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Represent '-1' indices as empty strings in StringArrayEncoding #1052

Represent '-1' indices as empty strings in StringArrayEncoding

Represent '-1' indices as empty strings in StringArrayEncoding #1052

Triggered via pull request October 4, 2025 16:21
Status Failure
Total duration 25m 6s
Artifacts 7

test_and_deploy.yml

on: pull_request
Build CCD and wheel for reusing it in several CI jobs
10m 58s
Build CCD and wheel for reusing it in several CI jobs
Check code style
27s
Check code style
Generate wheels matrix
11s
Generate wheels matrix
Build source distribution
37s
Build source distribution
Test interfaces to databases and applications
4m 42s
Test interfaces to databases and applications
Test interface to Muscle 5
1m 3s
Test interface to Muscle 5
Build documentation
4m 56s
Build documentation
Run benchmarks
9m 34s
Run benchmarks
Upload CCD to GitHub Releases
4s
Upload CCD to GitHub Releases
Matrix: Build & Test
Upload documentation to GitHub Releases and documentation website
0s
Upload documentation to GitHub Releases and documentation website
Upload package to GitHub Releases & PyPI
0s
Upload package to GitHub Releases & PyPI
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18 errors and 13 warnings
Build & Test (cp313-win_amd64, windows-latest)
Process completed with exit code 1.
Build & Test (cp313-win_amd64, windows-latest)
Command pytest D:\a\biotite\biotite --durations=50 --ignore=D:\a\biotite\biotite//tests//sequence//align//test_statistics.py --ignore=D:\a\biotite\biotite//tests//application --ignore=D:\a\biotite\biotite//tests//interface --ignore=D:\a\biotite\biotite//tests//database --ignore=D:\a\biotite\biotite//tests//test_doctest.py --ignore=D:\a\biotite\biotite//tests//test_modname.py
Build & Test (cp311-win_amd64, windows-latest)
The operation was canceled.
Build & Test (cp311-win_amd64, windows-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp312-win_amd64, windows-latest)
The operation was canceled.
Build & Test (cp312-win_amd64, windows-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp311-macosx_x86_64, macos-latest)
The operation was canceled.
Build & Test (cp311-macosx_x86_64, macos-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
The operation was canceled.
Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp312-macosx_x86_64, macos-latest)
The operation was canceled.
Build & Test (cp312-macosx_x86_64, macos-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp313-macosx_x86_64, macos-latest)
The operation was canceled.
Build & Test (cp313-macosx_x86_64, macos-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp311-manylinux_x86_64, ubuntu-latest)
The operation was canceled.
Build & Test (cp311-manylinux_x86_64, ubuntu-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
The operation was canceled.
Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
The strategy configuration was canceled because "test-and-build.cp313-win_amd64_windows-l" failed
Test interface to Muscle 5
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'.
Test interfaces to databases and applications
warning libmamba You are using 'pip' as an additional package manager. Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.
Test interfaces to databases and applications
warning libmamba [dssp-4.5.6-py312h36e4239_2] The following files were already present in the environment: - share/libcifpp/mmcif_ddl.dic - share/libcifpp/mmcif_ma.dic - share/libcifpp/mmcif_pdbx.dic
Test interfaces to databases and applications
warning libmamba [ossuuid-1.6.2-h5888daf_1001] The following files were already present in the environment: - lib/libuuid.a - lib/libuuid.so - lib/pkgconfig/uuid.pc
Test interfaces to databases and applications
warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used. warning libmamba Please make sure you understand Anaconda Terms of Services. warning libmamba See: https://legal.anaconda.com/policies/en/
Test interfaces to databases and applications
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'.
Test interfaces to databases and applications
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.9. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
Build documentation
warning libmamba You are using 'pip' as an additional package manager. Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.
Build documentation
warning libmamba [dssp-4.5.6-py312h36e4239_2] The following files were already present in the environment: - share/libcifpp/mmcif_ddl.dic - share/libcifpp/mmcif_ma.dic - share/libcifpp/mmcif_pdbx.dic
Build documentation
warning libmamba [ossuuid-1.6.2-h5888daf_1001] The following files were already present in the environment: - lib/libuuid.a - lib/libuuid.so - lib/pkgconfig/uuid.pc
Build documentation
warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used. warning libmamba Please make sure you understand Anaconda Terms of Services. warning libmamba See: https://legal.anaconda.com/policies/en/
Build documentation
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'.
Build documentation
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.9. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(

Artifacts

Produced during runtime
Name Size Digest
ccd Expired
35.4 MB
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documentation Expired
73.9 MB
sha256:447e3bcb006abfdf88ce41ec1b514d3703647ed6e59a613fe33855ddd1ae8450
internal-build Expired
53.2 MB
sha256:8b46ce29122c19b36c6720f3e145c77152412df213f5e260d6aeab499d5e3303
release-cp311-macosx_arm64 Expired
38.9 MB
sha256:8474fe9287514534ad8f399208bd13d8f413c19118e9f5b85ac2e05963c23004
release-cp312-macosx_arm64 Expired
38.9 MB
sha256:86b3d42065fd98ddb79666f8987e12e84debfea9739ade077336f3d37cc0144a
release-cp313-macosx_arm64 Expired
38.9 MB
sha256:78a19a84306b9ce3bef8346e94d5531eb33245b2867eb3c47026ce06ee0a6f9d
release-sdist Expired
35.9 MB
sha256:a812311287d8f113c0dd29e3f9b4ff681f97abfbc1243dda587f9ee818c32fe7