-params' import { WindowHistoryAdapter } from 'use-query-params/adapters/window' import { Image, createCanvas } from 'canvas' diff --git a/yarn.lock b/yarn.lock index b8aabe3511..f17ed1c5e1 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2877,9 +2877,9 @@ react-is "^18.3.1" "@mui/x-charts-vendor@^7.12.0": - version "7.16.0" - resolved "https://registry.yarnpkg.com/@mui/x-charts-vendor/-/x-charts-vendor-7.16.0.tgz#6f745457eac05955bfcfc6180562ceab576a8abf" - integrity sha512-MyMCCl7eAM53rLbjqP4zbMy5hYtdeqCjAYCH2jpvBKdgugm2eaPLKOPM8bUVfen0wHA8BXleQrIrNceytFPyZA== + version "7.18.0" + resolved "https://registry.yarnpkg.com/@mui/x-charts-vendor/-/x-charts-vendor-7.18.0.tgz#f8e26840bdc29311af629326063ea854b7a4608a" + integrity sha512-YPL7SP6W7t9jBIrK8WjmCtW/YoUmgr0BA7j2QE9bKX4VJLEUU498fEKik0ZJZyzyR7ov0MD3m7S+YCw1o5sqkw== dependencies: "@babel/runtime" "^7.25.6" "@types/d3-color" "^3.1.3" @@ -2898,21 +2898,21 @@ robust-predicates "^3.0.2" "@mui/x-data-grid@^7.0.0": - version "7.17.0" - resolved "https://registry.yarnpkg.com/@mui/x-data-grid/-/x-data-grid-7.17.0.tgz#26cb4b0b978e44e4488e2a0f2a4dd6810c147b74" - integrity sha512-d3pFdrQlNR+8waol7iM6LlNIpvqo9SgYeKcMIOSQ3etpue9iRFNy8s1HCHd9Nxnhzgr+fqMy/v3bXZnd196qig== + version "7.18.0" + resolved "https://registry.yarnpkg.com/@mui/x-data-grid/-/x-data-grid-7.18.0.tgz#9be96110e0334eb347b09eef68f1d61d3720bb13" + integrity sha512-41UjJbRxWk+Yk/lfvaO55Pwo5p+F5s3rOTiHLl53ikCT5GuJ5OCCvik0Bi3c6DzTuUBdrEucae2618rydc2DGw== dependencies: "@babel/runtime" "^7.25.6" "@mui/utils" "^5.16.6" - "@mui/x-internals" "7.17.0" + "@mui/x-internals" "7.18.0" clsx "^2.1.1" prop-types "^15.8.1" reselect "^5.1.1" -"@mui/x-internals@7.17.0": - version "7.17.0" - resolved 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"21.1.1" optionalDependencies: - "@nx/nx-darwin-arm64" "19.7.4" - "@nx/nx-darwin-x64" "19.7.4" - "@nx/nx-freebsd-x64" "19.7.4" - "@nx/nx-linux-arm-gnueabihf" "19.7.4" - "@nx/nx-linux-arm64-gnu" "19.7.4" - "@nx/nx-linux-arm64-musl" "19.7.4" - "@nx/nx-linux-x64-gnu" "19.7.4" - "@nx/nx-linux-x64-musl" "19.7.4" - "@nx/nx-win32-arm64-msvc" "19.7.4" - "@nx/nx-win32-x64-msvc" "19.7.4" + "@nx/nx-darwin-arm64" "19.8.0" + "@nx/nx-darwin-x64" "19.8.0" + "@nx/nx-freebsd-x64" "19.8.0" + "@nx/nx-linux-arm-gnueabihf" "19.8.0" + "@nx/nx-linux-arm64-gnu" "19.8.0" + "@nx/nx-linux-arm64-musl" "19.8.0" + "@nx/nx-linux-x64-gnu" "19.8.0" + "@nx/nx-linux-x64-musl" "19.8.0" + "@nx/nx-win32-arm64-msvc" "19.8.0" + "@nx/nx-win32-x64-msvc" "19.8.0" object-assign@^4, object-assign@^4.0.1, object-assign@^4.1.1: version "4.1.1" From 7d6caba2e6ec01985a757191f66b5e641714c045 Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 12:44:26 -0400 Subject: [PATCH 32/38] [skip ci] Release --- website/release_announcement_drafts/v2.15.4.md | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 website/release_announcement_drafts/v2.15.4.md diff --git a/website/release_announcement_drafts/v2.15.4.md b/website/release_announcement_drafts/v2.15.4.md new file mode 100644 index 0000000000..3a2def9c47 --- /dev/null +++ b/website/release_announcement_drafts/v2.15.4.md @@ -0,0 +1,2 @@ +Fixes Hi-C files failing to load in v2.15.3 and also fixes text indexing on +JBrowse Desktop on Windows machines From b32ffcb8a92ed9b7e7603b0e96186f18ddd0c359 Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 16:54:48 +0000 Subject: [PATCH 33/38] Prepare for v2.15.4 release --- CHANGELOG.md | 17 +++++++++++ website/blog/2024-09-20-v2.15.4-release.md | 34 ++++++++++++++++++++++ website/docusaurus.config.json | 2 +- 3 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 website/blog/2024-09-20-v2.15.4-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 3a2875d51f..e3d49686cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,20 @@ +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.4 + +## 2.15.4 (2024-09-20) + +#### :bug: Bug Fix + +- Other + - [#4582](https://github.com/GMOD/jbrowse-components/pull/4582) Fix text + indexing on Windows ([@cmdcolin](https://github.com/cmdcolin)) +- `text-indexing` + - [#4580](https://github.com/GMOD/jbrowse-components/pull/4580) Fix indexing + plaintext gff/vcf on desktop ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.22s. + yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3 Done in 0.57s. diff --git a/website/blog/2024-09-20-v2.15.4-release.md b/website/blog/2024-09-20-v2.15.4-release.md new file mode 100644 index 0000000000..0e2557e38a --- /dev/null +++ b/website/blog/2024-09-20-v2.15.4-release.md @@ -0,0 +1,34 @@ +--- +title: v2.15.4 Release +date: 2024-09-20 16:54:16 +tags: ['release', 'jbrowse 2'] +--- + +Fixes Hi-C files failing to load in v2.15.3 and also fixes text indexing on +JBrowse Desktop on Windows machines + +## Downloads + +- [v2.15.4](https://github.com/GMOD/jbrowse-components/releases/tag/v2.15.4) + +To install JBrowse 2 for the web, you can download the link above, or you can +use the JBrowse CLI to automatically download the latest version. See the +[JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more +details. + +yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.4 + +## 2.15.4 (2024-09-20) + +#### :bug: Bug Fix + +- Other + - [#4582](https://github.com/GMOD/jbrowse-components/pull/4582) Fix text + indexing on Windows ([@cmdcolin](https://github.com/cmdcolin)) +- `text-indexing` + - [#4580](https://github.com/GMOD/jbrowse-components/pull/4580) Fix indexing + plaintext gff/vcf on desktop ([@cmdcolin](https://github.com/cmdcolin)) + +#### Committers: 1 + +- Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) Done in 1.22s. diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index e6a814856f..1c3a8b7bd0 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,6 +9,6 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.15.3" + "currentVersion": "v2.15.4" } } From 686b4ad9016b3586e8230180f7adb44c238ba4fb Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 17:16:51 +0000 Subject: [PATCH 34/38] [update docs] v2.15.4 --- lerna.json | 2 +- packages/app-core/package.json | 4 +- packages/core/package.json | 2 +- packages/embedded-core/package.json | 6 +- packages/product-core/package.json | 4 +- packages/sv-core/package.json | 4 +- packages/text-indexing/package.json | 4 +- packages/web-core/package.json | 6 +- plugins/alignments/package.json | 4 +- plugins/arc/package.json | 2 +- plugins/authentication/package.json | 2 +- plugins/bed/package.json | 2 +- plugins/breakpoint-split-view/package.json | 2 +- plugins/circular-view/package.json | 2 +- plugins/comparative-adapters/package.json | 2 +- plugins/config/package.json | 2 +- plugins/data-management/package.json | 2 +- plugins/dotplot-view/package.json | 2 +- plugins/gccontent/package.json | 2 +- plugins/gff3/package.json | 2 +- plugins/grid-bookmark/package.json | 2 +- plugins/gtf/package.json | 2 +- plugins/hic/package.json | 2 +- plugins/jobs-management/package.json | 4 +- plugins/legacy-jbrowse/package.json | 2 +- plugins/linear-comparative-view/package.json | 2 +- plugins/linear-genome-view/package.json | 2 +- plugins/lollipop/package.json | 2 +- plugins/menus/package.json | 2 +- plugins/rdf/package.json | 2 +- plugins/sequence/package.json | 2 +- plugins/spreadsheet-view/package.json | 4 +- plugins/sv-inspector/package.json | 2 +- plugins/svg/package.json | 2 +- plugins/text-indexing/package.json | 4 +- plugins/trix/package.json | 2 +- plugins/variants/package.json | 4 +- plugins/wiggle/package.json | 2 +- products/jbrowse-cli/README.md | 24 +++---- products/jbrowse-cli/package.json | 2 +- products/jbrowse-desktop/package.json | 70 +++++++++---------- products/jbrowse-img/package.json | 6 +- .../jbrowse-predefined-sessions/package.json | 2 +- products/jbrowse-react-app/package.json | 66 ++++++++--------- .../package.json | 24 +++---- .../package.json | 40 +++++------ products/jbrowse-web/package.json | 66 ++++++++--------- 47 files changed, 201 insertions(+), 201 deletions(-) diff --git a/lerna.json b/lerna.json index 41bdf3d775..163448f924 100644 --- a/lerna.json +++ b/lerna.json @@ -1,5 +1,5 @@ { - "version": "2.15.3", + "version": "2.15.4", "npmClient": "yarn", "$schema": "node_modules/lerna/schemas/lerna-schema.json" } diff --git a/packages/app-core/package.json b/packages/app-core/package.json index 9424e6c846..51b4097ef4 100644 --- a/packages/app-core/package.json +++ b/packages/app-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/app-core", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/product-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/core/package.json b/packages/core/package.json index acf48565ae..7508e58452 100644 --- a/packages/core/package.json +++ b/packages/core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/core", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 core libraries used by plugins", "keywords": [ "jbrowse", diff --git a/packages/embedded-core/package.json b/packages/embedded-core/package.json index a578a19767..1f5a75edba 100644 --- a/packages/embedded-core/package.json +++ b/packages/embedded-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/embedded-core", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 code shared between embedded products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/product-core/package.json b/packages/product-core/package.json index f1e636503c..2d7512f899 100644 --- a/packages/product-core/package.json +++ b/packages/product-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/product-core", - "version": "2.15.3", + "version": "2.15.4", "sideEffects": false, "description": "JBrowse 2 code shared between products but not used by plugins", "keywords": [ @@ -43,7 +43,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", + "@jbrowse/core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "copy-to-clipboard": "^3.3.1", diff --git a/packages/sv-core/package.json b/packages/sv-core/package.json index e6914bdad5..5ae33bdc99 100644 --- a/packages/sv-core/package.json +++ b/packages/sv-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/sv-core", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 code shared between sv type code", "keywords": [ "jbrowse", @@ -41,7 +41,7 @@ "useSrc": "node ../../scripts/useSrc.js" }, "dependencies": { - "@jbrowse/plugin-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0" }, diff --git a/packages/text-indexing/package.json b/packages/text-indexing/package.json index f2885e5f10..1acb7d9fd9 100644 --- a/packages/text-indexing/package.json +++ b/packages/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/text-indexing", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 text indexing for desktop", "keywords": [ "jbrowse", @@ -42,7 +42,7 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/core": "^2.15.3", + "@jbrowse/core": "^2.15.4", "ixixx": "^2.0.1", "node-fetch": "^2.6.0", "sanitize-filename": "^1.6.3" diff --git a/packages/web-core/package.json b/packages/web-core/package.json index 190c0bf5ce..101fd9468a 100644 --- a/packages/web-core/package.json +++ b/packages/web-core/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web-core", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 code shared between web-app type products", "keywords": [ "jbrowse", @@ -42,8 +42,8 @@ }, "dependencies": { "@babel/runtime": "^7.16.3", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "clone": "^2.0.0", diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json index 9d61dc6ab9..8cc7b47dea 100644 --- a/plugins/alignments/package.json +++ b/plugins/alignments/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-alignments", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 alignments adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bam": "^2.0.0", "@gmod/cram": "^3.0.3", - "@jbrowse/sv-core": "^2.15.3", + "@jbrowse/sv-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "canvas2svg": "^1.0.16", "clone": "^2.1.2", diff --git a/plugins/arc/package.json b/plugins/arc/package.json index df5e78e4f5..69c3662dc3 100644 --- a/plugins/arc/package.json +++ b/plugins/arc/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-arc", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 arc adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/authentication/package.json b/plugins/authentication/package.json index 8d2389fe31..16ea9b5e5f 100644 --- a/plugins/authentication/package.json +++ b/plugins/authentication/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-authentication", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 Authentication", "keywords": [ "jbrowse", diff --git a/plugins/bed/package.json b/plugins/bed/package.json index 82859b3759..dab3b38e97 100644 --- a/plugins/bed/package.json +++ b/plugins/bed/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-bed", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 bed adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/breakpoint-split-view/package.json b/plugins/breakpoint-split-view/package.json index 205f71e445..f98792ffbc 100644 --- a/plugins/breakpoint-split-view/package.json +++ b/plugins/breakpoint-split-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-breakpoint-split-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 breakpoint detail split view", "keywords": [ "jbrowse", diff --git a/plugins/circular-view/package.json b/plugins/circular-view/package.json index 526ccd84de..b101736ca0 100644 --- a/plugins/circular-view/package.json +++ b/plugins/circular-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-circular-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 circular view", "keywords": [ "jbrowse", diff --git a/plugins/comparative-adapters/package.json b/plugins/comparative-adapters/package.json index 8ace6e37b9..e81f7a5a2d 100644 --- a/plugins/comparative-adapters/package.json +++ b/plugins/comparative-adapters/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-comparative-adapters", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 comparative adapters", "keywords": [ "jbrowse", diff --git a/plugins/config/package.json b/plugins/config/package.json index 4bf197f8cd..b85b14885f 100644 --- a/plugins/config/package.json +++ b/plugins/config/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-config", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 config utilities", "keywords": [ "jbrowse", diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json index 530385f2c3..715021fe35 100644 --- a/plugins/data-management/package.json +++ b/plugins/data-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-data-management", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/dotplot-view/package.json b/plugins/dotplot-view/package.json index 020c353870..6016a1b6c2 100644 --- a/plugins/dotplot-view/package.json +++ b/plugins/dotplot-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-dotplot-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 dotplot view", "keywords": [ "jbrowse", diff --git a/plugins/gccontent/package.json b/plugins/gccontent/package.json index a9f567a86d..e0624cf9a8 100644 --- a/plugins/gccontent/package.json +++ b/plugins/gccontent/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gccontent", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 gccontent concepts", "keywords": [ "jbrowse", diff --git a/plugins/gff3/package.json b/plugins/gff3/package.json index a9a0068554..d768ed3242 100644 --- a/plugins/gff3/package.json +++ b/plugins/gff3/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gff3", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 gff3.", "keywords": [ "jbrowse", diff --git a/plugins/grid-bookmark/package.json b/plugins/grid-bookmark/package.json index d604c6357d..973dfde16b 100644 --- a/plugins/grid-bookmark/package.json +++ b/plugins/grid-bookmark/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-grid-bookmark", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 grid bookmark widget", "keywords": [ "jbrowse", diff --git a/plugins/gtf/package.json b/plugins/gtf/package.json index 345bdc7315..bdcd7d1824 100644 --- a/plugins/gtf/package.json +++ b/plugins/gtf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-gtf", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 gtf feature adapter", "keywords": [ "jbrowse", diff --git a/plugins/hic/package.json b/plugins/hic/package.json index 2b5e0b25f9..967885386a 100644 --- a/plugins/hic/package.json +++ b/plugins/hic/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-hic", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 hic adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/jobs-management/package.json b/plugins/jobs-management/package.json index 43bc82b21d..f18f2630fa 100644 --- a/plugins/jobs-management/package.json +++ b/plugins/jobs-management/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-jobs-management", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 jobs management", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.3", + "@jbrowse/text-indexing": "^2.15.4", "@mui/icons-material": "^6.0.0" }, "peerDependencies": { diff --git a/plugins/legacy-jbrowse/package.json b/plugins/legacy-jbrowse/package.json index bf19fd4f01..bd02c92cb3 100644 --- a/plugins/legacy-jbrowse/package.json +++ b/plugins/legacy-jbrowse/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-legacy-jbrowse", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data", "keywords": [ "jbrowse", diff --git a/plugins/linear-comparative-view/package.json b/plugins/linear-comparative-view/package.json index d7b778ee65..600e8fc1f2 100644 --- a/plugins/linear-comparative-view/package.json +++ b/plugins/linear-comparative-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-comparative-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 linear comparative view", "keywords": [ "jbrowse", diff --git a/plugins/linear-genome-view/package.json b/plugins/linear-genome-view/package.json index e61561e631..4c912dea87 100644 --- a/plugins/linear-genome-view/package.json +++ b/plugins/linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-linear-genome-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 linear genome view", "keywords": [ "jbrowse", diff --git a/plugins/lollipop/package.json b/plugins/lollipop/package.json index 40cff9244a..ef246861ae 100644 --- a/plugins/lollipop/package.json +++ b/plugins/lollipop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-lollipop", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 plugin for lollipops", "keywords": [ "jbrowse", diff --git a/plugins/menus/package.json b/plugins/menus/package.json index 12681b6d91..c0159b4b74 100644 --- a/plugins/menus/package.json +++ b/plugins/menus/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-menus", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 basic menus", "keywords": [ "jbrowse", diff --git a/plugins/rdf/package.json b/plugins/rdf/package.json index 9beff555ed..45cf863817 100644 --- a/plugins/rdf/package.json +++ b/plugins/rdf/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-rdf", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 RDF resources", "keywords": [ "jbrowse", diff --git a/plugins/sequence/package.json b/plugins/sequence/package.json index f0e53718f6..964614d3e0 100644 --- a/plugins/sequence/package.json +++ b/plugins/sequence/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sequence", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 sequence adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/plugins/spreadsheet-view/package.json b/plugins/spreadsheet-view/package.json index 72d45b1209..cece3476d6 100644 --- a/plugins/spreadsheet-view/package.json +++ b/plugins/spreadsheet-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-spreadsheet-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 spreadsheet view", "keywords": [ "jbrowse", @@ -38,7 +38,7 @@ "dependencies": { "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/vcf": "^5.0.9", - "@jbrowse/plugin-variants": "^2.15.3", + "@jbrowse/plugin-variants": "^2.15.4", "@mui/icons-material": "^6.0.0", "csvtojson": "^2.0.10" }, diff --git a/plugins/sv-inspector/package.json b/plugins/sv-inspector/package.json index c87438e6b2..82d5d8a8d0 100644 --- a/plugins/sv-inspector/package.json +++ b/plugins/sv-inspector/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-sv-inspector", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 SV inspector view", "keywords": [ "jbrowse", diff --git a/plugins/svg/package.json b/plugins/svg/package.json index 1b60f1186b..11bfbc7add 100644 --- a/plugins/svg/package.json +++ b/plugins/svg/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-svg", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 plugin for svg features", "keywords": [ "jbrowse", diff --git a/plugins/text-indexing/package.json b/plugins/text-indexing/package.json index acf031cfec..03f2ab1720 100644 --- a/plugins/text-indexing/package.json +++ b/plugins/text-indexing/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-text-indexing", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 text indexing rpc method", "keywords": [ "jbrowse", @@ -36,7 +36,7 @@ "clean": "rimraf dist esm *.tsbuildinfo" }, "dependencies": { - "@jbrowse/text-indexing": "^2.15.3" + "@jbrowse/text-indexing": "^2.15.4" }, "peerDependencies": { "@jbrowse/core": "^2.0.0", diff --git a/plugins/trix/package.json b/plugins/trix/package.json index d8fbc008cc..2f128b5472 100644 --- a/plugins/trix/package.json +++ b/plugins/trix/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-trix", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 trix text search adapter", "keywords": [ "jbrowse", diff --git a/plugins/variants/package.json b/plugins/variants/package.json index 6e1042b688..46143c8a53 100644 --- a/plugins/variants/package.json +++ b/plugins/variants/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-variants", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 variant adapters, tracks, etc.", "keywords": [ "jbrowse", @@ -40,7 +40,7 @@ "@gmod/bgzf-filehandle": "^1.4.3", "@gmod/tabix": "^1.5.6", "@gmod/vcf": "^5.0.9", - "@jbrowse/sv-core": "^2.15.3", + "@jbrowse/sv-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", "generic-filehandle": "^3.0.0" diff --git a/plugins/wiggle/package.json b/plugins/wiggle/package.json index f9e0e2fce0..c4fb91d824 100644 --- a/plugins/wiggle/package.json +++ b/plugins/wiggle/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/plugin-wiggle", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 wiggle adapters, tracks, etc.", "keywords": [ "jbrowse", diff --git a/products/jbrowse-cli/README.md b/products/jbrowse-cli/README.md index 3252df5292..471ad4bb2d 100644 --- a/products/jbrowse-cli/README.md +++ b/products/jbrowse-cli/README.md @@ -205,7 +205,7 @@ EXAMPLES ``` _See code: -[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-assembly.ts)_ +[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` @@ -256,7 +256,7 @@ EXAMPLES ``` _See code: -[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-connection.ts)_ +[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/add-connection.ts)_ ## `jbrowse add-track TRACK` @@ -337,7 +337,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track.ts)_ +[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/add-track.ts)_ ## `jbrowse add-track-json TRACK` @@ -367,7 +367,7 @@ EXAMPLES ``` _See code: -[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/add-track-json.ts)_ +[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/add-track-json.ts)_ ## `jbrowse admin-server` @@ -399,7 +399,7 @@ EXAMPLES ``` _See code: -[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/admin-server.ts)_ +[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/admin-server.ts)_ ## `jbrowse create LOCALPATH` @@ -456,7 +456,7 @@ EXAMPLES ``` _See code: -[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/create.ts)_ +[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/create.ts)_ ## `jbrowse help [COMMAND]` @@ -507,7 +507,7 @@ EXAMPLES ``` _See code: -[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/make-pif.ts)_ +[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/make-pif.ts)_ ## `jbrowse remove-track TRACK` @@ -535,7 +535,7 @@ EXAMPLES ``` _See code: -[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/remove-track.ts)_ +[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/remove-track.ts)_ ## `jbrowse set-default-session` @@ -577,7 +577,7 @@ EXAMPLES ``` _See code: -[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/set-default-session.ts)_ +[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/set-default-session.ts)_ ## `jbrowse sort-gff FILE` @@ -608,7 +608,7 @@ EXAMPLES ``` _See code: -[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/sort-gff.ts)_ +[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/sort-gff.ts)_ ## `jbrowse text-index` @@ -675,7 +675,7 @@ EXAMPLES ``` _See code: -[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/text-index.ts)_ +[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/text-index.ts)_ ## `jbrowse upgrade [LOCALPATH]` @@ -738,7 +738,7 @@ EXAMPLES ``` _See code: -[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.3/products/jbrowse-cli/src/commands/upgrade.ts)_ +[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.15.4/products/jbrowse-cli/src/commands/upgrade.ts)_ diff --git a/products/jbrowse-cli/package.json b/products/jbrowse-cli/package.json index 68ab6bcdd3..97abd07793 100644 --- a/products/jbrowse-cli/package.json +++ b/products/jbrowse-cli/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/cli", - "version": "2.15.3", + "version": "2.15.4", "description": "A command line tool for working with JBrowse 2", "keywords": [ "jbrowse", diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json index 0b842a4dc3..aa4efeb85a 100644 --- a/products/jbrowse-desktop/package.json +++ b/products/jbrowse-desktop/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/desktop", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse desktop application specialized to inspect structural variants", "license": "Apache-2.0", "homepage": "./", @@ -42,40 +42,40 @@ "@emotion/react": "^11.9.0", "@fontsource/roboto": "^5.0.2", "@gmod/faidx": "^1.0.1", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-jobs-management": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-text-indexing": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/text-indexing": "^2.15.3", + "@jbrowse/app-core": "^2.15.4", + "@jbrowse/core": "^2.15.4", + "@jbrowse/plugin-alignments": "^2.15.4", + "@jbrowse/plugin-arc": "^2.15.4", + "@jbrowse/plugin-authentication": "^2.15.4", + "@jbrowse/plugin-bed": "^2.15.4", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.4", + "@jbrowse/plugin-circular-view": "^2.15.4", + "@jbrowse/plugin-comparative-adapters": "^2.15.4", + "@jbrowse/plugin-config": "^2.15.4", + "@jbrowse/plugin-data-management": "^2.15.4", + "@jbrowse/plugin-dotplot-view": "^2.15.4", + "@jbrowse/plugin-gccontent": "^2.15.4", + "@jbrowse/plugin-gff3": "^2.15.4", + "@jbrowse/plugin-grid-bookmark": "^2.15.4", + "@jbrowse/plugin-gtf": "^2.15.4", + "@jbrowse/plugin-hic": "^2.15.4", + "@jbrowse/plugin-jobs-management": "^2.15.4", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.4", + "@jbrowse/plugin-linear-comparative-view": "^2.15.4", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", + "@jbrowse/plugin-lollipop": "^2.15.4", + "@jbrowse/plugin-menus": "^2.15.4", + "@jbrowse/plugin-rdf": "^2.15.4", + "@jbrowse/plugin-sequence": "^2.15.4", + "@jbrowse/plugin-spreadsheet-view": "^2.15.4", + "@jbrowse/plugin-sv-inspector": "^2.15.4", + "@jbrowse/plugin-svg": "^2.15.4", + "@jbrowse/plugin-text-indexing": "^2.15.4", + "@jbrowse/plugin-trix": "^2.15.4", + "@jbrowse/plugin-variants": "^2.15.4", + "@jbrowse/plugin-wiggle": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", + "@jbrowse/text-indexing": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", diff --git a/products/jbrowse-img/package.json b/products/jbrowse-img/package.json index 295255df9e..e4bc2ee2bd 100644 --- a/products/jbrowse-img/package.json +++ b/products/jbrowse-img/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/img", - "version": "2.15.3", + "version": "2.15.4", "main": "dist/index.js", "module": "esm/index.js", "author": "JBrowse Team", @@ -27,8 +27,8 @@ "@babel/runtime": "^7.17.9", "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/react-linear-genome-view": "^2.15.3", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", + "@jbrowse/react-linear-genome-view": "^2.15.4", "canvas": "^2.9.1", "jsdom": "^24.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-predefined-sessions/package.json b/products/jbrowse-predefined-sessions/package.json index 99397cfb21..98209f617a 100644 --- a/products/jbrowse-predefined-sessions/package.json +++ b/products/jbrowse-predefined-sessions/package.json @@ -1,6 +1,6 @@ { "name": "jbrowse-predefined-sessions", - "version": "2.15.3", + "version": "2.15.4", "main": "index.js", "author": "JBrowse Team", "license": "MIT", diff --git a/products/jbrowse-react-app/package.json b/products/jbrowse-react-app/package.json index b03ea4b796..f6978f8647 100644 --- a/products/jbrowse-react-app/package.json +++ b/products/jbrowse-react-app/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-app", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 app React component", "keywords": [ "jbrowse", @@ -48,38 +48,38 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/web-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.4", + "@jbrowse/core": "^2.15.4", + "@jbrowse/plugin-alignments": "^2.15.4", + "@jbrowse/plugin-arc": "^2.15.4", + "@jbrowse/plugin-authentication": "^2.15.4", + "@jbrowse/plugin-bed": "^2.15.4", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.4", + "@jbrowse/plugin-circular-view": "^2.15.4", + "@jbrowse/plugin-comparative-adapters": "^2.15.4", + "@jbrowse/plugin-config": "^2.15.4", + "@jbrowse/plugin-data-management": "^2.15.4", + "@jbrowse/plugin-dotplot-view": "^2.15.4", + "@jbrowse/plugin-gccontent": "^2.15.4", + "@jbrowse/plugin-gff3": "^2.15.4", + "@jbrowse/plugin-grid-bookmark": "^2.15.4", + "@jbrowse/plugin-gtf": "^2.15.4", + "@jbrowse/plugin-hic": "^2.15.4", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.4", + "@jbrowse/plugin-linear-comparative-view": "^2.15.4", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", + "@jbrowse/plugin-lollipop": "^2.15.4", + "@jbrowse/plugin-menus": "^2.15.4", + "@jbrowse/plugin-rdf": "^2.15.4", + "@jbrowse/plugin-sequence": "^2.15.4", + "@jbrowse/plugin-spreadsheet-view": "^2.15.4", + "@jbrowse/plugin-sv-inspector": "^2.15.4", + "@jbrowse/plugin-svg": "^2.15.4", + "@jbrowse/plugin-trix": "^2.15.4", + "@jbrowse/plugin-variants": "^2.15.4", + "@jbrowse/plugin-wiggle": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", + "@jbrowse/web-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "base64-js": "^1.0.0", diff --git a/products/jbrowse-react-circular-genome-view/package.json b/products/jbrowse-react-circular-genome-view/package.json index 7b6b472b95..ca8b8c237c 100644 --- a/products/jbrowse-react-circular-genome-view/package.json +++ b/products/jbrowse-react-circular-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-circular-genome-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 circular genome view React component", "keywords": [ "jbrowse", @@ -41,17 +41,17 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.3", - "@jbrowse/embedded-core": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.4", + "@jbrowse/embedded-core": "^2.15.4", + "@jbrowse/plugin-authentication": "^2.15.4", + "@jbrowse/plugin-circular-view": "^2.15.4", + "@jbrowse/plugin-config": "^2.15.4", + "@jbrowse/plugin-data-management": "^2.15.4", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", + "@jbrowse/plugin-sequence": "^2.15.4", + "@jbrowse/plugin-variants": "^2.15.4", + "@jbrowse/plugin-wiggle": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-react-linear-genome-view/package.json b/products/jbrowse-react-linear-genome-view/package.json index e03b6966bd..92b7cd1563 100644 --- a/products/jbrowse-react-linear-genome-view/package.json +++ b/products/jbrowse-react-linear-genome-view/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/react-linear-genome-view", - "version": "2.15.3", + "version": "2.15.4", "description": "JBrowse 2 linear genome view React component", "keywords": [ "jbrowse", @@ -48,25 +48,25 @@ "@emotion/cache": "^11.7.1", "@emotion/react": "^11.9.0", "@emotion/styled": "^11.8.1", - "@jbrowse/core": "^2.15.3", - "@jbrowse/embedded-core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", + "@jbrowse/core": "^2.15.4", + "@jbrowse/embedded-core": "^2.15.4", + "@jbrowse/plugin-alignments": "^2.15.4", + "@jbrowse/plugin-arc": "^2.15.4", + "@jbrowse/plugin-authentication": "^2.15.4", + "@jbrowse/plugin-bed": "^2.15.4", + "@jbrowse/plugin-circular-view": "^2.15.4", + "@jbrowse/plugin-config": "^2.15.4", + "@jbrowse/plugin-data-management": "^2.15.4", + "@jbrowse/plugin-gccontent": "^2.15.4", + "@jbrowse/plugin-gff3": "^2.15.4", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.4", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", + "@jbrowse/plugin-sequence": "^2.15.4", + "@jbrowse/plugin-svg": "^2.15.4", + "@jbrowse/plugin-trix": "^2.15.4", + "@jbrowse/plugin-variants": "^2.15.4", + "@jbrowse/plugin-wiggle": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "mobx": "^6.6.0", diff --git a/products/jbrowse-web/package.json b/products/jbrowse-web/package.json index b0c998ee10..0d0d9b8e8b 100644 --- a/products/jbrowse-web/package.json +++ b/products/jbrowse-web/package.json @@ -1,6 +1,6 @@ { "name": "@jbrowse/web", - "version": "2.15.3", + "version": "2.15.4", "license": "Apache-2.0", "homepage": ".", "main": "build", @@ -15,38 +15,38 @@ }, "dependencies": { "@fontsource/roboto": "^5.0.2", - "@jbrowse/app-core": "^2.15.3", - "@jbrowse/core": "^2.15.3", - "@jbrowse/plugin-alignments": "^2.15.3", - "@jbrowse/plugin-arc": "^2.15.3", - "@jbrowse/plugin-authentication": "^2.15.3", - "@jbrowse/plugin-bed": "^2.15.3", - "@jbrowse/plugin-breakpoint-split-view": "^2.15.3", - "@jbrowse/plugin-circular-view": "^2.15.3", - "@jbrowse/plugin-comparative-adapters": "^2.15.3", - "@jbrowse/plugin-config": "^2.15.3", - "@jbrowse/plugin-data-management": "^2.15.3", - "@jbrowse/plugin-dotplot-view": "^2.15.3", - "@jbrowse/plugin-gccontent": "^2.15.3", - "@jbrowse/plugin-gff3": "^2.15.3", - "@jbrowse/plugin-grid-bookmark": "^2.15.3", - "@jbrowse/plugin-gtf": "^2.15.3", - "@jbrowse/plugin-hic": "^2.15.3", - "@jbrowse/plugin-legacy-jbrowse": "^2.15.3", - "@jbrowse/plugin-linear-comparative-view": "^2.15.3", - "@jbrowse/plugin-linear-genome-view": "^2.15.3", - "@jbrowse/plugin-lollipop": "^2.15.3", - "@jbrowse/plugin-menus": "^2.15.3", - "@jbrowse/plugin-rdf": "^2.15.3", - "@jbrowse/plugin-sequence": "^2.15.3", - "@jbrowse/plugin-spreadsheet-view": "^2.15.3", - "@jbrowse/plugin-sv-inspector": "^2.15.3", - "@jbrowse/plugin-svg": "^2.15.3", - "@jbrowse/plugin-trix": "^2.15.3", - "@jbrowse/plugin-variants": "^2.15.3", - "@jbrowse/plugin-wiggle": "^2.15.3", - "@jbrowse/product-core": "^2.15.3", - "@jbrowse/web-core": "^2.15.3", + "@jbrowse/app-core": "^2.15.4", + "@jbrowse/core": "^2.15.4", + "@jbrowse/plugin-alignments": "^2.15.4", + "@jbrowse/plugin-arc": "^2.15.4", + "@jbrowse/plugin-authentication": "^2.15.4", + "@jbrowse/plugin-bed": "^2.15.4", + "@jbrowse/plugin-breakpoint-split-view": "^2.15.4", + "@jbrowse/plugin-circular-view": "^2.15.4", + "@jbrowse/plugin-comparative-adapters": "^2.15.4", + "@jbrowse/plugin-config": "^2.15.4", + "@jbrowse/plugin-data-management": "^2.15.4", + "@jbrowse/plugin-dotplot-view": "^2.15.4", + "@jbrowse/plugin-gccontent": "^2.15.4", + "@jbrowse/plugin-gff3": "^2.15.4", + "@jbrowse/plugin-grid-bookmark": "^2.15.4", + "@jbrowse/plugin-gtf": "^2.15.4", + "@jbrowse/plugin-hic": "^2.15.4", + "@jbrowse/plugin-legacy-jbrowse": "^2.15.4", + "@jbrowse/plugin-linear-comparative-view": "^2.15.4", + "@jbrowse/plugin-linear-genome-view": "^2.15.4", + "@jbrowse/plugin-lollipop": "^2.15.4", + "@jbrowse/plugin-menus": "^2.15.4", + "@jbrowse/plugin-rdf": "^2.15.4", + "@jbrowse/plugin-sequence": "^2.15.4", + "@jbrowse/plugin-spreadsheet-view": "^2.15.4", + "@jbrowse/plugin-sv-inspector": "^2.15.4", + "@jbrowse/plugin-svg": "^2.15.4", + "@jbrowse/plugin-trix": "^2.15.4", + "@jbrowse/plugin-variants": "^2.15.4", + "@jbrowse/plugin-wiggle": "^2.15.4", + "@jbrowse/product-core": "^2.15.4", + "@jbrowse/web-core": "^2.15.4", "@mui/icons-material": "^6.0.0", "@mui/material": "^6.0.0", "@mui/x-data-grid": "^7.0.0", From 7cfd512f0277cf3c6ff03dd2327f89bea2a24dec Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 17:28:49 +0000 Subject: [PATCH 35/38] [skip ci] Bump version.js --- products/jbrowse-react-circular-genome-view/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-circular-genome-view/src/version.js b/products/jbrowse-react-circular-genome-view/src/version.js index 626d897e35..0ec209c466 100644 --- a/products/jbrowse-react-circular-genome-view/src/version.js +++ b/products/jbrowse-react-circular-genome-view/src/version.js @@ -1 +1 @@ -export const version = '2.15.3' +export const version = '2.15.4' From ecd3b7a1d0be3db93fd18afe05f1b576e0f4e48a Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 17:28:49 +0000 Subject: [PATCH 36/38] [skip ci] Bump version.js --- products/jbrowse-react-linear-genome-view/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-linear-genome-view/src/version.js b/products/jbrowse-react-linear-genome-view/src/version.js index 626d897e35..0ec209c466 100644 --- a/products/jbrowse-react-linear-genome-view/src/version.js +++ b/products/jbrowse-react-linear-genome-view/src/version.js @@ -1 +1 @@ -export const version = '2.15.3' +export const version = '2.15.4' From 429e131cf716ef3e745d5ccebe0785abc5eac79f Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 17:34:34 +0000 Subject: [PATCH 37/38] [skip ci] Bump version.js --- products/jbrowse-react-app/src/version.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/products/jbrowse-react-app/src/version.js b/products/jbrowse-react-app/src/version.js index 626d897e35..0ec209c466 100644 --- a/products/jbrowse-react-app/src/version.js +++ b/products/jbrowse-react-app/src/version.js @@ -1 +1 @@ -export const version = '2.15.3' +export const version = '2.15.4' From fadc05e6ab7ccd927037bc75a328e9c5e96fb91b Mon Sep 17 00:00:00 2001 From: Colin Date: Fri, 20 Sep 2024 13:50:33 -0400 Subject: [PATCH 38/38] [skip ci] Create command for auto-creating release notes for github --- PUBLISHING.md | 22 ++++++---------------- package.json | 3 ++- 2 files changed, 8 insertions(+), 17 deletions(-) diff --git a/PUBLISHING.md b/PUBLISHING.md index 5a5cdfca65..6b0f2ad5dc 100644 --- a/PUBLISHING.md +++ b/PUBLISHING.md @@ -93,16 +93,9 @@ mac, windows, and linux desktop builds) have been added to the release, click workflows will refuse to add them to the published release since it looks for draft releases) -Once the draft release has been created (you can look for it -[here](https://github.com/GMOD/jbrowse-components/releases)), go to the release -and click "Edit," then add a description to the release. Usually you can copy -the content of the blog post that was generated (it will be named something like -`website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the "Downloads" -section. - -Note also that I edit the .prettierrc.json file to change "proseWrap":"always" -to "proseWrap":"never", format the blogpost, then copy to the github release, -because they make markdown newlines into actual newlines in these release notes +Then run `yarn --silent releasenotes|pbcopy` to get the release notes in a +copy-and-pasteable way for the github release (it is slightly different than the +blogpost format) ### Step 5. Update embedded demos @@ -111,12 +104,9 @@ automated, but you can run each step and check that there aren't any errors ```bash cd embedded_demos -export NODE_OPTIONS=--openssl-legacy-provider # needed to deploy the CRA4 demos -export JB2TMP=~/jb2tmp # the embedded demo repos are cloned to this folder instead of the embedded_demos folder to avoid typescript and eslint complaining about ../ related weirdness -./clone_demos.sh # clones embedded demo repos to local folder -./update_demos.sh # runs yarn upgrade in each embedded demo to get latest jbrowse code -./deploy_demos.sh # runs build and uploads to amazon s3 bucket -./push_demos.sh # pushes updated yarn.locks to the github repos so consumers get same lock file +export JB2TMP=~/jb2tmp +./clone_demos.sh +./update_all.sh ``` Then you can manually check e.g. https://jbrowse.org/demos/lgv and see that the diff --git a/package.json b/package.json index 58fba0dcf5..7273f77835 100644 --- a/package.json +++ b/package.json @@ -23,7 +23,8 @@ "prepare": "husky", "configdocs": "rm -rf website/docs/config && mkdir website/docs/config && yarn tsx docs/generateConfigDocs.ts", "statedocs": "rm -rf website/docs/models && mkdir website/docs/models && yarn tsx docs/generateStateModelDocs.ts", - "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website" + "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website", + "releasenotes": "npx prettier --prose-wrap never website/blog/$(ls -Art website/blog/ | tail -n 1)|sed -e '/## Downloads/,+7d'|tail -n +7" }, "devDependencies": { "@babel/core": "^7.3.4",