From 5d0fd2303193e339f880c0a36dd7adc688f69a34 Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Tue, 23 Apr 2024 11:14:57 -0700 Subject: [PATCH 1/5] PREP: python 3.9 update (amplicon) --- .../passed/seed-environment-conda.yml | 35 ++++++++++--------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/2024.5/amplicon/passed/seed-environment-conda.yml b/2024.5/amplicon/passed/seed-environment-conda.yml index fed66548..ed49a22a 100644 --- a/2024.5/amplicon/passed/seed-environment-conda.yml +++ b/2024.5/amplicon/passed/seed-environment-conda.yml @@ -4,18 +4,18 @@ channels: - bioconda - defaults dependencies: -- biom-format=2.1.14 -- h5py=3.8.0 -- hdf5=1.14.0 -- mafft=7.520 -- matplotlib=3.6.0 +- biom-format=2.1.15 +- h5py=3.11.0 +- hdf5=1.14.3 +- mafft=7.525 +- matplotlib=3.8.4 - notebook=6.5.5 -- numpy=1.24.4 -- pandas=1.5.3 -- parsl=2023.12.04 -- patsy=0.5.3 -- pillow=9.4.0 -- python=3.8 +- numpy=1.26.4 +- pandas=2.2.2 +- parsl=2024.4.15 +- patsy=0.5.6 +- pillow=10.3.0 +- python=3.9.19 - q2-alignment=2024.5.0.dev0+1.g3a9c58b - q2-composition=2024.5.0.dev0 - q2-cutadapt=2024.5.0.dev0 @@ -42,13 +42,14 @@ dependencies: - q2galaxy=2024.5.0.dev0+2.ga124fa1 - q2templates=2024.5.0.dev0 - qiime2=2024.5.0.dev0+2.g27f5ec0 -- r-base=4.2.2 +- r-base=4.3.3 +- r-reticulate=1.36.0 - rescript=2024.5.0.dev0+3.g6e87cfe -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 -- seaborn=0.12.2 -- unifrac-binaries=1.3.2 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 +- seaborn=0.13.2 +- unifrac-binaries=1.4 - unifrac=1.3 extras: variant_override: From 2e2953f74986b2005473b3a1754436c9b2235331 Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Tue, 23 Apr 2024 14:04:11 -0700 Subject: [PATCH 2/5] looks like we need python_abi after all --- 2024.5/amplicon/passed/seed-environment-conda.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/2024.5/amplicon/passed/seed-environment-conda.yml b/2024.5/amplicon/passed/seed-environment-conda.yml index ed49a22a..10874b9c 100644 --- a/2024.5/amplicon/passed/seed-environment-conda.yml +++ b/2024.5/amplicon/passed/seed-environment-conda.yml @@ -16,6 +16,7 @@ dependencies: - patsy=0.5.6 - pillow=10.3.0 - python=3.9.19 +- python_abi=3.9 - q2-alignment=2024.5.0.dev0+1.g3a9c58b - q2-composition=2024.5.0.dev0 - q2-cutadapt=2024.5.0.dev0 From 7683490208be96f7aad365cc83885b03bcd0536c Mon Sep 17 00:00:00 2001 From: Liz Gehret <54517601+lizgehret@users.noreply.github.com> Date: Tue, 30 Apr 2024 11:39:28 -0700 Subject: [PATCH 3/5] Update 2024.5/amplicon/passed/seed-environment-conda.yml --- 2024.5/amplicon/passed/seed-environment-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/2024.5/amplicon/passed/seed-environment-conda.yml b/2024.5/amplicon/passed/seed-environment-conda.yml index 10874b9c..a3291151 100644 --- a/2024.5/amplicon/passed/seed-environment-conda.yml +++ b/2024.5/amplicon/passed/seed-environment-conda.yml @@ -7,7 +7,7 @@ dependencies: - biom-format=2.1.15 - h5py=3.11.0 - hdf5=1.14.3 -- mafft=7.525 +- mafft=7.520 - matplotlib=3.8.4 - notebook=6.5.5 - numpy=1.26.4 From 3ce1798ddb35e296205faf9cbcf57d0a6dee3426 Mon Sep 17 00:00:00 2001 From: Liz Gehret <54517601+lizgehret@users.noreply.github.com> Date: Tue, 30 Apr 2024 16:08:50 -0700 Subject: [PATCH 4/5] pin: keep prior seaborn version --- 2024.5/amplicon/passed/seed-environment-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/2024.5/amplicon/passed/seed-environment-conda.yml b/2024.5/amplicon/passed/seed-environment-conda.yml index a3291151..d10cf55a 100644 --- a/2024.5/amplicon/passed/seed-environment-conda.yml +++ b/2024.5/amplicon/passed/seed-environment-conda.yml @@ -49,7 +49,7 @@ dependencies: - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0 -- seaborn=0.13.2 +- seaborn=0.12.2 - unifrac-binaries=1.4 - unifrac=1.3 extras: From 9e4b926e9a1ff2d2e6e0c040868b90f4d0912624 Mon Sep 17 00:00:00 2001 From: q2d2 Date: Thu, 2 May 2024 01:09:08 +0000 Subject: [PATCH 5/5] Update conda environments (Language-python39-update/amplicon) --- .../qiime2-amplicon-macos-latest-conda.yml | 352 +++++++++-------- .../qiime2-amplicon-ubuntu-latest-conda.yml | 374 +++++++++--------- .../passed/seed-environment-conda.yml | 26 +- .../staged/seed-environment-conda.yml | 58 +-- 4 files changed, 411 insertions(+), 399 deletions(-) diff --git a/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml b/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml index 28195185..09b5a2a1 100644 --- a/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml +++ b/2024.5/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml @@ -18,59 +18,61 @@ dependencies: - asttokens=2.4.1 - atpublic=3.0.1 - attrs=23.2.0 -- backcall=0.2.0 - bcrypt=4.1.2 - beautifulsoup4=4.12.3 - bibtexparser=1.4.1 -- bioconductor-ancombc=2.0.1 -- bioconductor-beachmat=2.14.0 -- bioconductor-biobase=2.58.0 -- bioconductor-biocbaseutils=1.0.0 -- bioconductor-biocgenerics=0.44.0 -- bioconductor-biocneighbors=1.16.0 -- bioconductor-biocparallel=1.32.5 -- bioconductor-biocsingular=1.14.0 -- bioconductor-biomformat=1.26.0 -- bioconductor-biostrings=2.66.0 -- bioconductor-dada2=1.26.0 +- bioconductor-ancombc=2.4.0 +- bioconductor-beachmat=2.18.0 +- bioconductor-biobase=2.62.0 +- bioconductor-biocbaseutils=1.4.0 +- bioconductor-biocgenerics=0.48.1 +- bioconductor-biocneighbors=1.20.0 +- bioconductor-biocparallel=1.36.0 +- bioconductor-biocsingular=1.18.0 +- bioconductor-biomformat=1.30.0 +- bioconductor-biostrings=2.70.1 +- bioconductor-bluster=1.12.0 +- bioconductor-dada2=1.30.0 - bioconductor-data-packages=20231203 -- bioconductor-decipher=2.26.0 -- bioconductor-decontam=1.18.0 -- bioconductor-delayedarray=0.24.0 -- bioconductor-delayedmatrixstats=1.20.0 -- bioconductor-dirichletmultinomial=1.40.0 -- bioconductor-genomeinfodb=1.34.9 -- bioconductor-genomeinfodbdata=1.2.9 -- bioconductor-genomicalignments=1.34.0 -- bioconductor-genomicranges=1.50.0 -- bioconductor-iranges=2.32.0 -- bioconductor-matrixgenerics=1.10.0 -- bioconductor-mia=1.6.0 -- bioconductor-multiassayexperiment=1.24.0 -- bioconductor-multtest=2.54.0 -- bioconductor-phyloseq=1.42.0 -- bioconductor-rhdf5=2.42.0 -- bioconductor-rhdf5filters=1.10.0 -- bioconductor-rhdf5lib=1.20.0 -- bioconductor-rhtslib=2.0.0 -- bioconductor-rsamtools=2.14.0 -- bioconductor-s4vectors=0.36.0 -- bioconductor-scaledmatrix=1.6.0 -- bioconductor-scater=1.26.0 -- bioconductor-scuttle=1.8.0 -- bioconductor-shortread=1.56.0 -- bioconductor-singlecellexperiment=1.20.0 -- bioconductor-sparsematrixstats=1.10.0 -- bioconductor-summarizedexperiment=1.28.0 -- bioconductor-treeio=1.22.0 -- bioconductor-treesummarizedexperiment=2.6.0 -- bioconductor-xvector=0.38.0 -- bioconductor-zlibbioc=1.44.0 -- biom-format=2.1.14 +- bioconductor-decipher=2.30.0 +- bioconductor-decontam=1.22.0 +- bioconductor-delayedarray=0.28.0 +- bioconductor-delayedmatrixstats=1.24.0 +- bioconductor-dirichletmultinomial=1.44.0 +- bioconductor-genomeinfodb=1.38.1 +- bioconductor-genomeinfodbdata=1.2.11 +- bioconductor-genomicalignments=1.38.0 +- bioconductor-genomicranges=1.54.1 +- bioconductor-iranges=2.36.0 +- bioconductor-matrixgenerics=1.14.0 +- bioconductor-mia=1.10.0 +- bioconductor-multiassayexperiment=1.28.0 +- bioconductor-multtest=2.58.0 +- bioconductor-phyloseq=1.46.0 +- bioconductor-rhdf5=2.46.1 +- bioconductor-rhdf5filters=1.14.1 +- bioconductor-rhdf5lib=1.24.0 +- bioconductor-rhtslib=2.4.0 +- bioconductor-rsamtools=2.18.0 +- bioconductor-s4arrays=1.2.0 +- bioconductor-s4vectors=0.40.2 +- bioconductor-scaledmatrix=1.10.0 +- bioconductor-scater=1.30.1 +- bioconductor-scuttle=1.12.0 +- bioconductor-shortread=1.60.0 +- bioconductor-singlecellexperiment=1.24.0 +- bioconductor-sparsearray=1.2.2 +- bioconductor-sparsematrixstats=1.14.0 +- bioconductor-summarizedexperiment=1.32.0 +- bioconductor-treeio=1.26.0 +- bioconductor-treesummarizedexperiment=2.10.0 +- bioconductor-xvector=0.42.0 +- bioconductor-zlibbioc=1.48.0 +- biom-format=2.1.15 - biopython=1.83 - blast=2.15.0 - bleach=6.1.0 -- bowtie2=2.5.2 +- bowtie2=2.5.3 - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 @@ -78,30 +80,29 @@ dependencies: - bzip2=1.0.8 - c-ares=1.28.1 - ca-certificates=2024.2.2 -- cachecontrol=0.14.0 - cached-property=1.5.2 - cached_property=1.5.2 -- cairo=1.16.0 +- cairo=1.18.0 - cctools_osx-64=986 - certifi=2024.2.2 - cffi=1.16.0 - 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=18.1.3 +- clang-18=18.1.3 +- clang_impl_osx-64=18.1.3 +- clang_osx-64=18.1.3 +- clangxx=18.1.3 +- clangxx_impl_osx-64=18.1.3 +- clangxx_osx-64=18.1.3 - click=8.1.7 - colorama=0.4.6 - comm=0.2.2 -- compiler-rt=17.0.6 -- compiler-rt_osx-64=17.0.6 +- compiler-rt=18.1.3 +- compiler-rt_osx-64=18.1.3 - conda-pack=0.7.0 -- contourpy=1.1.1 +- contourpy=1.2.1 - cryptography=42.0.5 -- curl=7.88.1 +- curl=8.7.1 - cutadapt=4.8 - cycler=0.12.1 - deblur=1.1.1 @@ -119,6 +120,7 @@ dependencies: - expat=2.6.2 - fastcluster=1.2.6 - fasttree=2.1.11 +- filelock=3.14.0 - flufl.lock=7.1 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 @@ -137,56 +139,57 @@ dependencies: - gettext=0.22.5 - gettext-tools=0.22.5 - gffutils=0.10.1 -- gfortran_impl_osx-64=11.4.0 -- gfortran_osx-64=11.4.0 -- globus-sdk=3.40.0 +- gfortran_impl_osx-64=12.3.0 +- gfortran_osx-64=12.3.0 +- globus-sdk=3.41.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 - graphlib-backport=1.0.3 - gsl=2.7 -- h5py=3.8.0 -- harfbuzz=6.0.0 -- hdf5=1.14.0 +- h5py=3.11.0 +- harfbuzz=8.4.0 +- hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.1b2 -- htslib=1.17 -- icu=70.1 +- htslib=1.20 +- icu=73.2 - idna=3.7 - ijson=3.2.3 - importlib-metadata=7.1.0 +- importlib-resources=6.4.0 +- importlib_metadata=7.1.0 - importlib_resources=6.4.0 - iniconfig=2.0.0 - interface_meta=1.3.0 - iow=1.0.5 - ipykernel=6.29.3 -- ipython=8.12.2 +- ipython=8.18.1 - ipython_genutils=0.2.0 - ipywidgets=8.1.2 -- iqtree=2.3.0 +- iqtree=2.3.3 - isa-l=2.31.0 -- isl=0.25 +- isl=0.26 - isoduration=20.11.0 - jedi=0.19.1 - jinja2=3.1.3 - joblib=1.4.0 -- jpeg=9e - jq=1.7.1 - jsonlines=3.0.0 - jsonpointer=2.4 -- jsonschema=4.21.1 +- jsonschema=4.22.0 - jsonschema-specifications=2023.12.1 -- jsonschema-with-format-nongpl=4.21.1 +- jsonschema-with-format-nongpl=4.22.0 - jupyter_client=7.4.9 -- jupyter_core=5.7.2 +- jupyter_core=5.7.1 - jupyter_events=0.10.0 - jupyter_server=2.14.0 - jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 - jupyterlab_widgets=3.0.10 - kiwisolver=1.4.5 -- krb5=1.20.1 -- lcms2=2.15 +- krb5=1.21.2 +- lcms2=2.16 - ld64_osx-64=711 - lerc=4.0.0 - libaec=1.1.3 @@ -197,69 +200,69 @@ dependencies: - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 -- libclang-cpp17=17.0.6 -- libcurl=7.88.1 +- libclang-cpp18.1=18.1.3 +- libcurl=8.7.1 - libcxx=16.0.6 -- libdeflate=1.17 +- libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 - libexpat=2.6.2 -- libffi=3.4.4 +- libffi=3.4.2 - libgettextpo=0.22.5 - libgettextpo-devel=0.22.5 - libgfortran=5.0.0 -- libgfortran-devel_osx-64=11.4.0 +- libgfortran-devel_osx-64=12.3.0 - libgfortran5=13.2.0 -- libglib=2.78.1 +- libglib=2.80.0 +- libhwloc=2.10.0 - libiconv=1.17 - libidn2=2.3.7 - libintl=0.22.5 - libintl-devel=0.22.5 +- libjpeg-turbo=3.0.0 - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 -- libllvm17=17.0.6 +- libllvm18=18.1.3 - libnghttp2=1.58.0 -- libopenblas=0.3.25 +- libopenblas=0.3.27 - libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 - libsqlite=3.45.3 - libssh2=1.11.0 -- libtiff=4.5.0 +- libtiff=4.6.0 - libunistring=0.9.10 - libwebp-base=1.4.0 -- libxcb=1.13 -- libxml2=2.10.3 -- libxslt=1.1.37 +- libxcb=1.15 +- libxml2=2.12.6 +- libxslt=1.1.39 - libzlib=1.2.13 - llvm-openmp=18.1.3 -- llvm-tools=17.0.6 -- llvmlite=0.41.1 -- lockfile=0.12.2 -- lxml=4.9.2 +- llvm-tools=18.1.3 +- llvmlite=0.42.0 +- lxml=5.2.1 - lz4=4.3.3 - lz4-c=1.9.4 - mafft=7.520 - make=4.3 - markupsafe=2.1.5 -- matplotlib=3.6.0 -- matplotlib-base=3.6.0 +- matplotlib=3.8.4 +- matplotlib-base=3.8.4 - matplotlib-inline=0.1.7 - mistune=3.0.2 - mpc=1.3.1 - mpfr=4.2.1 - mpi=1.0 -- msgpack-python=1.0.7 - munkres=1.1.4 - natsort=8.4.0 - nbclassic=1.0.0 - nbclient=0.10.0 -- nbconvert=7.16.3 -- nbconvert-core=7.16.3 -- nbconvert-pandoc=7.16.3 +- nbconvert=7.16.4 +- nbconvert-core=7.16.4 +- nbconvert-pandoc=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.0 +- ncbi-datasets-pylib=16.6.1 - ncbi-vdb=3.1.0 - ncurses=6.4.20240210 - nest-asyncio=1.6.0 @@ -267,25 +270,25 @@ dependencies: - nlopt=2.7.1 - notebook=6.5.5 - notebook-shim=0.2.4 -- numba=0.58.1 -- numpy=1.24.4 +- numba=0.59.1 +- numpy=1.26.4 - oniguruma=6.9.9 -- openjdk=21.0.3 -- openjpeg=2.5.0 -- openssl=3.2.1 +- openjdk=22.0.1 +- openjpeg=2.5.2 +- openssl=3.3.0 - overrides=7.7.0 - packaging=24.0 -- pandas=1.5.3 +- pandas=2.2.2 - pandoc=3.1.13 - pandocfilters=1.5.0 -- pango=1.50.14 +- pango=1.52.2 - paramiko=3.4.0 -- parsl=2023.12.4 +- parsl=2024.4.15 - parso=0.8.4 -- patsy=0.5.3 +- patsy=0.5.6 - pbzip2=1.1.13 - pcre=8.45 -- pcre2=10.40 +- pcre2=10.43 - perl=5.32.1 - perl-archive-tar=2.40 - perl-carp=1.50 @@ -310,16 +313,14 @@ dependencies: - pexpect=4.9.0 - pickleshare=0.7.5 - pigz=2.8 -- pillow=9.4.0 +- pillow=10.3.0 - pip=24.0 - pixman=0.43.4 - pkgutil-resolve-name=1.3.10 -- platformdirs=4.2.0 -- pluggy=1.4.0 -- pooch=1.8.1 +- platformdirs=4.2.1 +- pluggy=1.5.0 - prometheus_client=0.20.0 - prompt-toolkit=3.0.42 -- prompt_toolkit=3.0.42 - protobuf=3.20.3 - psutil=5.9.8 - pthread-stubs=0.4 @@ -335,14 +336,15 @@ dependencies: - pyobjc-framework-cocoa=10.2 - pyparsing=3.1.2 - pysocks=1.7.1 -- pytest=8.1.1 -- python=3.8.19 +- pytest=8.2.0 +- python=3.9.19 - python-dateutil=2.8.2 - python-fastjsonschema=2.19.1 - python-isal=1.6.1 - python-json-logger=2.0.7 +- python-tzdata=2024.1 - python-zlib-ng=0.4.3 -- python_abi=3.8 +- python_abi=3.9 - pytz=2024.1 - pyvcf3=1.0.3 - pyyaml=6.0.1 @@ -353,32 +355,33 @@ dependencies: - q2-dada2=2024.5.0.dev0 - q2-deblur=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca -- q2-diversity-lib=2024.5.0.dev0 +- q2-diversity=2024.5.0.dev0+4.gf6b6556 +- q2-diversity-lib=2024.5.0.dev0+6.gf6acf9f - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fragment-insertion=2024.5.0.dev0 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad - q2-mystery-stew=2024.5.0.dev0 - q2-phylogeny=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 +- q2cli=2024.5.0.dev0+1.gafe71da - q2galaxy=2024.5.0.dev0+2.ga124fa1 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa +- r-abind=1.4_5 - r-ade4=1.7_22 -- r-ape=5.7_1 +- r-ape=5.8 - r-askpass=1.2.0 - r-assertthat=0.2.1 - r-backports=1.4.1 -- r-base=4.2.2 +- r-base=4.3.3 - r-base64enc=0.1_3 - r-beeswarm=0.4.0 - r-bh=1.84.0_0 @@ -391,7 +394,7 @@ dependencies: - r-broom=1.0.5 - r-bslib=0.7.0 - r-cachem=1.0.8 -- r-cairo=1.6_0 +- r-cairo=1.6_2 - r-callr=3.7.6 - r-cellranger=1.1.0 - r-checkmate=2.3.1 @@ -404,13 +407,13 @@ dependencies: - r-conflicted=1.2.0 - r-cpp11=0.4.7 - r-crayon=1.5.2 -- r-curl=4.3.3 +- r-curl=5.1.0 - r-cvxr=1.0_12 - r-data.table=1.15.2 - r-dbi=1.2.2 -- r-dbplyr=2.4.0 +- r-dbplyr=2.5.0 - r-deldir=2.0_4 -- r-desctools=0.99.51 +- r-desctools=0.99.54 - r-digest=0.6.35 - r-doparallel=1.0.17 - r-dorng=1.8.6 @@ -420,9 +423,7 @@ dependencies: - r-e1071=1.7_14 - r-ecosolver=0.5.5 - r-ellipsis=0.3.2 -- r-emmeans=1.10.1 - r-energy=1.7_11 -- r-estimability=1.4.1 - r-evaluate=0.23 - r-exact=3.2 - r-expm=0.999_9 @@ -437,7 +438,7 @@ dependencies: - r-formatr=1.14 - r-formula=1.2_5 - r-frictionless=1.1.0 -- r-fs=1.6.3 +- r-fs=1.6.4 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 - r-gargle=1.5.2 @@ -445,7 +446,7 @@ dependencies: - r-generics=0.1.3 - r-getopt=1.20.4 - r-ggbeeswarm=0.7.2 -- r-ggplot2=3.5.0 +- r-ggplot2=3.5.1 - r-ggrastr=1.0.2 - r-ggrepel=0.9.5 - r-gld=2.6.6 @@ -455,8 +456,10 @@ dependencies: - r-googlesheets4=1.1.1 - r-gridextra=2.3 - r-gsl=2.1_8 -- r-gtable=0.3.4 +- r-gtable=0.3.5 +- r-gtools=3.9.5 - r-haven=2.5.4 +- r-here=1.0.1 - r-highr=0.10 - r-hmisc=5.1_2 - r-hms=1.1.3 @@ -466,7 +469,7 @@ dependencies: - r-httr=1.4.7 - r-hwriter=1.3.2.1 - r-ids=1.0.1 -- r-igraph=1.4.2 +- r-igraph=2.0.3 - r-interp=1.1_6 - r-irlba=2.3.5.1 - r-isoband=0.2.7 @@ -486,7 +489,7 @@ dependencies: - r-lmom=3.0 - r-lubridate=1.9.3 - r-magrittr=2.0.3 -- r-mass=7.3_60.0.1 +- r-mass=7.3_60 - r-matrix=1.6_5 - r-matrixstats=1.3.0 - r-memoise=2.0.1 @@ -494,13 +497,14 @@ dependencies: - r-mime=0.12 - r-minqa=1.2.6 - r-modelr=0.1.11 +- r-multcomp=1.4_25 - r-munsell=0.5.1 - r-mvtnorm=1.2_4 - r-nlme=3.1_164 - r-nloptr=2.0.3 - r-nnet=7.3_19 - r-numderiv=2016.8_1.1 -- r-openssl=2.1.1 +- r-openssl=2.1.2 - r-optparse=1.7.5 - r-osqp=0.6.3.2 - r-permute=0.9_7 @@ -519,7 +523,7 @@ dependencies: - r-ps=1.7.6 - r-purrr=1.0.2 - r-r6=2.5.1 -- r-ragg=1.2.5 +- r-ragg=1.3.0 - r-rappdirs=0.3.3 - r-rbibutils=2.2.16 - r-rcolorbrewer=1.1_3 @@ -530,7 +534,8 @@ dependencies: - r-rcppml=0.3.7 - r-rcppparallel=5.1.6 - r-rcppprogress=0.4.2 -- r-rcurl=1.98_1.12 +- r-rcpptoml=0.2.2 +- r-rcurl=1.98_1.14 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 @@ -539,33 +544,37 @@ dependencies: - r-rematch2=2.1.2 - r-reprex=2.1.0 - r-reshape2=1.4.4 +- r-reticulate=1.36.0 - r-rlang=1.1.3 -- r-rmarkdown=2.25 +- r-rmarkdown=2.26 - r-rmpfr=0.9_5 - r-rngtools=1.5.2 - r-rootsolve=1.8.2.4 - r-rpart=4.1.23 +- r-rprojroot=2.0.4 - r-rsqlite=2.3.4 - r-rstudioapi=0.16.0 - r-rsvd=1.0.5 - r-rtsne=0.17 - r-rvest=1.0.4 +- r-sandwich=3.1_0 - r-sass=0.4.9 - r-scales=1.3.0 - r-scs=3.2.4 - r-selectr=0.4_2 - r-sitmo=2.0.2 - r-snow=0.4_4 -- r-sp=2.1_3 -- r-stringi=1.7.12 +- r-sp=2.1_4 +- r-stringi=1.8.3 - r-stringr=1.5.1 -- r-survival=3.5_8 +- r-survival=3.6_4 - r-sys=3.4.2 - r-systemfonts=1.0.5 -- r-textshaping=0.3.6 +- r-textshaping=0.3.7 +- r-th.data=1.1_2 - r-tibble=3.2.1 - r-tidyr=1.3.1 -- r-tidyselect=1.2.0 +- r-tidyselect=1.2.1 - r-tidytree=0.4.6 - r-tidyverse=2.0.0 - r-timechange=0.3.0 @@ -582,26 +591,27 @@ dependencies: - r-vroom=1.6.5 - r-withr=3.0.0 - r-xfun=0.43 -- r-xml2=1.3.3 +- r-xml2=1.3.6 - r-xtable=1.8_4 - r-yaml=2.3.8 - r-yulab.utils=0.1.4 +- r-zoo=1.8_12 - raxml=8.2.13 - readline=8.2 -- referencing=0.34.0 +- referencing=0.35.0 - requests=2.31.0 - rescript=2024.5.0.dev0+3.g6e87cfe - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rpds-py=0.18.0 -- samtools=1.18 -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- samtools=1.20 +- 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=4.3.10 +- sepp=4.4.0 - setproctitle=1.3.3 - setuptools=69.5.1 - sigtool=0.1.3 @@ -611,13 +621,13 @@ dependencies: - sortmerna=2.0 - soupsieve=2.5 - stack_data=0.6.2 -- statsmodels=0.14.0 +- statsmodels=0.14.1 - tapi=1100.0.11 -- tbb=2021.10.0 +- tbb=2021.12.0 - tblib=3.0.0 - terminado=0.18.1 -- threadpoolctl=3.4.0 -- tinycss2=1.2.1 +- threadpoolctl=3.5.0 +- tinycss2=1.3.0 - tk=8.6.13 - tktable=2.10 - toml=0.10.2 @@ -627,41 +637,35 @@ dependencies: - tornado=6.4 - tqdm=4.66.2 - traitlets=5.9.0 -- typeguard=2.13.3 +- typeguard=4.2.1 - types-python-dateutil=2.9.0.20240316 - typing-extensions=4.11.0 - typing_extensions=4.11.0 - typing_utils=0.1.0 +- tzdata=2024a - tzlocal=2.1 - umap-learn=0.5.5 - unicodedata2=15.1.0 - unifrac=1.3 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - uri-template=1.3.0 - urllib3=1.26.18 - vsearch=2.22.1 - wcwidth=0.2.13 - webcolors=1.13 - webencodings=0.5.1 -- websocket-client=1.7.0 +- websocket-client=1.8.0 - wget=1.21.4 - wheel=0.43.0 - widgetsnbextension=4.0.10 - wrapt=1.16.0 - xmltodict=0.13.0 - xopen=2.0.1 -- xorg-kbproto=1.0.7 -- xorg-libice=1.0.10 -- xorg-libsm=1.2.3 -- xorg-libx11=1.8.4 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 -- xorg-libxt=1.3.0 -- xorg-xextproto=7.3.0 -- xorg-xproto=7.0.31 - xz=5.2.6 - yaml=0.2.5 -- yq=3.4.1 +- yq=3.4.3 - zeromq=4.3.5 - zipp=3.17.0 - zlib=1.2.13 diff --git a/2024.5/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml b/2024.5/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml index eb72ad4b..63676a2d 100644 --- a/2024.5/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml +++ b/2024.5/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml @@ -7,7 +7,7 @@ dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - _r-mutex=1.0.1 -- alsa-lib=1.2.8 +- alsa-lib=1.2.11 - altair=5.3.0 - anyio=4.3.0 - appdirs=1.4.4 @@ -21,60 +21,62 @@ dependencies: - atpublic=3.0.1 - attr=2.5.1 - attrs=23.2.0 -- backcall=0.2.0 - bcrypt=4.1.2 - beautifulsoup4=4.12.3 - bibtexparser=1.4.1 - binutils_impl_linux-64=2.40 -- bioconductor-ancombc=2.0.1 -- bioconductor-beachmat=2.14.0 -- bioconductor-biobase=2.58.0 -- bioconductor-biocbaseutils=1.0.0 -- bioconductor-biocgenerics=0.44.0 -- bioconductor-biocneighbors=1.16.0 -- bioconductor-biocparallel=1.32.5 -- bioconductor-biocsingular=1.14.0 -- bioconductor-biomformat=1.26.0 -- bioconductor-biostrings=2.66.0 -- bioconductor-dada2=1.26.0 +- bioconductor-ancombc=2.4.0 +- bioconductor-beachmat=2.18.0 +- bioconductor-biobase=2.62.0 +- bioconductor-biocbaseutils=1.4.0 +- bioconductor-biocgenerics=0.48.1 +- bioconductor-biocneighbors=1.20.0 +- bioconductor-biocparallel=1.36.0 +- bioconductor-biocsingular=1.18.0 +- bioconductor-biomformat=1.30.0 +- bioconductor-biostrings=2.70.1 +- bioconductor-bluster=1.12.0 +- bioconductor-dada2=1.30.0 - bioconductor-data-packages=20231203 -- bioconductor-decipher=2.26.0 -- bioconductor-decontam=1.18.0 -- bioconductor-delayedarray=0.24.0 -- bioconductor-delayedmatrixstats=1.20.0 -- bioconductor-dirichletmultinomial=1.40.0 -- bioconductor-genomeinfodb=1.34.9 -- bioconductor-genomeinfodbdata=1.2.9 -- bioconductor-genomicalignments=1.34.0 -- bioconductor-genomicranges=1.50.0 -- bioconductor-iranges=2.32.0 -- bioconductor-matrixgenerics=1.10.0 -- bioconductor-mia=1.6.0 -- bioconductor-multiassayexperiment=1.24.0 -- bioconductor-multtest=2.54.0 -- bioconductor-phyloseq=1.42.0 -- bioconductor-rhdf5=2.42.0 -- bioconductor-rhdf5filters=1.10.0 -- bioconductor-rhdf5lib=1.20.0 -- bioconductor-rhtslib=2.0.0 -- bioconductor-rsamtools=2.14.0 -- bioconductor-s4vectors=0.36.0 -- bioconductor-scaledmatrix=1.6.0 -- bioconductor-scater=1.26.0 -- bioconductor-scuttle=1.8.0 -- bioconductor-shortread=1.56.0 -- bioconductor-singlecellexperiment=1.20.0 -- bioconductor-sparsematrixstats=1.10.0 -- bioconductor-summarizedexperiment=1.28.0 -- bioconductor-treeio=1.22.0 -- bioconductor-treesummarizedexperiment=2.6.0 -- bioconductor-xvector=0.38.0 -- bioconductor-zlibbioc=1.44.0 -- biom-format=2.1.14 +- bioconductor-decipher=2.30.0 +- bioconductor-decontam=1.22.0 +- bioconductor-delayedarray=0.28.0 +- bioconductor-delayedmatrixstats=1.24.0 +- bioconductor-dirichletmultinomial=1.44.0 +- bioconductor-genomeinfodb=1.38.1 +- bioconductor-genomeinfodbdata=1.2.11 +- bioconductor-genomicalignments=1.38.0 +- bioconductor-genomicranges=1.54.1 +- bioconductor-iranges=2.36.0 +- bioconductor-matrixgenerics=1.14.0 +- bioconductor-mia=1.10.0 +- bioconductor-multiassayexperiment=1.28.0 +- bioconductor-multtest=2.58.0 +- bioconductor-phyloseq=1.46.0 +- bioconductor-rhdf5=2.46.1 +- bioconductor-rhdf5filters=1.14.1 +- bioconductor-rhdf5lib=1.24.0 +- bioconductor-rhtslib=2.4.0 +- bioconductor-rsamtools=2.18.0 +- bioconductor-s4arrays=1.2.0 +- bioconductor-s4vectors=0.40.2 +- bioconductor-scaledmatrix=1.10.0 +- bioconductor-scater=1.30.1 +- bioconductor-scuttle=1.12.0 +- bioconductor-shortread=1.60.0 +- bioconductor-singlecellexperiment=1.24.0 +- bioconductor-sparsearray=1.2.2 +- bioconductor-sparsematrixstats=1.14.0 +- bioconductor-summarizedexperiment=1.32.0 +- bioconductor-treeio=1.26.0 +- bioconductor-treesummarizedexperiment=2.10.0 +- bioconductor-xvector=0.42.0 +- bioconductor-zlibbioc=1.48.0 +- biom-format=2.1.15 - biopython=1.83 - blast=2.15.0 - bleach=6.1.0 -- bowtie2=2.5.1 +- bowtie2=2.5.3 - brotli=1.1.0 - brotli-bin=1.1.0 - brotli-python=1.1.0 @@ -82,10 +84,9 @@ dependencies: - bzip2=1.0.8 - c-ares=1.28.1 - ca-certificates=2024.2.2 -- cachecontrol=0.14.0 - cached-property=1.5.2 - cached_property=1.5.2 -- cairo=1.16.0 +- cairo=1.18.0 - certifi=2024.2.2 - cffi=1.16.0 - charset-normalizer=3.3.2 @@ -93,9 +94,9 @@ dependencies: - colorama=0.4.6 - comm=0.2.2 - conda-pack=0.7.0 -- contourpy=1.1.1 -- cryptography=39.0.0 -- curl=7.88.1 +- contourpy=1.2.1 +- cryptography=42.0.5 +- curl=8.7.1 - cutadapt=4.8 - cycler=0.12.1 - dbus=1.13.6 @@ -114,7 +115,7 @@ dependencies: - expat=2.6.2 - fastcluster=1.2.6 - fasttree=2.1.11 -- fftw=3.3.10 +- filelock=3.14.0 - flufl.lock=7.1 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 @@ -136,50 +137,49 @@ dependencies: - gffutils=0.10.1 - gfortran_impl_linux-64=13.2.0 - giflib=5.2.2 -- glib=2.78.1 -- glib-tools=2.78.1 -- globus-sdk=3.40.0 +- glib=2.80.0 +- glib-tools=2.80.0 +- globus-sdk=3.41.0 - glpk=5.0 - gmp=6.3.0 - graphite2=1.3.13 - graphlib-backport=1.0.3 - gsl=2.7 -- gst-plugins-base=1.21.3 -- gstreamer=1.21.3 -- gstreamer-orc=0.4.38 +- gst-plugins-base=1.24.1 +- gstreamer=1.24.1 - gxx_impl_linux-64=13.2.0 -- h5py=3.8.0 -- harfbuzz=6.0.0 -- hdf5=1.14.0 +- h5py=3.11.0 +- harfbuzz=8.4.0 +- hdf5=1.14.3 - hdmedians=0.14.2 - hmmer=3.1b2 -- htslib=1.17 -- icu=70.1 +- htslib=1.20 +- icu=73.2 - idna=3.7 - ijson=3.2.3 - importlib-metadata=7.1.0 +- importlib-resources=6.4.0 +- importlib_metadata=7.1.0 - importlib_resources=6.4.0 - iniconfig=2.0.0 - interface_meta=1.3.0 - iow=1.0.5 - ipykernel=6.29.3 -- ipython=8.12.2 +- ipython=8.18.1 - ipython_genutils=0.2.0 - ipywidgets=8.1.2 -- iqtree=2.3.0 +- iqtree=2.3.3 - isa-l=2.31.0 - isoduration=20.11.0 -- jack=1.9.22 - jedi=0.19.1 - jinja2=3.1.3 - joblib=1.4.0 -- jpeg=9e - jq=1.7.1 - jsonlines=3.0.0 - jsonpointer=2.4 -- jsonschema=4.21.1 +- jsonschema=4.22.0 - jsonschema-specifications=2023.12.1 -- jsonschema-with-format-nongpl=4.21.1 +- jsonschema-with-format-nongpl=4.22.0 - jupyter_client=7.4.9 - jupyter_core=5.7.2 - jupyter_events=0.10.0 @@ -190,9 +190,9 @@ dependencies: - kernel-headers_linux-64=2.6.32 - keyutils=1.6.1 - kiwisolver=1.4.5 -- krb5=1.20.1 +- krb5=1.21.2 - lame=3.100 -- lcms2=2.15 +- lcms2=2.16 - ld_impl_linux-64=2.40 - lerc=4.0.0 - libaec=1.1.3 @@ -202,17 +202,16 @@ dependencies: - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 -- libcap=2.66 +- libcap=2.69 - libcblas=3.9.0 -- libclang=15.0.7 -- libclang13=15.0.7 +- libclang-cpp15=15.0.7 +- libclang13=18.1.4 - libcups=2.3.3 -- libcurl=7.88.1 -- libdb=6.2.32 -- libdeflate=1.17 +- libcurl=8.7.1 +- libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 -- libevent=2.1.10 +- libevent=2.1.12 - libexpat=2.6.2 - libffi=3.4.2 - libflac=1.4.3 @@ -223,72 +222,70 @@ dependencies: - libgettextpo-devel=0.22.5 - libgfortran-ng=13.2.0 - libgfortran5=13.2.0 -- libglib=2.78.1 +- libglib=2.80.0 - libgomp=13.2.0 -- libgpg-error=1.48 -- libhwloc=2.9.1 +- libgpg-error=1.49 +- libhwloc=2.10.0 - libiconv=1.17 - libidn2=2.3.7 +- libjpeg-turbo=3.0.0 - liblapack=3.9.0 - liblapacke=3.9.0 - libllvm14=14.0.6 - libllvm15=15.0.7 -- libnghttp2=1.52.0 +- libllvm18=18.1.4 +- libnghttp2=1.58.0 - libnsl=2.0.1 - libogg=1.3.4 -- libopenblas=0.3.25 +- libopenblas=0.3.27 - libopus=1.3.1 - libpng=1.6.43 -- libpq=15.1 +- libpq=16.2 - libprotobuf=3.20.3 - libsanitizer=13.2.0 - libsndfile=1.2.2 - libsodium=1.0.18 - libsqlite=3.45.3 -- libssh2=1.10.0 +- libssh2=1.11.0 - libstdcxx-devel_linux-64=13.2.0 - libstdcxx-ng=13.2.0 -- libsystemd0=252 -- libtiff=4.5.0 -- libtool=2.4.7 -- libudev1=253 +- libsystemd0=255 +- libtiff=4.6.0 - libunistring=0.9.10 - libuuid=2.38.1 - libvorbis=1.3.7 - libwebp-base=1.4.0 -- libxcb=1.13 +- libxcb=1.15 - libxcrypt=4.4.36 -- libxkbcommon=1.5.0 -- libxml2=2.10.3 -- libxslt=1.1.37 +- libxkbcommon=1.7.0 +- libxml2=2.12.6 +- libxslt=1.1.39 - libzlib=1.2.13 -- llvmlite=0.41.1 -- lockfile=0.12.2 -- lxml=4.9.2 +- llvmlite=0.42.0 +- lxml=5.2.1 - lz4=4.3.3 - lz4-c=1.9.4 - mafft=7.520 - make=4.3 - markupsafe=2.1.5 -- matplotlib=3.6.0 -- matplotlib-base=3.6.0 +- matplotlib=3.8.4 +- matplotlib-base=3.8.4 - matplotlib-inline=0.1.7 - mistune=3.0.2 - mpfr=4.2.1 - mpg123=1.32.6 - mpi=1.0 -- msgpack-python=1.0.7 - munkres=1.1.4 -- mysql-common=8.0.32 -- mysql-libs=8.0.32 +- mysql-common=8.3.0 +- mysql-libs=8.3.0 - natsort=8.4.0 - nbclassic=1.0.0 - nbclient=0.10.0 -- nbconvert=7.16.3 -- nbconvert-core=7.16.3 -- nbconvert-pandoc=7.16.3 +- nbconvert=7.16.4 +- nbconvert-core=7.16.4 +- nbconvert-pandoc=7.16.4 - nbformat=5.10.4 -- ncbi-datasets-pylib=16.6.0 +- ncbi-datasets-pylib=16.6.1 - ncbi-vdb=3.1.0 - ncurses=6.4.20240210 - nest-asyncio=1.6.0 @@ -298,25 +295,25 @@ dependencies: - notebook-shim=0.2.4 - nspr=4.35 - nss=3.98 -- numba=0.58.1 -- numpy=1.24.4 +- numba=0.59.1 +- numpy=1.26.4 - oniguruma=6.9.9 -- openjdk=17.0.3 -- openjpeg=2.5.0 -- openssl=1.1.1w +- openjdk=22.0.1 +- openjpeg=2.5.2 +- openssl=3.3.0 - overrides=7.7.0 - packaging=24.0 -- pandas=1.5.3 +- pandas=2.2.2 - pandoc=3.1.13 - pandocfilters=1.5.0 -- pango=1.50.14 +- pango=1.52.2 - paramiko=3.4.0 -- parsl=2023.12.4 +- parsl=2024.4.15 - parso=0.8.4 -- patsy=0.5.3 +- patsy=0.5.6 - pbzip2=1.1.13 - pcre=8.45 -- pcre2=10.40 +- pcre2=10.43 - perl=5.32.1 - perl-archive-tar=2.40 - perl-carp=1.50 @@ -341,22 +338,20 @@ dependencies: - pexpect=4.9.0 - pickleshare=0.7.5 - pigz=2.8 -- pillow=9.4.0 +- pillow=10.3.0 - pip=24.0 - pixman=0.43.2 - pkgutil-resolve-name=1.3.10 -- platformdirs=4.2.0 -- pluggy=1.4.0 +- platformdirs=4.2.1 +- pluggy=1.5.0 - ply=3.11 -- pooch=1.8.1 - prometheus_client=0.20.0 - prompt-toolkit=3.0.42 -- prompt_toolkit=3.0.42 - protobuf=3.20.3 - psutil=5.9.8 - pthread-stubs=0.4 - ptyprocess=0.7.0 -- pulseaudio=16.1 +- pulseaudio-client=17.0 - pure_eval=0.2.2 - pycparser=2.22 - pyfaidx=0.8.1.1 @@ -365,17 +360,18 @@ dependencies: - pynacl=1.5.0 - pynndescent=0.5.12 - pyparsing=3.1.2 -- pyqt=5.15.7 -- pyqt5-sip=12.11.0 +- pyqt=5.15.9 +- pyqt5-sip=12.12.2 - pysocks=1.7.1 -- pytest=8.1.1 -- python=3.8.15 +- pytest=8.2.0 +- python=3.9.19 - python-dateutil=2.8.2 - python-fastjsonschema=2.19.1 - python-isal=1.6.1 - python-json-logger=2.0.7 +- python-tzdata=2024.1 - python-zlib-ng=0.4.3 -- python_abi=3.8 +- python_abi=3.9 - pytz=2024.1 - pyvcf3=1.0.3 - pyyaml=6.0.1 @@ -386,33 +382,34 @@ dependencies: - q2-dada2=2024.5.0.dev0 - q2-deblur=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca -- q2-diversity-lib=2024.5.0.dev0 +- q2-diversity=2024.5.0.dev0+4.gf6b6556 +- q2-diversity-lib=2024.5.0.dev0+6.gf6acf9f - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fragment-insertion=2024.5.0.dev0 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad - q2-mystery-stew=2024.5.0.dev0 - q2-phylogeny=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 +- q2cli=2024.5.0.dev0+1.gafe71da - q2galaxy=2024.5.0.dev0+2.ga124fa1 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 -- qt-main=5.15.6 +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa +- qt-main=5.15.8 +- r-abind=1.4_5 - r-ade4=1.7_22 -- r-ape=5.7_1 +- r-ape=5.8 - r-askpass=1.2.0 - r-assertthat=0.2.1 - r-backports=1.4.1 -- r-base=4.2.2 +- r-base=4.3.3 - r-base64enc=0.1_3 - r-beeswarm=0.4.0 - r-bh=1.84.0_0 @@ -425,7 +422,7 @@ dependencies: - r-broom=1.0.5 - r-bslib=0.7.0 - r-cachem=1.0.8 -- r-cairo=1.6_0 +- r-cairo=1.6_2 - r-callr=3.7.6 - r-cellranger=1.1.0 - r-checkmate=2.3.0 @@ -438,13 +435,13 @@ dependencies: - r-conflicted=1.2.0 - r-cpp11=0.4.7 - r-crayon=1.5.2 -- r-curl=4.3.3 +- r-curl=5.1.0 - r-cvxr=1.0_12 - r-data.table=1.15.2 - r-dbi=1.2.2 -- r-dbplyr=2.4.0 +- r-dbplyr=2.5.0 - r-deldir=2.0_4 -- r-desctools=0.99.51 +- r-desctools=0.99.54 - r-digest=0.6.35 - r-doparallel=1.0.17 - r-dorng=1.8.6 @@ -454,9 +451,7 @@ dependencies: - r-e1071=1.7_14 - r-ecosolver=0.5.5 - r-ellipsis=0.3.2 -- r-emmeans=1.10.1 - r-energy=1.7_11 -- r-estimability=1.4.1 - r-evaluate=0.23 - r-exact=3.2 - r-expm=0.999_9 @@ -471,7 +466,7 @@ dependencies: - r-formatr=1.14 - r-formula=1.2_5 - r-frictionless=1.1.0 -- r-fs=1.6.3 +- r-fs=1.6.4 - r-futile.logger=1.4.3 - r-futile.options=1.0.1 - r-gargle=1.5.2 @@ -479,7 +474,7 @@ dependencies: - r-generics=0.1.3 - r-getopt=1.20.4 - r-ggbeeswarm=0.7.2 -- r-ggplot2=3.5.0 +- r-ggplot2=3.5.1 - r-ggrastr=1.0.2 - r-ggrepel=0.9.5 - r-gld=2.6.6 @@ -489,8 +484,10 @@ dependencies: - r-googlesheets4=1.1.1 - r-gridextra=2.3 - r-gsl=2.1_8 -- r-gtable=0.3.4 +- r-gtable=0.3.5 +- r-gtools=3.9.5 - r-haven=2.5.4 +- r-here=1.0.1 - r-highr=0.10 - r-hmisc=5.1_2 - r-hms=1.1.3 @@ -500,7 +497,7 @@ dependencies: - r-httr=1.4.7 - r-hwriter=1.3.2.1 - r-ids=1.0.1 -- r-igraph=1.4.2 +- r-igraph=2.0.3 - r-interp=1.1_6 - r-irlba=2.3.5.1 - r-isoband=0.2.7 @@ -520,7 +517,7 @@ dependencies: - r-lmom=3.0 - r-lubridate=1.9.3 - r-magrittr=2.0.3 -- r-mass=7.3_60.0.1 +- r-mass=7.3_60 - r-matrix=1.6_5 - r-matrixstats=1.3.0 - r-memoise=2.0.1 @@ -528,13 +525,14 @@ dependencies: - r-mime=0.12 - r-minqa=1.2.6 - r-modelr=0.1.11 +- r-multcomp=1.4_25 - r-munsell=0.5.1 - r-mvtnorm=1.2_4 - r-nlme=3.1_164 - r-nloptr=2.0.3 - r-nnet=7.3_19 - r-numderiv=2016.8_1.1 -- r-openssl=2.0.5 +- r-openssl=2.1.2 - r-optparse=1.7.5 - r-osqp=0.6.3.2 - r-permute=0.9_7 @@ -553,7 +551,7 @@ dependencies: - r-ps=1.7.6 - r-purrr=1.0.2 - r-r6=2.5.1 -- r-ragg=1.2.5 +- r-ragg=1.3.0 - r-rappdirs=0.3.3 - r-rbibutils=2.2.16 - r-rcolorbrewer=1.1_3 @@ -564,7 +562,8 @@ dependencies: - r-rcppml=0.3.7 - r-rcppparallel=5.1.6 - r-rcppprogress=0.4.2 -- r-rcurl=1.98_1.12 +- r-rcpptoml=0.2.2 +- r-rcurl=1.98_1.14 - r-rdpack=2.6 - r-readr=2.1.5 - r-readxl=1.4.3 @@ -573,33 +572,37 @@ dependencies: - r-rematch2=2.1.2 - r-reprex=2.1.0 - r-reshape2=1.4.4 +- r-reticulate=1.36.0 - r-rlang=1.1.3 -- r-rmarkdown=2.25 +- r-rmarkdown=2.26 - r-rmpfr=0.9_5 - r-rngtools=1.5.2 - r-rootsolve=1.8.2.4 - r-rpart=4.1.23 +- r-rprojroot=2.0.4 - r-rsqlite=2.3.4 - r-rstudioapi=0.16.0 - r-rsvd=1.0.5 - r-rtsne=0.17 - r-rvest=1.0.4 +- r-sandwich=3.1_0 - r-sass=0.4.9 - r-scales=1.3.0 - r-scs=3.2.4 - r-selectr=0.4_2 - r-sitmo=2.0.2 - r-snow=0.4_4 -- r-sp=2.1_3 -- r-stringi=1.7.12 +- r-sp=2.1_4 +- r-stringi=1.8.3 - r-stringr=1.5.1 -- r-survival=3.5_8 +- r-survival=3.6_4 - r-sys=3.4.2 - r-systemfonts=1.0.5 -- r-textshaping=0.3.6 +- r-textshaping=0.3.7 +- r-th.data=1.1_2 - r-tibble=3.2.1 - r-tidyr=1.3.1 -- r-tidyselect=1.2.0 +- r-tidyselect=1.2.1 - r-tidytree=0.4.6 - r-tidyverse=2.0.0 - r-timechange=0.3.0 @@ -616,27 +619,28 @@ dependencies: - r-vroom=1.6.5 - r-withr=3.0.0 - r-xfun=0.43 -- r-xml2=1.3.3 +- r-xml2=1.3.6 - r-xtable=1.8_4 - r-yaml=2.3.8 - r-yulab.utils=0.1.4 +- r-zoo=1.8_12 - raxml=8.2.13 - readline=8.2 -- referencing=0.34.0 +- referencing=0.35.0 - requests=2.31.0 - rescript=2024.5.0.dev0+3.g6e87cfe - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rpds-py=0.18.0 -- samtools=1.18 -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- samtools=1.20 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 - seaborn=0.12.2 - seaborn-base=0.12.2 - sed=4.8 - send2trash=1.8.3 -- sepp=4.3.10 +- sepp=4.4.0 - setproctitle=1.3.3 - setuptools=69.5.1 - simplejson=3.19.2 @@ -646,13 +650,13 @@ dependencies: - sortmerna=2.0 - soupsieve=2.5 - stack_data=0.6.2 -- statsmodels=0.14.0 +- statsmodels=0.14.1 - sysroot_linux-64=2.12 -- tbb=2021.9.0 +- tbb=2021.12.0 - tblib=3.0.0 - terminado=0.18.1 -- threadpoolctl=3.4.0 -- tinycss2=1.2.1 +- threadpoolctl=3.5.0 +- tinycss2=1.3.0 - tk=8.6.13 - tktable=2.10 - toml=0.10.2 @@ -662,24 +666,25 @@ dependencies: - tornado=6.4 - tqdm=4.66.2 - traitlets=5.9.0 -- typeguard=2.13.3 +- typeguard=4.2.1 - types-python-dateutil=2.9.0.20240316 - typing-extensions=4.11.0 - typing_extensions=4.11.0 - typing_utils=0.1.0 +- tzdata=2024a - tzlocal=2.1 - umap-learn=0.5.5 - unicodedata2=15.1.0 - unifrac=1.3 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - uri-template=1.3.0 - urllib3=1.26.18 - vsearch=2.22.1 - wcwidth=0.2.13 - webcolors=1.13 - webencodings=0.5.1 -- websocket-client=1.7.0 -- wget=1.20.3 +- websocket-client=1.8.0 +- wget=1.21.4 - wheel=0.43.0 - widgetsnbextension=4.0.10 - wrapt=1.16.0 @@ -688,30 +693,31 @@ dependencies: - xcb-util-keysyms=0.4.0 - xcb-util-renderutil=0.3.9 - xcb-util-wm=0.4.1 -- xkeyboard-config=2.38 +- xkeyboard-config=2.41 - xmltodict=0.13.0 - xopen=2.0.1 - xorg-fixesproto=5.0 - xorg-inputproto=2.3.2 - xorg-kbproto=1.0.7 -- xorg-libice=1.0.10 -- xorg-libsm=1.2.3 -- xorg-libx11=1.8.4 +- xorg-libice=1.1.1 +- xorg-libsm=1.2.4 +- xorg-libx11=1.8.9 - xorg-libxau=1.0.11 - xorg-libxdmcp=1.1.3 - xorg-libxext=1.3.4 - xorg-libxfixes=5.0.3 - xorg-libxi=1.7.10 -- xorg-libxrender=0.9.10 +- xorg-libxrender=0.9.11 - xorg-libxt=1.3.0 - xorg-libxtst=1.2.3 - xorg-recordproto=1.14.2 - xorg-renderproto=0.11.1 - xorg-xextproto=7.3.0 +- xorg-xf86vidmodeproto=2.3.1 - xorg-xproto=7.0.31 - xz=5.2.6 - yaml=0.2.5 -- yq=3.4.1 +- yq=3.4.3 - zeromq=4.3.5 - zipp=3.17.0 - zlib=1.2.13 diff --git a/2024.5/amplicon/passed/seed-environment-conda.yml b/2024.5/amplicon/passed/seed-environment-conda.yml index d10cf55a..f2879c8e 100644 --- a/2024.5/amplicon/passed/seed-environment-conda.yml +++ b/2024.5/amplicon/passed/seed-environment-conda.yml @@ -23,26 +23,26 @@ dependencies: - q2-dada2=2024.5.0.dev0 - q2-deblur=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity-lib=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca +- q2-diversity-lib=2024.5.0.dev0+6.gf6acf9f +- q2-diversity=2024.5.0.dev0+4.gf6b6556 - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fragment-insertion=2024.5.0.dev0 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad - q2-mystery-stew=2024.5.0.dev0 - q2-phylogeny=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 +- q2cli=2024.5.0.dev0+1.gafe71da - q2galaxy=2024.5.0.dev0+2.ga124fa1 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa - r-base=4.3.3 - r-reticulate=1.36.0 - rescript=2024.5.0.dev0+3.g6e87cfe diff --git a/2024.5/amplicon/staged/seed-environment-conda.yml b/2024.5/amplicon/staged/seed-environment-conda.yml index e87d28b1..a32db4cb 100644 --- a/2024.5/amplicon/staged/seed-environment-conda.yml +++ b/2024.5/amplicon/staged/seed-environment-conda.yml @@ -4,51 +4,53 @@ channels: - bioconda - defaults dependencies: -- biom-format=2.1.14 -- h5py=3.8.0 -- hdf5=1.14.0 +- biom-format=2.1.15 +- h5py=3.11.0 +- hdf5=1.14.3 - mafft=7.520 -- matplotlib=3.6.0 +- matplotlib=3.8.4 - notebook=6.5.5 -- numpy=1.24.4 -- pandas=1.5.3 -- parsl=2023.12.04 -- patsy=0.5.3 -- pillow=9.4.0 -- python=3.8 +- numpy=1.26.4 +- pandas=2.2.2 +- parsl=2024.4.15 +- patsy=0.5.6 +- pillow=10.3.0 +- python=3.9.19 +- python_abi=3.9 - q2-alignment=2024.5.0.dev0+1.g3a9c58b - q2-composition=2024.5.0.dev0 - q2-cutadapt=2024.5.0.dev0 - q2-dada2=2024.5.0.dev0 - q2-deblur=2024.5.0.dev0 - q2-demux=2024.5.0.dev0 -- q2-diversity-lib=2024.5.0.dev0 -- q2-diversity=2024.5.0.dev0+1.g99a0cca +- q2-diversity-lib=2024.5.0.dev0+6.gf6acf9f +- q2-diversity=2024.5.0.dev0+4.gf6b6556 - q2-emperor=2024.5.0.dev0 -- q2-feature-classifier=2024.5.0.dev0 -- q2-feature-table=2024.5.0.dev0+2.g65222bd +- q2-feature-classifier=2024.5.0.dev0+1.g0efbd37 +- q2-feature-table=2024.5.0.dev0+3.g85719af - q2-fragment-insertion=2024.5.0.dev0 -- q2-longitudinal=2024.5.0.dev0 -- q2-metadata=2024.5.0.dev0 +- q2-longitudinal=2024.5.0.dev0+1.g438df87 +- q2-metadata=2024.5.0.dev0+1.g2766cad - q2-mystery-stew=2024.5.0.dev0 - q2-phylogeny=2024.5.0.dev0 -- q2-quality-control=2024.5.0.dev0 +- q2-quality-control=2024.5.0.dev0+1.gf23ff9e - q2-quality-filter=2024.5.0.dev0 -- q2-sample-classifier=2024.5.0.dev0 -- q2-taxa=2024.5.0.dev0 -- q2-types=2024.5.0.dev0+5.gd24a69d +- q2-sample-classifier=2024.5.0.dev0+8.gc4e186c +- q2-taxa=2024.5.0.dev0+1.g127c848 +- q2-types=2024.5.0.dev0+6.g8551927 - q2-vsearch=2024.5.0.dev0 -- q2cli=2024.5.0.dev0 +- q2cli=2024.5.0.dev0+1.gafe71da - q2galaxy=2024.5.0.dev0+2.ga124fa1 -- q2templates=2024.5.0.dev0 -- qiime2=2024.5.0.dev0+2.g27f5ec0 -- r-base=4.2.2 +- q2templates=2024.5.0.dev0+1.g9aff160 +- qiime2=2024.5.0.dev0+4.gc35a5aa +- r-base=4.3.3 +- r-reticulate=1.36.0 - rescript=2024.5.0.dev0+3.g6e87cfe -- scikit-bio=0.5.8 -- scikit-learn=0.24.1 -- scipy=1.10.0 +- scikit-bio=0.6.0 +- scikit-learn=1.4.2 +- scipy=1.13.0 - seaborn=0.12.2 -- unifrac-binaries=1.3.2 +- unifrac-binaries=1.4 - unifrac=1.3 extras: variant_override: