From 826d8af5ea54a6d12a3163a9e8fa9cf62de4aa6e Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Tue, 17 Dec 2024 12:16:02 -0700 Subject: [PATCH 1/2] test update of biom dependency --- 2025.4/amplicon/passed/seed-environment-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/2025.4/amplicon/passed/seed-environment-conda.yml b/2025.4/amplicon/passed/seed-environment-conda.yml index ed18387d..8e83c4fd 100644 --- a/2025.4/amplicon/passed/seed-environment-conda.yml +++ b/2025.4/amplicon/passed/seed-environment-conda.yml @@ -3,7 +3,7 @@ channels: - conda-forge - bioconda dependencies: -- biom-format=2.1.15 +- biom-format=2.1.16 - h5py=3.11.0 - hdf5=1.14.3 - mafft=7.526 From 2b749ae183acbcc3d04b9951f2561dc5b8263780 Mon Sep 17 00:00:00 2001 From: q2d2 Date: Wed, 18 Dec 2024 17:40:26 +0000 Subject: [PATCH 2/2] Update conda environments (update-biom) --- .../qiime2-amplicon-macos-latest-conda.yml | 18 +++++++++--------- .../qiime2-amplicon-ubuntu-latest-conda.yml | 14 +++++++------- .../amplicon/staged/seed-environment-conda.yml | 2 +- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml b/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml index 561dab5e..6fdfb97f 100644 --- a/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml +++ b/2025.4/amplicon/passed/qiime2-amplicon-macos-latest-conda.yml @@ -17,7 +17,7 @@ dependencies: - astor=0.8.1 - asttokens=3.0.0 - atpublic=5.0 -- attrs=24.2.0 +- attrs=24.3.0 - bcrypt=4.2.1 - beautifulsoup4=4.12.3 - bibtexparser=1.4.2 @@ -33,7 +33,7 @@ dependencies: - bioconductor-biostrings=2.70.1 - bioconductor-bluster=1.12.0 - bioconductor-dada2=1.30.0 -- bioconductor-data-packages=20231203 +- bioconductor-data-packages=20241103 - bioconductor-decipher=2.30.0 - bioconductor-decontam=1.22.0 - bioconductor-delayedarray=0.28.0 @@ -68,7 +68,7 @@ dependencies: - bioconductor-treesummarizedexperiment=2.10.0 - bioconductor-xvector=0.42.0 - bioconductor-zlibbioc=1.48.0 -- biom-format=2.1.15 +- biom-format=2.1.16 - biopython=1.84 - blast=2.16.0 - bleach=6.2.0 @@ -84,7 +84,7 @@ dependencies: - cached_property=1.5.2 - cairo=1.18.0 - cctools_osx-64=986 -- certifi=2024.8.30 +- certifi=2024.12.14 - cffi=1.17.1 - chardet=5.2.0 - charset-normalizer=3.4.0 @@ -189,7 +189,7 @@ dependencies: - jsonschema-with-format-nongpl=4.23.0 - jupyter_client=7.4.9 - jupyter_core=5.7.2 -- jupyter_events=0.10.0 +- jupyter_events=0.11.0 - jupyter_server=2.14.2 - jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 @@ -209,7 +209,7 @@ dependencies: - libcblas=3.9.0 - libclang-cpp18.1=18.1.7 - libcurl=8.8.0 -- libcxx=19.1.5 +- libcxx=19.1.6 - libdeflate=1.20 - libedit=3.1.20191231 - libev=4.33 @@ -247,7 +247,7 @@ dependencies: - libxml2=2.12.7 - libxslt=1.1.39 - libzlib=1.2.13 -- llvm-openmp=19.1.5 +- llvm-openmp=19.1.6 - llvm-tools=18.1.7 - llvmlite=0.42.0 - lxml=5.2.2 @@ -270,7 +270,7 @@ dependencies: - munkres=1.1.4 - muscle=3.8.1551 - mypy_extensions=1.0.0 -- narwhals=1.18.3 +- narwhals=1.18.4 - natsort=8.4.0 - nbclassic=1.1.0 - nbclient=0.10.1 @@ -403,7 +403,7 @@ dependencies: - qiime2=2025.4.0.dev0+5.gdb970dd - r-abind=1.4_5 - r-ade4=1.7_22 -- r-ape=5.8 +- r-ape=5.8_1 - r-askpass=1.2.1 - r-assertthat=0.2.1 - r-backports=1.5.0 diff --git a/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml b/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml index d2386056..3292d094 100644 --- a/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml +++ b/2025.4/amplicon/passed/qiime2-amplicon-ubuntu-latest-conda.yml @@ -20,7 +20,7 @@ dependencies: - asttokens=3.0.0 - atpublic=5.0 - attr=2.5.1 -- attrs=24.2.0 +- attrs=24.3.0 - bcrypt=4.2.1 - beautifulsoup4=4.12.3 - bibtexparser=1.4.2 @@ -37,7 +37,7 @@ dependencies: - bioconductor-biostrings=2.70.1 - bioconductor-bluster=1.12.0 - bioconductor-dada2=1.30.0 -- bioconductor-data-packages=20231203 +- bioconductor-data-packages=20241103 - bioconductor-decipher=2.30.0 - bioconductor-decontam=1.22.0 - bioconductor-delayedarray=0.28.0 @@ -72,7 +72,7 @@ dependencies: - bioconductor-treesummarizedexperiment=2.10.0 - bioconductor-xvector=0.42.0 - bioconductor-zlibbioc=1.48.0 -- biom-format=2.1.15 +- biom-format=2.1.16 - biopython=1.84 - blast=2.16.0 - bleach=6.2.0 @@ -87,7 +87,7 @@ dependencies: - cached-property=1.5.2 - cached_property=1.5.2 - cairo=1.18.0 -- certifi=2024.8.30 +- certifi=2024.12.14 - cffi=1.17.1 - chardet=5.2.0 - charset-normalizer=3.4.0 @@ -189,7 +189,7 @@ dependencies: - jsonschema-with-format-nongpl=4.23.0 - jupyter_client=7.4.9 - jupyter_core=5.7.2 -- jupyter_events=0.10.0 +- jupyter_events=0.11.0 - jupyter_server=2.14.2 - jupyter_server_terminals=0.5.3 - jupyterlab_pygments=0.3.0 @@ -296,7 +296,7 @@ dependencies: - mypy_extensions=1.0.0 - mysql-common=8.3.0 - mysql-libs=8.3.0 -- narwhals=1.18.3 +- narwhals=1.18.4 - natsort=8.4.0 - nbclassic=1.1.0 - nbclient=0.10.1 @@ -434,7 +434,7 @@ dependencies: - qt-main=5.15.8 - r-abind=1.4_5 - r-ade4=1.7_22 -- r-ape=5.8 +- r-ape=5.8_1 - r-askpass=1.2.1 - r-assertthat=0.2.1 - r-backports=1.5.0 diff --git a/2025.4/amplicon/staged/seed-environment-conda.yml b/2025.4/amplicon/staged/seed-environment-conda.yml index 8830df18..d6643667 100644 --- a/2025.4/amplicon/staged/seed-environment-conda.yml +++ b/2025.4/amplicon/staged/seed-environment-conda.yml @@ -3,7 +3,7 @@ channels: - conda-forge - bioconda dependencies: -- biom-format=2.1.15 +- biom-format=2.1.16 - h5py=3.11.0 - hdf5=1.14.3 - mafft=7.526