fix: support alternative atom names within connect_via_residue_names #668
nscorleytest_and_deploy.yml
on: pull_request
Build CCD and wheel for reusing it in several CI jobs
4m 56s
Generate wheels matrix
9s
Check code style
10s
Build source distribution
30s
Test interfaces to databases and applications
2m 25s
Test interface to Muscle 5
59s
Matrix: Build & Test
Upload documentation to GitHub Releases and documentation website
0s
Upload package to GitHub Releases & PyPI
0s
Annotations
16 errors and 21 warnings
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Test interfaces to databases and applications
Process completed with exit code 1.
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Run benchmarks
Error: failed to execute the benchmark process
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Run benchmarks
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Build & Test (cp311-macosx_x86_64, macos-latest)
Command ['arch', '-x86_64', '/bin/sh', '-c', 'pytest /Users/runner/work/biotite/biotite --durations=50 --ignore=/Users/runner/work/biotite/biotite//tests//sequence//align//test_statistics.py --ignore=/Users/runner/work/biotite/biotite//tests//application --ignore=/Users/runner/work/biotite/biotite//tests//database --ignore=/Users/runner/work/biotite/biotite//tests//test_doctest.py --ignore=/Users/runner/work/biotite/biotite//tests//test_modname.py\n'] failed with code 1.
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Build & Test (cp311-macosx_x86_64, macos-latest)
Process completed with exit code 1.
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Build & Test (cp310-win_amd64, windows-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp313-win_amd64, windows-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp312-win_amd64, windows-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp311-win_amd64, windows-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp313-manylinux_x86_64, ubuntu-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp312-manylinux_x86_64, ubuntu-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp311-manylinux_x86_64, ubuntu-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp312-macosx_x86_64, macos-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp313-macosx_x86_64, macos-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp310-manylinux_x86_64, ubuntu-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Build & Test (cp310-macosx_x86_64, macos-latest)
The job was canceled because "cp311-macosx_x86_64_macos" failed.
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Check code style
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Generate wheels matrix
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Build CCD and wheel for reusing it in several CI jobs
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Upload CCD to GitHub Releases
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Build source distribution
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Test interface to Muscle 5
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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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'.
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Test interfaces to databases and applications
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Test interfaces to databases and applications
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:200: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
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(
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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'.
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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/
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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/
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/
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/
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Test interfaces to databases and applications
warning libmamba [expat-2.6.4-h6a678d5_0] The following files were already present in the environment:
- lib/libexpat.so.1
- lib/libexpat.so.1.10.0
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Test interfaces to databases and applications
warning libmamba [gobject-introspection-1.78.1-py312h42194e9_1] The following files were already present in the environment:
- lib/girepository-1.0/GLib-2.0.typelib
- lib/girepository-1.0/GModule-2.0.typelib
- lib/girepository-1.0/GObject-2.0.typelib
- lib/girepository-1.0/Gio-2.0.typelib
- share/gir-1.0/GLib-2.0.gir
- share/gir-1.0/GModule-2.0.gir
- share/gir-1.0/GObject-2.0.gir
- share/gir-1.0/Gio-2.0.gir
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Build documentation
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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Build documentation
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:200: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
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(
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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'.
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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/
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
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/
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
warning libmamba [expat-2.6.4-h6a678d5_0] The following files were already present in the environment:
- lib/libexpat.so.1
- lib/libexpat.so.1.10.0
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Build documentation
warning libmamba [gobject-introspection-1.78.1-py312h42194e9_1] The following files were already present in the environment:
- lib/girepository-1.0/GLib-2.0.typelib
- lib/girepository-1.0/GModule-2.0.typelib
- lib/girepository-1.0/GObject-2.0.typelib
- lib/girepository-1.0/Gio-2.0.typelib
- share/gir-1.0/GLib-2.0.gir
- share/gir-1.0/GModule-2.0.gir
- share/gir-1.0/GObject-2.0.gir
- share/gir-1.0/Gio-2.0.gir
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Artifacts
Produced during runtime
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ccd
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33 MB |
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documentation
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74.3 MB |
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internal-build
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51.1 MB |
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release-cp310-macosx_arm64
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36.4 MB |
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release-cp311-macosx_arm64
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36.4 MB |
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release-cp312-macosx_arm64
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36.4 MB |
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release-cp313-macosx_arm64
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36.4 MB |
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release-sdist
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33.5 MB |
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