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GMOD · Sep 24, 2024 · 1e9c443 · 1e9c443
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diff --git 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: |
@@ -65,15 +71,29 @@ 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/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,50 @@
+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.
+
+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/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/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',
@@ -169,6 +170,7 @@ 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',
@@ -179,6 +181,7 @@ export default tseslint.config(
  },
  },
  rules: {
+ 'no-restricted-globals': ['off'],
  '@typescript-eslint/no-require-imports': 'off',
  'no-console': 'off',
  },

diff --git a/lerna.json b/lerna.json
@@ -1,5 +1,5 @@
 {
- "version": "2.15.1",
+ "version": "2.15.4",
  "npmClient": "yarn",
  "$schema": "node_modules/lerna/schemas/lerna-schema.json"
 }
diff --git a/package.json b/package.json
@@ -23,7 +23,8 @@
  "prepare": "husky",
  "configdocs": "rm -rf website/docs/config && mkdir website/docs/config && yarn tsx docs/generateConfigDocs.ts",
  "statedocs": "rm -rf website/docs/models && mkdir website/docs/models && yarn tsx docs/generateStateModelDocs.ts",
- "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website"
+ "autogen": "yarn statedocs && yarn configdocs && yarn prettier --write website",
+ "releasenotes": "npx prettier --prose-wrap never website/blog/$(ls -Art website/blog/ | tail -n 1)|sed -e '/## Downloads/,+7d'|tail -n +7"
  },
  "devDependencies": {
  "@babel/core": "^7.3.4",

diff --git 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": "2.15.4",
  "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": "^2.15.1",
+ "@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
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/core",
- "version": "2.15.1",
+ "version": "2.15.4",
  "description": "JBrowse 2 core libraries used by plugins",
  "keywords": [
  "jbrowse",

diff --git 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,
@@ -1426,8 +1427,7 @@ 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/packages/embedded-core/package.json b/packages/embedded-core/package.json
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/embedded-core",
- "version": "2.15.1",
+ "version": "2.15.4",
  "description": "JBrowse 2 code shared between embedded products",
  "keywords": [
  "jbrowse",
@@ -42,8 +42,8 @@
  },
  "dependencies": {
  "@babel/runtime": "^7.16.3",
- "@jbrowse/core": "^2.15.1",
- "@jbrowse/product-core": "^2.15.1",
+ "@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
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/product-core",
- "version": "2.15.1",
+ "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": "^2.15.1",
+ "@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
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/sv-core",
- "version": "2.15.1",
+ "version": "2.15.4",
  "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": "^2.15.4",
  "@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
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/text-indexing",
- "version": "2.15.1",
+ "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": "^2.15.1",
+ "@jbrowse/core": "^2.15.4",
  "ixixx": "^2.0.1",
  "node-fetch": "^2.6.0",
  "sanitize-filename": "^1.6.3"

diff --git 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/packages/web-core/package.json b/packages/web-core/package.json
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/web-core",
- "version": "2.15.1",
+ "version": "2.15.4",
  "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": "^2.15.1",
- "@jbrowse/product-core": "^2.15.1",
+ "@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
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/plugin-alignments",
- "version": "2.15.1",
+ "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": "^2.15.1",
+ "@jbrowse/sv-core": "^2.15.4",
  "@mui/icons-material": "^6.0.0",
  "canvas2svg": "^1.0.16",
  "clone": "^2.1.2",

diff --git 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/arc/package.json b/plugins/arc/package.json
@@ -1,6 +1,6 @@
 {
  "name": "@jbrowse/plugin-arc",
- "version": "2.15.1",
+ "version": "2.15.4",
  "description": "JBrowse 2 arc adapters, tracks, etc.",
  "keywords": [
  "jbrowse",