From 3e5396cccd728cc97eb9d1047acafa6d6c02dd0b Mon Sep 17 00:00:00 2001 From: Evan Bolyen Date: Wed, 24 Jul 2024 14:24:24 -0700 Subject: [PATCH 1/2] REF: q2-types --- 2024.10/metagenome/passed/seed-environment-conda.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/2024.10/metagenome/passed/seed-environment-conda.yml b/2024.10/metagenome/passed/seed-environment-conda.yml index 2bc59d99..5266c99f 100644 --- a/2024.10/metagenome/passed/seed-environment-conda.yml +++ b/2024.10/metagenome/passed/seed-environment-conda.yml @@ -1,3 +1,4 @@ +# Trial-type-refactor channels: - https://packages.qiime2.org/qiime2/2024.10/metagenome/passed - conda-forge From a7af51b18cc29b447b8ae290ad81f4fd6bcecd92 Mon Sep 17 00:00:00 2001 From: q2d2 Date: Fri, 26 Jul 2024 01:34:30 +0000 Subject: [PATCH 2/2] Update conda environments (Trial-type-refactor/metagenome) --- .../qiime2-metagenome-macos-latest-conda.yml | 210 +++++++++-------- .../qiime2-metagenome-ubuntu-latest-conda.yml | 215 +++++++++--------- .../passed/seed-environment-conda.yml | 13 +- .../staged/seed-environment-conda.yml | 12 +- 4 files changed, 231 insertions(+), 219 deletions(-) diff --git a/2024.10/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml b/2024.10/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml index 960c0b58..81cc6c63 100644 --- a/2024.10/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml +++ b/2024.10/metagenome/passed/qiime2-metagenome-macos-latest-conda.yml @@ -9,8 +9,8 @@ dependencies: - anyio=4.4.0 - appdirs=1.4.4 - appnope=0.1.4 -- argcomplete=3.3.0 -- argh=0.31.2 +- argcomplete=3.4.0 +- argh=0.31.3 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - aria2=1.37.0 @@ -20,9 +20,9 @@ dependencies: - atpublic=3.0.1 - attrs=23.2.0 - augustus=3.5.0 -- bamtools=2.5.1 +- bamtools=2.5.2 - bbmap=39.06 -- bcrypt=4.1.3 +- bcrypt=4.2.0 - beautifulsoup4=4.12.3 - bedtools=2.31.1 - bibtexparser=1.4.1 @@ -85,7 +85,7 @@ dependencies: - biopython=1.83 - blast=2.15.0 - bleach=6.1.0 -- boost-cpp=1.78.0 +- boost-cpp=1.85.0 - bowtie2=2.5.1 - bracken=1.0.0 - brotli=1.1.0 @@ -95,55 +95,55 @@ dependencies: - bwa=0.7.18 - bwidget=1.9.14 - bzip2=1.0.8 -- c-ares=1.28.1 -- ca-certificates=2024.6.2 +- c-ares=1.32.3 +- ca-certificates=2024.7.4 - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.18.0 - cctools_osx-64=986 - cdbtools=0.99 -- certifi=2024.2.2 +- certifi=2024.7.4 - cffi=1.16.0 - charset-normalizer=3.3.2 - circos=0.69.9 -- clang=18.1.6 -- clang-18=18.1.6 -- clang_impl_osx-64=18.1.6 -- clang_osx-64=18.1.6 -- clangxx=18.1.6 -- clangxx_impl_osx-64=18.1.6 -- clangxx_osx-64=18.1.6 +- 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 - colorama=0.4.6 - comm=0.2.2 -- compiler-rt=18.1.6 -- compiler-rt_osx-64=18.1.6 +- compiler-rt=18.1.7 +- compiler-rt_osx-64=18.1.7 - conda-pack=0.7.0 - contourpy=1.2.1 -- cryptography=42.0.8 +- cryptography=43.0.0 - curl=8.8.0 -- cutadapt=4.8 +- cutadapt=4.9 - cycler=0.12.1 -- debugpy=1.8.1 +- debugpy=1.8.2 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=4.5.2 - diamond=2.1.9 - dill=0.3.8 -- dnaio=1.2.0 +- dnaio=1.2.1 - easel=0.49 - eggnog-mapper=2.1.12 - emperor=1.0.4 -- entrez-direct=22.1 +- entrez-direct=22.4 - entrezpy=2.1.2 - entrypoints=0.4 -- exceptiongroup=1.2.0 +- exceptiongroup=1.2.2 - executing=2.0.1 - expat=2.6.2 - fastcluster=1.2.6 - feedparser=6.0.11 -- filelock=3.14.0 -- flufl.lock=7.1 +- filelock=3.15.4 +- flufl.lock=8.0.2 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 - font-ttf-source-code-pro=2.038 @@ -151,8 +151,8 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.53.0 -- formulaic=1.0.1 +- fonttools=4.53.1 +- formulaic=1.0.2 - fqdn=1.5.1 - freetype=2.12.1 - fribidi=1.0.10 @@ -165,31 +165,33 @@ dependencies: - gfortran_osx-64=12.3.0 - giflib=5.2.2 - glimmerhmm=3.0.4 -- globus-sdk=3.41.0 +- globus-sdk=3.42.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 - graphlib-backport=1.0.3 - gridss=2.11.1 - gsl=2.7 +- h2=4.1.0 - h5py=3.11.0 - harfbuzz=8.5.0 - hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.1b2 +- hpack=4.0.0 - htslib=1.20 +- hyperframe=6.0.1 - icu=73.2 - idna=3.7 - ijson=3.3.0 -- importlib-metadata=7.1.0 +- importlib-metadata=8.2.0 - importlib-resources=6.4.0 -- importlib_metadata=7.1.0 - importlib_resources=6.4.0 - iniconfig=2.0.0 - insilicoseq=2.0.1 - interface_meta=1.3.0 - iow=1.0.5 -- ipykernel=6.29.3 +- ipykernel=6.29.5 - ipython=8.18.1 - ipython_genutils=0.2.0 - ipywidgets=8.1.3 @@ -201,14 +203,14 @@ dependencies: - joblib=1.4.2 - jq=1.7.1 - jsonlines=3.0.0 -- jsonpointer=2.4 -- jsonschema=4.22.0 +- jsonpointer=3.0.0 +- jsonschema=4.23.0 - jsonschema-specifications=2023.12.1 -- jsonschema-with-format-nongpl=4.22.0 +- jsonschema-with-format-nongpl=4.23.0 - jupyter_client=7.4.9 - jupyter_core=5.7.1 - jupyter_events=0.10.0 -- jupyter_server=2.14.1 +- jupyter_server=2.14.2 - jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 - jupyterlab_widgets=3.0.11 @@ -218,7 +220,7 @@ dependencies: - kmer-jellyfish=1.1.12 - kraken=1.1.1 - kraken2=2.1.3 -- krb5=1.21.2 +- krb5=1.21.3 - lcms2=2.16 - ld64_osx-64=711 - lerc=4.0.0 @@ -226,13 +228,16 @@ dependencies: - libasprintf=0.22.5 - libasprintf-devel=0.22.5 - libblas=3.9.0 +- libboost=1.85.0 +- libboost-devel=1.85.0 +- libboost-headers=1.85.0 - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 -- libclang-cpp18.1=18.1.6 +- libclang-cpp18.1=18.1.7 - libcurl=8.8.0 -- libcxx=17.0.6 +- libcxx=18.1.8 - libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 @@ -245,7 +250,7 @@ dependencies: - libgfortran-devel_osx-64=12.3.0 - libgfortran5=13.2.0 - libglib=2.80.2 -- libhwloc=2.10.0 +- libhwloc=2.11.1 - libiconv=1.17 - libidn2=2.3.7 - libintl=0.22.5 @@ -254,13 +259,13 @@ dependencies: - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 -- libllvm18=18.1.6 +- libllvm18=18.1.7 - libnghttp2=1.58.0 - libopenblas=0.3.27 - libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 -- libsqlite=3.45.3 +- libsqlite=3.46.0 - libssh2=1.11.0 - libtiff=4.6.0 - libunistring=0.9.10 @@ -270,9 +275,9 @@ dependencies: - libxml2=2.12.7 - libxslt=1.1.39 - libzlib=1.2.13 -- llvm-openmp=18.1.6 -- llvm-tools=18.1.6 -- llvmlite=0.42.0 +- llvm-openmp=18.1.8 +- llvm-tools=18.1.7 +- llvmlite=0.43.0 - lp_solve=5.5.2.11 - lxml=5.2.2 - lz4=4.3.3 @@ -299,7 +304,7 @@ dependencies: - nbclient=0.10.0 - nbconvert-core=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.1 +- ncbi-datasets-pylib=14.25.1 - ncbi-vdb=3.1.1 - ncurses=6.5 - nest-asyncio=1.6.0 @@ -307,18 +312,19 @@ dependencies: - nlopt=2.7.1 - notebook=6.5.5 - notebook-shim=0.2.4 -- numba=0.59.1 +- numba=0.60.0 - numpy=1.26.4 - oniguruma=6.9.9 - openjdk=22.0.1 - openjpeg=2.5.2 - openssl=3.3.1 - overrides=7.7.0 -- packaging=24.0 +- packaging=24.1 - pandas=2.2.2 -- pandoc=3.2 +- pandoc=3.2.1 - pandocfilters=1.5.0 -- pango=1.52.2 +- pango=1.54.0 +- parameterized=0.9.0 - paramiko=3.4.0 - parsl=2024.4.15 - parso=0.8.4 @@ -403,28 +409,29 @@ dependencies: - popt=1.16 - prodigal=2.6.3 - prometheus_client=0.20.0 -- prompt-toolkit=3.0.46 +- prompt-toolkit=3.0.47 - protobuf=3.20.3 -- psutil=5.9.8 +- psutil=6.0.0 - pthread-stubs=0.4 - ptyprocess=0.7.0 -- pure_eval=0.2.2 +- pure_eval=0.2.3 - pycparser=2.22 - pyfaidx=0.8.1.1 - pygments=2.18.0 +- pyhmmer=0.10.14 - pyjwt=2.8.0 - pynacl=1.5.0 -- pynndescent=0.5.12 -- pyobjc-core=10.2 -- pyobjc-framework-cocoa=10.2 +- pynndescent=0.5.13 +- pyobjc-core=10.3.1 +- pyobjc-framework-cocoa=10.3.1 - pyparsing=3.1.2 - pysam=0.22.1 - pysocks=1.7.1 -- pytest=8.2.2 +- pytest=8.3.2 - python=3.9.19 -- python-dateutil=2.8.2 +- python-dateutil=2.9.0 - python-dotenv=1.0.1 -- python-fastjsonschema=2.19.1 +- python-fastjsonschema=2.20.0 - python-isal=1.6.1 - python-json-logger=2.0.7 - python-tzdata=2024.1 @@ -435,26 +442,26 @@ dependencies: - pyyaml=6.0.1 - pyzmq=24.0.1 - pyzotero=1.5.19 -- q2-assembly=2024.10.0.dev0 +- q2-assembly=2024.10.0.dev0+5.gd6cbf5a - q2-composition=2024.10.0.dev0 - q2-cutadapt=2024.10.0.dev0 -- q2-demux=2024.10.0.dev0 +- q2-demux=2024.10.0.dev0+1.g037f78a - q2-diversity=2024.10.0.dev0 - q2-diversity-lib=2024.10.0.dev0 - q2-emperor=2024.10.0.dev0 -- q2-feature-classifier=2024.10.0.dev0 +- q2-feature-classifier=2024.10.0.dev0+1.ga00fe79 - q2-feature-table=2024.10.0.dev0 - q2-fondue=2024.10.0.dev0 - q2-longitudinal=2024.10.0.dev0 - q2-metadata=2024.10.0.dev0 -- q2-moshpit=2024.10.0.dev0+3.gfe14cc2 +- q2-moshpit=2024.10.0.dev0+15.ge99496e - q2-mystery-stew=2024.10.0.dev0 - q2-quality-control=2024.10.0.dev0 - q2-quality-filter=2024.10.0.dev0 - q2-sample-classifier=2024.10.0.dev0 - q2-sapienns=2024.10.0.dev0 - q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0 +- q2-types=2024.10.0.dev0+20.g5e0a3d3 - q2-vsearch=2024.10.0.dev0 - q2cli=2024.10.0.dev0+1.gefac9fc - q2templates=2024.10.0.dev0 @@ -486,15 +493,15 @@ dependencies: - r-cellranger=1.1.0 - r-checkmate=2.3.1 - r-class=7.3_22 -- r-cli=3.6.2 +- r-cli=3.6.3 - r-clipr=0.8.0 - r-cluster=2.1.6 - r-codetools=0.2_20 - r-colorspace=2.1_0 - r-conflicted=1.2.0 - r-cpp11=0.4.7 -- r-crayon=1.5.2 -- r-curl=5.1.0 +- r-crayon=1.5.3 +- r-curl=5.2.1 - r-cvxr=1.0_13 - r-data.table=1.15.2 - r-dbi=1.2.3 @@ -503,7 +510,7 @@ dependencies: - r-desc=1.4.3 - r-desctools=0.99.54 - r-diffobj=0.3.5 -- r-digest=0.6.35 +- r-digest=0.6.36 - r-doparallel=1.0.17 - r-dorng=1.8.6 - r-dplyr=1.1.4 @@ -513,8 +520,8 @@ dependencies: - r-ecosolver=0.5.5 - r-ellipsis=0.3.2 - r-energy=1.7_11 -- r-evaluate=0.23 -- r-exact=3.2 +- r-evaluate=0.24.0 +- r-exact=3.3 - r-expm=0.999_9 - r-fansi=1.0.6 - r-farver=2.1.2 @@ -524,7 +531,7 @@ dependencies: - r-fontawesome=0.5.2 - r-forcats=1.0.0 - r-foreach=1.5.2 -- r-foreign=0.8_86 +- r-foreign=0.8_87 - r-formatr=1.14 - r-formula=1.2_5 - r-frictionless=1.1.0 @@ -553,7 +560,7 @@ dependencies: - r-highr=0.11 - r-hmisc=5.1_3 - r-hms=1.1.3 -- r-htmltable=2.4.2 +- r-htmltable=2.4.3 - r-htmltools=0.5.8.1 - r-htmlwidgets=1.6.4 - r-httr=1.4.7 @@ -566,19 +573,19 @@ dependencies: - r-jpeg=0.1_10 - r-jquerylib=0.1.4 - r-jsonlite=1.8.8 -- r-knitr=1.47 +- r-knitr=1.48 - r-labeling=0.4.3 - r-lambda.r=1.2.4 - r-lattice=0.22_6 - r-latticeextra=0.6_30 - r-lazyeval=0.2.2 - r-lifecycle=1.0.4 -- r-lme4=1.1_35.3 +- r-lme4=1.1_35.5 - r-lmertest=3.1_3 - r-lmom=3.0 - r-lubridate=1.9.3 - r-magrittr=2.0.3 -- r-mass=7.3_60 +- r-mass=7.3_60.0.1 - r-matrix=1.6_5 - r-matrixstats=1.3.0 - r-memoise=2.0.1 @@ -586,16 +593,16 @@ dependencies: - r-mime=0.12 - r-minqa=1.2.7 - r-modelr=0.1.11 -- r-multcomp=1.4_25 +- r-multcomp=1.4_26 - r-munsell=0.5.1 - r-mvtnorm=1.2_5 -- r-nlme=3.1_164 -- r-nloptr=2.0.3 +- r-nlme=3.1_165 +- r-nloptr=2.1.1 - r-nnet=7.3_19 - r-numderiv=2016.8_1.1 - r-openssl=2.2.0 - r-optparse=1.7.5 -- r-osqp=0.6.3.2 +- r-osqp=0.6.3.3 - r-permute=0.9_7 - r-pheatmap=1.0.12 - r-pillar=1.9.0 @@ -612,28 +619,28 @@ dependencies: - r-processx=3.8.4 - r-progress=1.2.3 - r-proxy=0.4_27 -- r-ps=1.7.6 +- r-ps=1.7.7 - r-purrr=1.0.2 - r-r6=2.5.1 - r-ragg=1.3.2 - r-rappdirs=0.3.3 - r-rbibutils=2.2.16 - r-rcolorbrewer=1.1_3 -- r-rcpp=1.0.12 +- r-rcpp=1.0.13 - r-rcppannoy=0.0.22 - r-rcppeigen=0.3.4.0.0 - r-rcpphnsw=0.6.0 - r-rcppml=0.3.7 - r-rcppprogress=0.4.2 - r-rcpptoml=0.2.2 -- r-rcurl=1.98_1.14 +- r-rcurl=1.98_1.16 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 - r-registry=0.5_1 - r-rematch=2.0.0 - r-rematch2=2.1.2 -- r-reprex=2.1.0 +- r-reprex=2.1.1 - r-reshape2=1.4.4 - r-restfulr=0.0.15 - r-reticulate=1.36.0 @@ -645,7 +652,7 @@ dependencies: - r-rootsolve=1.8.2.4 - r-rpart=4.1.23 - r-rprojroot=2.0.4 -- r-rsqlite=2.3.4 +- r-rsqlite=2.3.7 - r-rstudioapi=0.16.0 - r-rsvd=1.0.5 - r-rtsne=0.17 @@ -658,7 +665,7 @@ dependencies: - r-sitmo=2.0.2 - r-snow=0.4_4 - r-sp=2.1_4 -- r-stringdist=0.9.10 +- r-stringdist=0.9.12 - r-stringi=1.8.4 - r-stringr=1.5.1 - r-survival=3.7_0 @@ -673,7 +680,7 @@ dependencies: - r-tidytree=0.4.6 - r-tidyverse=2.0.0 - r-timechange=0.3.0 -- r-tinytex=0.51 +- r-tinytex=0.52 - r-tzdb=0.4.0 - r-utf8=1.2.4 - r-uuid=1.2_0 @@ -686,20 +693,20 @@ dependencies: - r-vroom=1.6.5 - r-waldo=0.5.2 - r-withr=3.0.0 -- r-xfun=0.44 -- r-xml=3.99_0.16.1 +- r-xfun=0.45 +- r-xml=3.99_0.17 - r-xml2=1.3.6 - r-xtable=1.8_4 -- r-yaml=2.3.8 +- r-yaml=2.3.9 - r-yulab.utils=0.1.4 - r-zoo=1.8_12 - readline=8.2 - referencing=0.35.1 - requests=2.32.3 -- rescript=2024.10.0.dev0+4.g14dd23a +- rescript=2024.10.0.dev0+9.g92fee7e - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 -- rpds-py=0.18.1 +- rpds-py=0.19.1 - rsync=3.3.0 - samtools=1.20 - scikit-bio=0.6.0 @@ -710,15 +717,16 @@ dependencies: - send2trash=1.8.3 - sepp=4.4.0 - setproctitle=1.3.3 -- setuptools=70.0.0 +- setuptools=71.0.4 - sgmllib3k=1.0.0 +- shortuuid=1.0.13 - sigtool=0.1.3 - simplejson=3.19.2 - six=1.16.0 - sniffio=1.3.1 - soupsieve=2.5 - spades=3.15.2 -- sqlite=3.45.3 +- sqlite=3.46.0 - stack_data=0.6.2 - statsmodels=0.14.2 - suitesparse=5.10.1 @@ -733,15 +741,15 @@ dependencies: - tktable=2.10 - toml=0.10.2 - tomli=2.0.1 -- tomlkit=0.12.5 +- tomlkit=0.13.0 - toolz=0.12.1 -- tornado=6.4 +- tornado=6.4.1 - tqdm=4.62.3 - traitlets=5.9.0 - typeguard=4.3.0 - types-python-dateutil=2.9.0.20240316 -- typing-extensions=4.12.1 -- typing_extensions=4.12.1 +- typing-extensions=4.12.2 +- typing_extensions=4.12.2 - typing_utils=0.1.0 - tzdata=2024a - tzlocal=2.1 @@ -752,7 +760,7 @@ dependencies: - unifrac=1.3 - unifrac-binaries=1.4 - uri-template=1.3.0 -- urllib3=1.26.18 +- urllib3=2.2.2 - vsearch=2.28.1 - wcwidth=0.2.13 - webcolors=24.6.0 @@ -764,7 +772,7 @@ dependencies: - wrapt=1.16.0 - xlsxwriter=3.1.9 - xmltodict=0.13.0 -- xopen=2.0.1 +- xopen=2.0.2 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xxhash=0.8.2 @@ -772,8 +780,8 @@ dependencies: - yaml=0.2.5 - yq=3.4.3 - zeromq=4.3.5 -- zipp=3.17.0 +- zipp=3.19.2 - zlib=1.2.13 -- zlib-ng=2.0.7 -- zstandard=0.19.0 +- zlib-ng=2.2.1 +- zstandard=0.23.0 - zstd=1.5.6 diff --git a/2024.10/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml b/2024.10/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml index a8403d5e..9e373124 100644 --- a/2024.10/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml +++ b/2024.10/metagenome/passed/qiime2-metagenome-ubuntu-latest-conda.yml @@ -12,8 +12,8 @@ dependencies: - altair=5.3.0 - anyio=4.4.0 - appdirs=1.4.4 -- argcomplete=3.3.0 -- argh=0.31.2 +- argcomplete=3.4.0 +- argh=0.31.3 - argon2-cffi=23.1.0 - argon2-cffi-bindings=21.2.0 - aria2=1.37.0 @@ -28,7 +28,7 @@ dependencies: - bbmap=39.06 - bc=1.07.1 - bcftools=1.20 -- bcrypt=4.1.3 +- bcrypt=4.2.0 - beautifulsoup4=4.12.3 - bedtools=2.31.1 - bibtexparser=1.4.1 @@ -90,11 +90,11 @@ dependencies: - bioconductor-zlibbioc=1.48.0 - biom-format=2.1.15 - biopython=1.83 -- blast=2.15.0 +- blast=2.16.0 - bleach=6.1.0 - boost-cpp=1.78.0 - bowtie2=2.5.1 -- bracken=2.9 +- bracken=3.0 - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 @@ -102,13 +102,13 @@ dependencies: - bwa=0.7.18 - bwidget=1.9.14 - bzip2=1.0.8 -- c-ares=1.28.1 -- ca-certificates=2024.6.2 +- c-ares=1.32.3 +- ca-certificates=2024.7.4 - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.18.0 - cdbtools=0.99 -- certifi=2024.2.2 +- certifi=2024.7.4 - cffi=1.16.0 - charset-normalizer=3.3.2 - circos=0.69.9 @@ -117,31 +117,31 @@ dependencies: - comm=0.2.2 - conda-pack=0.7.0 - contourpy=1.2.1 -- cryptography=42.0.8 +- cryptography=43.0.0 - curl=8.8.0 -- cutadapt=4.8 +- cutadapt=4.9 - cycler=0.12.1 - dbus=1.13.6 -- debugpy=1.8.1 +- debugpy=1.8.2 - decorator=4.4.2 - defusedxml=0.7.1 - dendropy=4.5.2 -- diamond=2.1.9 +- diamond=2.1.8 - dill=0.3.8 -- dnaio=1.2.0 +- dnaio=1.2.1 - easel=0.49 - eggnog-mapper=2.1.12 - emperor=1.0.4 -- entrez-direct=22.1 +- entrez-direct=22.4 - entrezpy=2.1.2 - entrypoints=0.4 -- exceptiongroup=1.2.0 +- exceptiongroup=1.2.2 - executing=2.0.1 - expat=2.6.2 - fastcluster=1.2.6 - feedparser=6.0.11 -- filelock=3.14.0 -- flufl.lock=7.1 +- filelock=3.15.4 +- flufl.lock=8.0.2 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 - font-ttf-source-code-pro=2.038 @@ -149,23 +149,23 @@ dependencies: - fontconfig=2.14.2 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 -- fonttools=4.53.0 -- formulaic=1.0.1 +- fonttools=4.53.1 +- formulaic=1.0.2 - fqdn=1.5.1 - freetype=2.12.1 - fribidi=1.0.10 - future=1.0.0 - gawk=5.3.0 -- gcc_impl_linux-64=13.2.0 +- gcc_impl_linux-64=14.1.0 - gettext=0.22.5 - gettext-tools=0.22.5 - gffutils=0.10.1 -- gfortran_impl_linux-64=13.2.0 +- gfortran_impl_linux-64=14.1.0 - giflib=5.2.2 - glib=2.80.2 - glib-tools=2.80.2 - glimmerhmm=3.0.4 -- globus-sdk=3.41.0 +- globus-sdk=3.42.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 @@ -174,25 +174,27 @@ dependencies: - gsl=2.7 - gst-plugins-base=1.24.4 - gstreamer=1.24.4 -- gxx_impl_linux-64=13.2.0 +- gxx_impl_linux-64=14.1.0 +- h2=4.1.0 - h5py=3.11.0 - harfbuzz=8.5.0 - hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.1b2 +- hpack=4.0.0 - htslib=1.20 +- hyperframe=6.0.1 - icu=73.2 - idna=3.7 - ijson=3.3.0 -- importlib-metadata=7.1.0 +- importlib-metadata=8.2.0 - importlib-resources=6.4.0 -- importlib_metadata=7.1.0 - importlib_resources=6.4.0 - iniconfig=2.0.0 - insilicoseq=2.0.1 - interface_meta=1.3.0 - iow=1.0.5 -- ipykernel=6.29.3 +- ipykernel=6.29.5 - ipython=8.18.1 - ipython_genutils=0.2.0 - ipywidgets=8.1.3 @@ -203,14 +205,14 @@ dependencies: - joblib=1.4.2 - jq=1.7.1 - jsonlines=3.0.0 -- jsonpointer=2.4 -- jsonschema=4.22.0 +- jsonpointer=3.0.0 +- jsonschema=4.23.0 - jsonschema-specifications=2023.12.1 -- jsonschema-with-format-nongpl=4.22.0 +- jsonschema-with-format-nongpl=4.23.0 - jupyter_client=7.4.9 - jupyter_core=5.7.2 - jupyter_events=0.10.0 -- jupyter_server=2.14.1 +- jupyter_server=2.14.2 - jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 - jupyterlab_widgets=3.0.11 @@ -220,7 +222,7 @@ dependencies: - keyutils=1.6.1 - kiwisolver=1.4.5 - kraken2=2.1.3 -- krb5=1.21.2 +- krb5=1.21.3 - lame=3.100 - lcms2=2.16 - ld_impl_linux-64=2.40 @@ -235,7 +237,7 @@ dependencies: - libcap=2.69 - libcblas=3.9.0 - libclang-cpp15=15.0.7 -- libclang13=18.1.6 +- libclang13=18.1.7 - libcups=2.3.3 - libcurl=8.8.0 - libdeflate=1.20 @@ -245,18 +247,18 @@ dependencies: - libexpat=2.6.2 - libffi=3.4.2 - libflac=1.4.3 -- libgcc-devel_linux-64=13.2.0 -- libgcc-ng=13.2.0 -- libgcrypt=1.10.3 +- libgcc-devel_linux-64=14.1.0 +- libgcc-ng=14.1.0 +- libgcrypt=1.11.0 - libgd=2.3.3 - libgettextpo=0.22.5 - libgettextpo-devel=0.22.5 -- libgfortran-ng=13.2.0 -- libgfortran5=13.2.0 +- libgfortran-ng=14.1.0 +- libgfortran5=14.1.0 - libglib=2.80.2 -- libgomp=13.2.0 -- libgpg-error=1.49 -- libhwloc=2.10.0 +- libgomp=14.1.0 +- libgpg-error=1.50 +- libhwloc=2.11.1 - libiconv=1.17 - libidn2=2.3.7 - libjpeg-turbo=3.0.0 @@ -264,22 +266,22 @@ dependencies: - liblapacke=3.9.0 - libllvm14=14.0.6 - libllvm15=15.0.7 -- libllvm18=18.1.6 +- libllvm18=18.1.7 - libnghttp2=1.58.0 - libnsl=2.0.1 -- libogg=1.3.4 +- libogg=1.3.5 - libopenblas=0.3.27 - libopus=1.3.1 - libpng=1.6.43 - libpq=16.3 - libprotobuf=3.20.3 -- libsanitizer=13.2.0 +- libsanitizer=14.1.0 - libsndfile=1.2.2 - libsodium=1.0.18 -- libsqlite=3.45.3 +- libsqlite=3.46.0 - libssh2=1.11.0 -- libstdcxx-devel_linux-64=13.2.0 -- libstdcxx-ng=13.2.0 +- libstdcxx-devel_linux-64=14.1.0 +- libstdcxx-ng=14.1.0 - libsystemd0=255 - libtiff=4.6.0 - libunistring=0.9.10 @@ -294,7 +296,7 @@ dependencies: - libxslt=1.1.39 - libzlib=1.2.13 - llvm-openmp=8.0.1 -- llvmlite=0.42.0 +- llvmlite=0.43.0 - lp_solve=5.5.2.11 - lxml=5.2.2 - lz4=4.3.3 @@ -305,7 +307,7 @@ dependencies: - matplotlib-base=3.8.4 - matplotlib-inline=0.1.7 - megahit=1.2.9 -- metabat2=2.15 +- metabat2=2.17 - metaeuk=7.bba0d80 - metis=5.1.0 - minimap2=2.28 @@ -324,7 +326,7 @@ dependencies: - nbclient=0.10.0 - nbconvert-core=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.1 +- ncbi-datasets-pylib=14.25.1 - ncbi-vdb=3.1.1 - ncurses=6.5 - nest-asyncio=1.6.0 @@ -334,7 +336,7 @@ dependencies: - notebook-shim=0.2.4 - nspr=4.35 - nss=3.100 -- numba=0.59.1 +- numba=0.60.0 - numpy=1.26.4 - oniguruma=6.9.9 - openjdk=22.0.1 @@ -342,11 +344,12 @@ dependencies: - openmp=8.0.1 - openssl=3.3.1 - overrides=7.7.0 -- packaging=24.0 +- packaging=24.1 - pandas=2.2.2 -- pandoc=3.2 +- pandoc=3.2.1 - pandocfilters=1.5.0 -- pango=1.52.2 +- pango=1.54.0 +- parameterized=0.9.0 - paramiko=3.4.0 - parsl=2024.4.15 - parso=0.8.4 @@ -432,29 +435,30 @@ dependencies: - popt=1.16 - prodigal=2.6.3 - prometheus_client=0.20.0 -- prompt-toolkit=3.0.46 +- prompt-toolkit=3.0.47 - protobuf=3.20.3 -- psutil=5.9.8 +- psutil=6.0.0 - pthread-stubs=0.4 - ptyprocess=0.7.0 - pulseaudio-client=17.0 -- pure_eval=0.2.2 +- pure_eval=0.2.3 - pycparser=2.22 - pyfaidx=0.8.1.1 - pygments=2.18.0 +- pyhmmer=0.10.14 - pyjwt=2.8.0 - pynacl=1.5.0 -- pynndescent=0.5.12 +- pynndescent=0.5.13 - pyparsing=3.1.2 - pyqt=5.15.9 - pyqt5-sip=12.12.2 - pysam=0.22.1 - pysocks=1.7.1 -- pytest=8.2.2 +- pytest=8.3.2 - python=3.9.19 -- python-dateutil=2.8.2 +- python-dateutil=2.9.0 - python-dotenv=1.0.1 -- python-fastjsonschema=2.19.1 +- python-fastjsonschema=2.20.0 - python-isal=1.6.1 - python-json-logger=2.0.7 - python-tzdata=2024.1 @@ -465,26 +469,26 @@ dependencies: - pyyaml=6.0.1 - pyzmq=24.0.1 - pyzotero=1.5.19 -- q2-assembly=2024.10.0.dev0 +- q2-assembly=2024.10.0.dev0+5.gd6cbf5a - q2-composition=2024.10.0.dev0 - q2-cutadapt=2024.10.0.dev0 -- q2-demux=2024.10.0.dev0 +- q2-demux=2024.10.0.dev0+1.g037f78a - q2-diversity=2024.10.0.dev0 - q2-diversity-lib=2024.10.0.dev0 - q2-emperor=2024.10.0.dev0 -- q2-feature-classifier=2024.10.0.dev0 +- q2-feature-classifier=2024.10.0.dev0+1.ga00fe79 - q2-feature-table=2024.10.0.dev0 - q2-fondue=2024.10.0.dev0 - q2-longitudinal=2024.10.0.dev0 - q2-metadata=2024.10.0.dev0 -- q2-moshpit=2024.10.0.dev0+3.gfe14cc2 +- q2-moshpit=2024.10.0.dev0+15.ge99496e - q2-mystery-stew=2024.10.0.dev0 - q2-quality-control=2024.10.0.dev0 - q2-quality-filter=2024.10.0.dev0 - q2-sample-classifier=2024.10.0.dev0 - q2-sapienns=2024.10.0.dev0 - q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0 +- q2-types=2024.10.0.dev0+20.g5e0a3d3 - q2-vsearch=2024.10.0.dev0 - q2cli=2024.10.0.dev0+1.gefac9fc - q2templates=2024.10.0.dev0 @@ -517,15 +521,15 @@ dependencies: - r-cellranger=1.1.0 - r-checkmate=2.3.1 - r-class=7.3_22 -- r-cli=3.6.2 +- r-cli=3.6.3 - r-clipr=0.8.0 - r-cluster=2.1.6 - r-codetools=0.2_20 - r-colorspace=2.1_0 - r-conflicted=1.2.0 - r-cpp11=0.4.7 -- r-crayon=1.5.2 -- r-curl=5.1.0 +- r-crayon=1.5.3 +- r-curl=5.2.1 - r-cvxr=1.0_13 - r-data.table=1.15.2 - r-dbi=1.2.3 @@ -534,7 +538,7 @@ dependencies: - r-desc=1.4.3 - r-desctools=0.99.54 - r-diffobj=0.3.5 -- r-digest=0.6.35 +- r-digest=0.6.36 - r-doparallel=1.0.17 - r-dorng=1.8.6 - r-dplyr=1.1.4 @@ -544,8 +548,8 @@ dependencies: - r-ecosolver=0.5.5 - r-ellipsis=0.3.2 - r-energy=1.7_11 -- r-evaluate=0.23 -- r-exact=3.2 +- r-evaluate=0.24.0 +- r-exact=3.3 - r-expm=0.999_9 - r-fansi=1.0.6 - r-farver=2.1.2 @@ -555,7 +559,7 @@ dependencies: - r-fontawesome=0.5.2 - r-forcats=1.0.0 - r-foreach=1.5.2 -- r-foreign=0.8_86 +- r-foreign=0.8_87 - r-formatr=1.14 - r-formula=1.2_5 - r-frictionless=1.1.0 @@ -584,7 +588,7 @@ dependencies: - r-highr=0.11 - r-hmisc=5.1_3 - r-hms=1.1.3 -- r-htmltable=2.4.2 +- r-htmltable=2.4.3 - r-htmltools=0.5.8.1 - r-htmlwidgets=1.6.4 - r-httr=1.4.7 @@ -597,19 +601,19 @@ dependencies: - r-jpeg=0.1_10 - r-jquerylib=0.1.4 - r-jsonlite=1.8.8 -- r-knitr=1.47 +- r-knitr=1.48 - r-labeling=0.4.3 - r-lambda.r=1.2.4 - r-lattice=0.22_6 - r-latticeextra=0.6_30 - r-lazyeval=0.2.2 - r-lifecycle=1.0.4 -- r-lme4=1.1_35.3 +- r-lme4=1.1_35.5 - r-lmertest=3.1_3 - r-lmom=3.0 - r-lubridate=1.9.3 - r-magrittr=2.0.3 -- r-mass=7.3_60 +- r-mass=7.3_60.0.1 - r-matrix=1.6_5 - r-matrixstats=1.3.0 - r-memoise=2.0.1 @@ -617,16 +621,16 @@ dependencies: - r-mime=0.12 - r-minqa=1.2.7 - r-modelr=0.1.11 -- r-multcomp=1.4_25 +- r-multcomp=1.4_26 - r-munsell=0.5.1 - r-mvtnorm=1.2_5 -- r-nlme=3.1_164 -- r-nloptr=2.0.3 +- r-nlme=3.1_165 +- r-nloptr=2.1.1 - r-nnet=7.3_19 - r-numderiv=2016.8_1.1 - r-openssl=2.2.0 - r-optparse=1.7.5 -- r-osqp=0.6.3.2 +- r-osqp=0.6.3.3 - r-permute=0.9_7 - r-pheatmap=1.0.12 - r-pillar=1.9.0 @@ -643,28 +647,28 @@ dependencies: - r-processx=3.8.4 - r-progress=1.2.3 - r-proxy=0.4_27 -- r-ps=1.7.6 +- r-ps=1.7.7 - r-purrr=1.0.2 - r-r6=2.5.1 - r-ragg=1.3.2 - r-rappdirs=0.3.3 - r-rbibutils=2.2.16 - r-rcolorbrewer=1.1_3 -- r-rcpp=1.0.12 +- r-rcpp=1.0.13 - r-rcppannoy=0.0.22 - r-rcppeigen=0.3.4.0.0 - r-rcpphnsw=0.6.0 - r-rcppml=0.3.7 - r-rcppprogress=0.4.2 - r-rcpptoml=0.2.2 -- r-rcurl=1.98_1.14 +- r-rcurl=1.98_1.16 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 - r-registry=0.5_1 - r-rematch=2.0.0 - r-rematch2=2.1.2 -- r-reprex=2.1.0 +- r-reprex=2.1.1 - r-reshape2=1.4.4 - r-restfulr=0.0.15 - r-reticulate=1.36.0 @@ -676,7 +680,7 @@ dependencies: - r-rootsolve=1.8.2.4 - r-rpart=4.1.23 - r-rprojroot=2.0.4 -- r-rsqlite=2.3.4 +- r-rsqlite=2.3.7 - r-rstudioapi=0.16.0 - r-rsvd=1.0.5 - r-rtsne=0.17 @@ -689,7 +693,7 @@ dependencies: - r-sitmo=2.0.2 - r-snow=0.4_4 - r-sp=2.1_4 -- r-stringdist=0.9.10 +- r-stringdist=0.9.12 - r-stringi=1.8.4 - r-stringr=1.5.1 - r-survival=3.7_0 @@ -704,7 +708,7 @@ dependencies: - r-tidytree=0.4.6 - r-tidyverse=2.0.0 - r-timechange=0.3.0 -- r-tinytex=0.51 +- r-tinytex=0.52 - r-tzdb=0.4.0 - r-utf8=1.2.4 - r-uuid=1.2_0 @@ -717,22 +721,22 @@ dependencies: - r-vroom=1.6.5 - r-waldo=0.5.2 - r-withr=3.0.0 -- r-xfun=0.44 -- r-xml=3.99_0.16.1 +- r-xfun=0.46 +- r-xml=3.99_0.17 - r-xml2=1.3.6 - r-xtable=1.8_4 -- r-yaml=2.3.8 +- r-yaml=2.3.9 - r-yulab.utils=0.1.4 - r-zoo=1.8_12 - readline=8.2 - referencing=0.35.1 - repeatmasker=4.1.5 - requests=2.32.3 -- rescript=2024.10.0.dev0+4.g14dd23a +- rescript=2024.10.0.dev0+9.g92fee7e - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rmblast=2.14.1 -- rpds-py=0.18.1 +- rpds-py=0.19.1 - rsync=3.3.0 - samtools=1.20 - scikit-bio=0.6.0 @@ -744,15 +748,16 @@ dependencies: - send2trash=1.8.3 - sepp=4.4.0 - setproctitle=1.3.3 -- setuptools=70.0.0 +- setuptools=71.0.4 - sgmllib3k=1.0.0 +- shortuuid=1.0.13 - simplejson=3.19.2 - sip=6.7.12 - six=1.16.0 - sniffio=1.3.1 - soupsieve=2.5 - spades=3.15.2 -- sqlite=3.45.3 +- sqlite=3.46.0 - stack_data=0.6.2 - statsmodels=0.14.2 - suitesparse=5.10.1 @@ -768,16 +773,16 @@ dependencies: - tktable=2.10 - toml=0.10.2 - tomli=2.0.1 -- tomlkit=0.12.5 +- tomlkit=0.13.0 - toolz=0.12.1 -- tornado=6.4 +- tornado=6.4.1 - tqdm=4.62.3 - traitlets=5.9.0 - trf=4.09.1 - typeguard=4.3.0 - types-python-dateutil=2.9.0.20240316 -- typing-extensions=4.12.1 -- typing_extensions=4.12.1 +- typing-extensions=4.12.2 +- typing_extensions=4.12.2 - typing_utils=0.1.0 - tzdata=2024a - tzlocal=2.1 @@ -788,7 +793,7 @@ dependencies: - unifrac=1.3 - unifrac-binaries=1.4 - uri-template=1.3.0 -- urllib3=1.26.18 +- urllib3=2.2.2 - vsearch=2.28.1 - wcwidth=0.2.13 - webcolors=24.6.0 @@ -803,10 +808,10 @@ dependencies: - xcb-util-keysyms=0.4.0 - xcb-util-renderutil=0.3.9 - xcb-util-wm=0.4.1 -- xkeyboard-config=2.41 +- xkeyboard-config=2.42 - xlsxwriter=3.1.9 - xmltodict=0.13.0 -- xopen=2.0.1 +- xopen=2.0.2 - xorg-fixesproto=5.0 - xorg-inputproto=2.3.2 - xorg-kbproto=1.0.7 @@ -820,7 +825,7 @@ dependencies: - xorg-libxi=1.7.10 - xorg-libxrender=0.9.11 - xorg-libxt=1.3.0 -- xorg-libxtst=1.2.3 +- xorg-libxtst=1.2.4 - xorg-recordproto=1.14.2 - xorg-renderproto=0.11.1 - xorg-xextproto=7.3.0 @@ -831,8 +836,8 @@ dependencies: - yaml=0.2.5 - yq=3.4.3 - zeromq=4.3.5 -- zipp=3.17.0 +- zipp=3.19.2 - zlib=1.2.13 -- zlib-ng=2.0.7 -- zstandard=0.19.0 +- zlib-ng=2.2.1 +- zstandard=0.23.0 - zstd=1.5.6 diff --git a/2024.10/metagenome/passed/seed-environment-conda.yml b/2024.10/metagenome/passed/seed-environment-conda.yml index 5266c99f..9f922ed9 100644 --- a/2024.10/metagenome/passed/seed-environment-conda.yml +++ b/2024.10/metagenome/passed/seed-environment-conda.yml @@ -1,4 +1,3 @@ -# Trial-type-refactor channels: - https://packages.qiime2.org/qiime2/2024.10/metagenome/passed - conda-forge @@ -21,33 +20,33 @@ dependencies: - pysam=0.22.1 - python=3.9.19 - python_abi=3.9 -- q2-assembly=2024.10.0.dev0 +- q2-assembly=2024.10.0.dev0+5.gd6cbf5a - q2-composition=2024.10.0.dev0 - q2-cutadapt=2024.10.0.dev0 -- q2-demux=2024.10.0.dev0 +- q2-demux=2024.10.0.dev0+1.g037f78a - q2-diversity-lib=2024.10.0.dev0 - q2-diversity=2024.10.0.dev0 - q2-emperor=2024.10.0.dev0 -- q2-feature-classifier=2024.10.0.dev0 +- q2-feature-classifier=2024.10.0.dev0+1.ga00fe79 - q2-feature-table=2024.10.0.dev0 - q2-fondue=2024.10.0.dev0 - q2-longitudinal=2024.10.0.dev0 - q2-metadata=2024.10.0.dev0 -- q2-moshpit=2024.10.0.dev0+3.gfe14cc2 +- q2-moshpit=2024.10.0.dev0+15.ge99496e - q2-mystery-stew=2024.10.0.dev0 - q2-quality-control=2024.10.0.dev0 - q2-quality-filter=2024.10.0.dev0 - q2-sample-classifier=2024.10.0.dev0 - q2-sapienns=2024.10.0.dev0 - q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0 +- q2-types=2024.10.0.dev0+20.g5e0a3d3 - q2-vsearch=2024.10.0.dev0 - q2cli=2024.10.0.dev0+1.gefac9fc - q2templates=2024.10.0.dev0 - qiime2=2024.10.0.dev0 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0.dev0+4.g14dd23a +- rescript=2024.10.0.dev0+9.g92fee7e - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0 diff --git a/2024.10/metagenome/staged/seed-environment-conda.yml b/2024.10/metagenome/staged/seed-environment-conda.yml index 8b54fb85..eb59492c 100644 --- a/2024.10/metagenome/staged/seed-environment-conda.yml +++ b/2024.10/metagenome/staged/seed-environment-conda.yml @@ -20,19 +20,19 @@ dependencies: - pysam=0.22.1 - python=3.9.19 - python_abi=3.9 -- q2-assembly=2024.10.0.dev0 +- q2-assembly=2024.10.0.dev0+5.gd6cbf5a - q2-composition=2024.10.0.dev0 - q2-cutadapt=2024.10.0.dev0 -- q2-demux=2024.10.0.dev0 +- q2-demux=2024.10.0.dev0+1.g037f78a - q2-diversity-lib=2024.10.0.dev0 - q2-diversity=2024.10.0.dev0 - q2-emperor=2024.10.0.dev0 -- q2-feature-classifier=2024.10.0.dev0 +- q2-feature-classifier=2024.10.0.dev0+1.ga00fe79 - q2-feature-table=2024.10.0.dev0 - q2-fondue=2024.10.0.dev0 - q2-longitudinal=2024.10.0.dev0 - q2-metadata=2024.10.0.dev0 -- q2-moshpit=2024.10.0.dev0+3.gfe14cc2 +- q2-moshpit=2024.10.0.dev0+15.ge99496e - q2-mystery-stew=2024.10.0.dev0 - q2-quality-control=2024.10.0.dev0 - q2-quality-filter=2024.10.0.dev0 @@ -40,14 +40,14 @@ dependencies: - q2-sapienns=2024.10.0.dev0 - q2-taxa=2024.10.0.dev0 - q2-types-genomics=2023.11.0.dev0+8.g3b993ed -- q2-types=2024.10.0.dev0 +- q2-types=2024.10.0.dev0+20.g5e0a3d3 - q2-vsearch=2024.10.0.dev0 - q2cli=2024.10.0.dev0+1.gefac9fc - q2templates=2024.10.0.dev0 - qiime2=2024.10.0.dev0 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0.dev0+4.g14dd23a +- rescript=2024.10.0.dev0+9.g92fee7e - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0