feat: update github CI workflows and config options #3
snakemake-tests.yml
on: pull_request
snakemake-tests
/
Formatting
1m 40s
snakemake-tests
/
Linting
41s
snakemake-tests
/
Testing
6m 22s
Annotations
15 warnings
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snakemake-tests / Linting
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, conda-incubator/setup-miniconda@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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snakemake-tests / Linting
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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snakemake-tests / Formatting
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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snakemake-tests / Testing
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, conda-incubator/setup-miniconda@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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snakemake-tests / Testing
warning libmamba [bzip2-1.0.8-hda65f42_9] The following files were already present in the environment:
- bin/bunzip2
- bin/bzcat
- bin/bzcmp
- bin/bzdiff
- bin/bzegrep
- bin/bzfgrep
- bin/bzgrep
- bin/bzip2
- bin/bzip2recover
- bin/bzless
- bin/bzmore
- include/bzlib.h
- lib/libbz2.a
- lib/libbz2.so
- lib/libbz2.so.1.0
- lib/libbz2.so.1.0.8
- share/man/man1/bzcmp.1
- share/man/man1/bzdiff.1
- share/man/man1/bzegrep.1
- share/man/man1/bzfgrep.1
- share/man/man1/bzgrep.1
- share/man/man1/bzip2.1
- share/man/man1/bzless.1
- share/man/man1/bzmore.1
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snakemake-tests / Testing
warning libmamba [libgcc-15.2.0-he0feb66_18] The following files were already present in the environment:
- lib/libatomic.so
- lib/libatomic.so.1
- lib/libatomic.so.1.2.0
- lib/libgcc_s.so
- lib/libgcc_s.so.1
- lib/libitm.so
- lib/libitm.so.1
- lib/libitm.so.1.0.0
- lib/libquadmath.so
- lib/libquadmath.so.0
- lib/libquadmath.so.0.0.0
- share/info/libgomp.info
- share/info/libquadmath.info
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION
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snakemake-tests / Testing
warning libmamba [ld_impl_linux-64-2.45.1-default_hbd61a6d_101] The following files were already present in the environment:
- bin/x86_64-conda-linux-gnu-ld
- x86_64-conda-linux-gnu/bin/ld
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snakemake-tests / Testing
warning libmamba [zstd-1.5.7-hb78ec9c_6] The following files were already present in the environment:
- bin/unzstd
- bin/zstd
- bin/zstdcat
- bin/zstdgrep
- bin/zstdless
- bin/zstdmt
- etc/conda/test-files/zstd/1/cf_test/CMakeLists.txt
- include/zdict.h
- include/zstd.h
- include/zstd_errors.h
- lib/cmake/zstd/zstdConfig.cmake
- lib/cmake/zstd/zstdConfigVersion.cmake
- lib/cmake/zstd/zstdTargets-release.cmake
- lib/cmake/zstd/zstdTargets.cmake
- lib/libzstd.so
- lib/libzstd.so.1
- lib/libzstd.so.1.5.7
- lib/pkgconfig/libzstd.pc
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snakemake-tests / Testing
warning libmamba [_openmp_mutex-4.5-20_gnu] The following files were already present in the environment:
- lib/libgomp.so.1
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snakemake-tests / Testing
warning libmamba [tzdata-2025c-hc9c84f9_1] The following files were already present in the environment:
- share/zoneinfo/Africa/Abidjan
- share/zoneinfo/Africa/Accra
- share/zoneinfo/Africa/Addis_Ababa
- share/zoneinfo/Africa/Algiers
- share/zoneinfo/Africa/Asmara
- share/zoneinfo/Africa/Asmera
- share/zoneinfo/Africa/Bamako
- share/zoneinfo/Africa/Bangui
- share/zoneinfo/Africa/Banjul
- share/zoneinfo/Africa/Bissau
- share/zoneinfo/Africa/Blantyre
- share/zoneinfo/Africa/Brazzaville
- share/zoneinfo/Africa/Bujumbura
- share/zoneinfo/Africa/Cairo
- share/zoneinfo/Africa/Casablanca
- share/zoneinfo/Africa/Ceuta
- share/zoneinfo/Africa/Conakry
- share/zoneinfo/Africa/Dakar
- share/zoneinfo/Africa/Dar_es_Salaam
- share/zoneinfo/Africa/Djibouti
- share/zoneinfo/Africa/Douala
- share/zoneinfo/Africa/El_Aaiun
- share/zoneinfo/Africa/Freetown
- share/zoneinfo/Africa/Gaborone
- share/zoneinfo/Africa/Harare
- share/zoneinfo/Africa/Johannesburg
- share/zoneinfo/Africa/Juba
- share/zoneinfo/Africa/Kampala
- share/zoneinfo/Africa/Khartoum
- share/zoneinfo/Africa/Kigali
- share/zoneinfo/Africa/Kinshasa
- share/zoneinfo/Africa/Lagos
- share/zoneinfo/Africa/Libreville
- share/zoneinfo/Africa/Lome
- share/zoneinfo/Africa/Luanda
- share/zoneinfo/Africa/Lubumbashi
- share/zoneinfo/Africa/Lusaka
- share/zoneinfo/Africa/Malabo
- share/zoneinfo/Africa/Maputo
- share/zoneinfo/Africa/Maseru
- share/zoneinfo/Africa/Mbabane
- share/zoneinfo/Africa/Mogadishu
- share/zoneinfo/Africa/Monrovia
- share/zoneinfo/Africa/Nairobi
- share/zoneinfo/Africa/Ndjamena
- share/zoneinfo/Africa/Niamey
- share/zoneinfo/Africa/Nouakchott
- share/zoneinfo/Africa/Ouagadougou
- share/zoneinfo/Africa/Porto-Novo
- share/zoneinfo/Africa/Sao_Tome
- share/zoneinfo/Africa/Timbuktu
- share/zoneinfo/Africa/Tripoli
- share/zoneinfo/Africa/Tunis
- share/zoneinfo/Africa/Windhoek
- share/zoneinfo/America/Adak
- share/zoneinfo/America/Anchorage
- share/zoneinfo/America/Anguilla
- share/zoneinfo/America/Antigua
- share/zoneinfo/America/Araguaina
- share/zoneinfo/America/Argentina/Buenos_Aires
- share/zoneinfo/America/Argentina/Catamarca
- share/zoneinfo/America/Argentina/ComodRivadavia
- share/zoneinfo/America/Argentina/Cordoba
- share/zoneinfo/America/Argentina/Jujuy
- share/zoneinfo/America/Argentina/La_Rioja
- share/zoneinfo/America/Argentina/Mendoza
- share/zoneinfo/America/Argentina/Rio_Gallegos
- share/zoneinfo/America/Argentina/Salta
- share/zoneinfo/America/Argentina/San_Juan
- share/zoneinfo/America/Argentina/San_Luis
- share/zoneinfo/America/Argentina/Tucuman
- share/zoneinfo/America/Argentina/Ushuaia
- share/zoneinfo/America/Aruba
- share/zoneinfo/America/Asuncion
- share/zoneinfo/America/Atikokan
- share/zoneinfo/America/Atka
- share/zoneinfo/America/Bahia
- share/zoneinfo/America/Bahia_Banderas
- share/zoneinfo/America/Barbados
- share/zoneinfo/America/Belem
- share/zoneinfo/America/Belize
- share/zoneinfo/America/Blanc-Sablon
- share/zoneinfo/America/Boa_Vista
- share/zoneinfo/America/Bogota
- share/zoneinfo/America/Boise
- share/zoneinfo/America/Buenos_Aires
- share/zoneinfo/America/Cambridge_Bay
- share/zoneinfo/America/Campo_Grande
- share/zoneinfo/America/Cancun
- share/zoneinfo/America/Caracas
- share/zoneinfo/America/Catamarca
- share/zoneinfo/America/Cayenne
- share/zoneinfo/America/Cayman
- share/zoneinfo/America/Chicago
- share/zoneinfo/America/Chihuahua
- share/zoneinfo/America/Ciudad_Juarez
- share/zoneinfo/America/Coral_Harbour
- share/zoneinfo/America/Cordoba
- share/zoneinfo/America/Costa_Rica
- share/zoneinfo/America/Coyhaique
- share/zoneinfo/America/Creston
- share/zoneinfo/America/Cuiaba
- share/zoneinfo/America/Curacao
- share/zoneinfo/Amer
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snakemake-tests / Testing
warning libmamba [pybind11-abi-11-hc364b38_1] The following files were already present in the environment:
- etc/conda/test-files/pybind11-abi/0/check_abi.py
- etc/conda/test-files/pybind11-abi/0/include/pybind11/detail/internals.h
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snakemake-tests / Testing
warning libmamba [libzlib-1.3.2-h25fd6f3_2] The following files were already present in the environment:
- lib/libz.so.1
- lib/libz.so.1.3.2
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snakemake-tests / Testing
warning libmamba [libgomp-15.2.0-he0feb66_18] The following files were already present in the environment:
- lib/libgomp.so
- lib/libgomp.so.1.0.0
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION.gomp_copy
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snakemake-tests / Testing
warning libmamba [ca-certificates-2026.2.25-hbd8a1cb_0] The following files were already present in the environment:
- ssl/cacert.pem
- ssl/cert.pem
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snakemake-tests / Testing
The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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