Merge pull request #391 from qiime2/update-latest-envs-from-PR-390

[amplicon] latest env updates from PR 390

latest/passed/qiime2-amplicon-macos-latest-conda.yml

@@ -16,7 +16,7 @@ dependencies:
 - arrow=1.3.0
 - astor=0.8.1
 - asttokens=2.4.1
-- atpublic=3.1.1
+- atpublic=5.0
 - attrs=24.2.0
 - bcrypt=4.2.0
 - beautifulsoup4=4.12.3
@@ -88,31 +88,33 @@ dependencies:
 - cffi=1.17.1
 - chardet=5.2.0
 - charset-normalizer=3.3.2
-- clang=17.0.6
-- clang-17=17.0.6
-- clang_impl_osx-64=17.0.6
-- clang_osx-64=17.0.6
-- clangxx=17.0.6
-- clangxx_impl_osx-64=17.0.6
-- clangxx_osx-64=17.0.6
+- clang=18.1.7
+- clang-18=18.1.7
+- clang_impl_osx-64=18.1.7
+- clang_osx-64=18.1.7
+- clangxx=18.1.7
+- clangxx_impl_osx-64=18.1.7
+- clangxx_osx-64=18.1.7
 - click=8.1.7
+- clustalw=2.1
 - colorama=0.4.6
 - comm=0.2.2
-- compiler-rt=17.0.6
-- compiler-rt_osx-64=17.0.6
+- compiler-rt=18.1.7
+- compiler-rt_osx-64=18.1.7
 - conda-pack=0.7.0
 - contourpy=1.3.0
 - cryptography=43.0.1
-- curl=8.9.1
+- curl=8.8.0
 - cutadapt=4.9
 - cycler=0.12.1
 - deblur=1.1.1
 - debugpy=1.8.5
 - decorator=4.4.2
 - defusedxml=0.7.1
-- dendropy=4.5.2
+- dendropy=5.0.1
 - dill=0.3.8
 - dnaio=1.2.1
+- dnspython=2.6.1
 - emperor=1.0.4
 - entrez-direct=22.4
 - entrypoints=0.4
@@ -121,7 +123,7 @@ dependencies:
 - expat=2.6.3
 - fastcluster=1.2.6
 - fasttree=2.1.11
-- filelock=3.15.4
+- filelock=3.16.1
 - flufl.lock=8.1.0
 - font-ttf-dejavu-sans-mono=2.37
 - font-ttf-inconsolata=3.000
@@ -137,13 +139,13 @@ dependencies:
 - fribidi=1.0.10
 - frictionless=5.5.0
 - future=1.0.0
-- gawk=5.3.0
+- gawk=5.3.1
 - gettext=0.22.5
 - gettext-tools=0.22.5
 - gffutils=0.10.1
 - gfortran_impl_osx-64=12.3.0
 - gfortran_osx-64=12.3.0
-- globus-sdk=3.44.0
+- globus-sdk=3.45.0
 - glpk=5.0
 - gmp=6.3.0
 - graphite2=1.3.13
@@ -153,20 +155,19 @@ dependencies:
 - harfbuzz=8.5.0
 - hdf5=1.14.3
 - hdmedians=0.14.2
-- hmmer=3.1b2
-- htslib=1.20
+- hmmer=3.4
+- htslib=1.21
 - humanize=4.10.0
 - icu=73.2
-- idna=3.8
+- idna=3.10
 - ijson=3.3.0
-- importlib-metadata=8.4.0
-- importlib-resources=6.4.4
-- importlib_resources=6.4.4
+- importlib-metadata=8.5.0
+- importlib_resources=6.4.5
 - iniconfig=2.0.0
 - interface_meta=1.3.0
 - iow=1.0.5
 - ipykernel=6.29.5
-- ipython=8.18.1
+- ipython=8.21.0
 - ipython_genutils=0.2.0
 - ipywidgets=8.1.5
 - iqtree=2.3.6
@@ -184,14 +185,14 @@ dependencies:
 - jsonschema-specifications=2023.12.1
 - jsonschema-with-format-nongpl=4.23.0
 - jupyter_client=7.4.9
-- jupyter_core=5.7.1
+- jupyter_core=5.7.2
 - jupyter_events=0.10.0
 - jupyter_server=2.14.2
 - jupyter_server_terminals=0.5.3
 - jupyterlab_pygments=0.3.0
 - jupyterlab_widgets=3.0.13
 - kiwisolver=1.4.7
-- krb5=1.20.1
+- krb5=1.21.3
 - lcms2=2.16
 - ld64_osx-64=711
 - lerc=4.0.0
@@ -203,10 +204,9 @@ dependencies:
 - libbrotlidec=1.1.0
 - libbrotlienc=1.1.0
 - libcblas=3.9.0
-- libclang-cpp17=17.0.6
-- libcurl=8.9.1
+- libclang-cpp18.1=18.1.7
+- libcurl=8.8.0
 - libcxx=18.1.8
-- libcxx-devel=17.0.6
 - libdeflate=1.20
 - libedit=3.1.20191231
 - libev=4.33
@@ -227,7 +227,7 @@ dependencies:
 - liblapack=3.9.0
 - liblapacke=3.9.0
 - libllvm14=14.0.6
-- libllvm17=17.0.6
+- libllvm18=18.1.7
 - libnghttp2=1.58.0
 - libopenblas=0.3.27
 - libpng=1.6.43
@@ -243,12 +243,12 @@ dependencies:
 - libxslt=1.1.39
 - libzlib=1.2.13
 - llvm-openmp=18.1.8
-- llvm-tools=17.0.6
+- llvm-tools=18.1.7
 - llvmlite=0.43.0
 - lxml=5.2.2
 - lz4=4.3.3
 - lz4-c=1.9.4
-- mafft=7.520
+- mafft=7.526
 - make=4.4.1
 - markdown-it-py=3.0.0
 - marko=2.1.2
@@ -262,7 +262,8 @@ dependencies:
 - mpfr=4.2.1
 - mpi=1.0
 - munkres=1.1.4
-- narwhals=1.6.2
+- muscle=3.8.1551
+- narwhals=1.8.1
 - natsort=8.4.0
 - nbclassic=1.1.0
 - nbclient=0.10.0
@@ -285,14 +286,16 @@ dependencies:
 - overrides=7.7.0
 - packaging=24.1
 - pandas=2.2.2
-- pandoc=3.3
+- pandoc=3.4
 - pandocfilters=1.5.0
 - pango=1.54.0
 - paramiko=3.4.1
 - parsl=2024.4.15
 - parso=0.8.4
+- pasta=1.9.2
 - patsy=0.5.6
 - pbzip2=1.1.13
+- pcre=8.45
 - pcre2=10.43
 - perl=5.32.1
 - perl-archive-tar=2.40
@@ -323,8 +326,9 @@ dependencies:
 - pip=24.2
 - pixman=0.43.4
 - pkgutil-resolve-name=1.3.10
-- platformdirs=4.2.2
+- platformdirs=4.3.6
 - pluggy=1.5.0
+- prank=170427
 - prometheus_client=0.20.0
 - prompt-toolkit=3.0.47
 - protobuf=3.20.3
@@ -337,23 +341,24 @@ dependencies:
 - pygments=2.18.0
 - pyhmmer=0.10.14
 - pyjwt=2.9.0
+- pymongo=4.9
 - pynacl=1.5.0
 - pynndescent=0.5.13
 - pyobjc-core=10.3.1
 - pyobjc-framework-cocoa=10.3.1
 - pyparsing=3.1.4
 - pysocks=1.7.1
-- pytest=8.3.2
-- python=3.9.19
+- pytest=8.3.3
+- python=3.10.14
 - python-dateutil=2.8.2
 - python-fastjsonschema=2.20.0
 - python-isal=1.7.0
 - python-json-logger=2.0.7
 - python-slugify=8.0.4
 - python-tzdata=2024.1
 - python-zlib-ng=0.5.0
-- python_abi=3.9
-- pytz=2024.1
+- python_abi=3.10
+- pytz=2024.2
 - pyvcf3=1.0.3
 - pyyaml=6.0.2
 - pyzmq=24.0.1
@@ -362,13 +367,13 @@ dependencies:
 - q2-cutadapt=2024.10.0.dev0
 - q2-dada2=2024.10.0.dev0+2.g7d89c3b
 - q2-deblur=2024.10.0.dev0
-- q2-demux=2024.10.0.dev0+2.gc13cafb
+- q2-demux=2024.10.0.dev0+3.g7c9b6d3
 - q2-diversity=2024.10.0.dev0+2.gc81c7a0
 - q2-diversity-lib=2024.10.0.dev0+1.gbd7e767
 - q2-emperor=2024.10.0.dev0
 - q2-feature-classifier=2024.10.0.dev0+1.g1caeb30
 - q2-feature-table=2024.10.0.dev0+2.ga4d0e2e
-- q2-fragment-insertion=2024.10.0.dev0
+- q2-fragment-insertion=2024.10.0.dev0+1.g7090abd
 - q2-longitudinal=2024.10.0.dev0+1.g207dda1
 - q2-metadata=2024.10.0.dev0
 - q2-mystery-stew=2024.10.0.dev0
@@ -379,11 +384,11 @@ dependencies:
 - q2-stats=2024.10.0.dev0+1.g6711b86
 - q2-taxa=2024.10.0.dev0
 - q2-types=2024.10.0.dev0+21.g0982c4a
-- q2-vsearch=2024.10.0.dev0
+- q2-vsearch=2024.10.0.dev0+1.g475bfd2
 - q2cli=2024.10.0.dev0+5.g76b8d1e
 - q2galaxy=2024.10.0.dev0+1.g324442b
 - q2templates=2024.10.0.dev0
-- qiime2=2024.10.0.dev0+12.g3581493
+- qiime2=2024.10.0.dev0+14.gd0ed13e
 - r-abind=1.4_5
 - r-ade4=1.7_22
 - r-ape=5.8
@@ -429,11 +434,11 @@ dependencies:
 - r-dplyr=1.1.4
 - r-dqrng=0.3.2
 - r-dtplyr=1.3.1
-- r-e1071=1.7_14
+- r-e1071=1.7_16
 - r-ecosolver=0.5.5
 - r-ellipsis=0.3.2
 - r-energy=1.7_12
-- r-evaluate=0.24.0
+- r-evaluate=1.0.0
 - r-exact=3.3
 - r-expm=1.0_0
 - r-fansi=1.0.6
@@ -457,7 +462,7 @@ dependencies:
 - r-ggbeeswarm=0.7.2
 - r-ggplot2=3.5.1
 - r-ggrastr=1.0.2
-- r-ggrepel=0.9.5
+- r-ggrepel=0.9.6
 - r-gld=2.6.6
 - r-glue=1.7.0
 - r-gmp=0.7_5
@@ -476,7 +481,7 @@ dependencies:
 - r-htmltools=0.5.8.1
 - r-htmlwidgets=1.6.4
 - r-httr=1.4.7
-- r-httr2=1.0.3
+- r-httr2=1.0.4
 - r-hwriter=1.3.2.1
 - r-ids=1.0.1
 - r-igraph=2.0.3
@@ -501,7 +506,7 @@ dependencies:
 - r-magrittr=2.0.3
 - r-mass=7.3_60.0.1
 - r-matrix=1.6_5
-- r-matrixstats=1.4.0
+- r-matrixstats=1.4.1
 - r-memoise=2.0.1
 - r-mgcv=1.9_1
 - r-mime=0.12
@@ -533,7 +538,7 @@ dependencies:
 - r-ps=1.7.7
 - r-purrr=1.0.2
 - r-r6=2.5.1
-- r-ragg=1.3.2
+- r-ragg=1.3.3
 - r-rappdirs=0.3.3
 - r-rbibutils=2.2.16
 - r-rcolorbrewer=1.1_3
@@ -567,7 +572,7 @@ dependencies:
 - r-rsvd=1.0.5
 - r-rtsne=0.17
 - r-rvest=1.0.4
-- r-sandwich=3.1_0
+- r-sandwich=3.1_1
 - r-sass=0.4.9
 - r-scales=1.3.0
 - r-scs=3.2.4
@@ -588,7 +593,7 @@ dependencies:
 - r-tidytree=0.4.6
 - r-tidyverse=2.0.0
 - r-timechange=0.3.0
-- r-tinytex=0.52
+- r-tinytex=0.53
 - r-tzdb=0.4.0
 - r-utf8=1.2.4
 - r-uuid=1.2_1
@@ -614,17 +619,17 @@ dependencies:
 - rfc3339-validator=0.1.4
 - rfc3986=2.0.0
 - rfc3986-validator=0.1.1
-- rich=13.7.1
+- rich=13.8.1
 - rpds-py=0.20.0
 - rpsbproc=0.5.0
-- samtools=1.20
+- samtools=1.21
 - scikit-bio=0.6.0
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - seaborn=0.12.2
 - seaborn-base=0.12.2
 - send2trash=1.8.3
-- sepp=4.4.0
+- sepp=4.5.5
 - setproctitle=1.3.3
 - setuptools=73.0.1
 - shellingham=1.5.4
@@ -636,10 +641,10 @@ dependencies:
 - sortmerna=2.0
 - soupsieve=2.5
 - stack_data=0.6.2
-- statsmodels=0.14.2
+- statsmodels=0.14.3
 - stringcase=1.2.0
 - tabulate=0.9.0
-- tapi=1300.6.5
+- tapi=1100.0.11
 - tbb=2021.13.0
 - tblib=3.0.0
 - terminado=0.18.1
@@ -688,8 +693,8 @@ dependencies:
 - yaml=0.2.5
 - yq=3.4.3
 - zeromq=4.3.5
-- zipp=3.20.1
+- zipp=3.20.2
 - zlib=1.2.13
-- zlib-ng=2.2.1
+- zlib-ng=2.2.2
 - zstandard=0.23.0
 - zstd=1.5.6