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Fix drawing errors for charged species by moving to rdkit geometry generation #5779

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Fix drawing errors for charged species by moving to rdkit geometry generation

Fix drawing errors for charged species by moving to rdkit geometry generation #5779

Triggered via pull request July 25, 2025 17:10
@jonwzhengjonwzheng
synchronize #2838
kirkbadger18:add_charged_bidentate_draw_test
Status Success
Total duration 5h 5m 52s
Artifacts 3

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on: pull_request
Matrix: build-and-test
Regression Test
1h 8m
Regression Test
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25 warnings and 12 notices
Python 3.9 ubuntu-latest Build and Test
/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(
Python 3.11 ubuntu-latest Build and Test
/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(
Python 3.10 ubuntu-latest Build and Test
/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(
Python 3.10 ubuntu-latest Build and Test with RMS
/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(
Python 3.11 ubuntu-latest Build and Test with RMS
/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(
Regression Test
/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(
Python 3.9 ubuntu-latest Build and Test with RMS
/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(
Python 3.10 macos-latest Build and Test with RMS
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.10 macos-latest Build and Test with RMS
/Users/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(
Python 3.9 macos-latest Build and Test
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.9 macos-latest Build and Test
/Users/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(
Python 3.10 macos-latest Build and Test
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.10 macos-latest Build and Test
/Users/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(
Python 3.11 macos-latest Build and Test with RMS
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.11 macos-latest Build and Test with RMS
/Users/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(
Python 3.11 macos-latest Build and Test
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.11 macos-latest Build and Test
/Users/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(
Python 3.10 macos-13 Build and Test
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.10 macos-13 Build and Test
/Users/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(
Python 3.9 macos-latest Build and Test with RMS
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.9 macos-latest Build and Test with RMS
/Users/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(
Python 3.11 macos-13 Build and Test
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.11 macos-13 Build and Test
/Users/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(
Python 3.9 macos-13 Build and Test
warning libmamba [pyutilib-6.0.0-pyh9f0ad1d_0] The following files were already present in the environment: - bin/replaceCopyright - bin/checkCopyright
Python 3.9 macos-13 Build and Test
/Users/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(
Python 3.10 macos-latest Build and Test with RMS
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.10 macos-latest Build and Test with RMS
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.9 macos-latest Build and Test
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.9 macos-latest Build and Test
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.10 macos-latest Build and Test
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.10 macos-latest Build and Test
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.11 macos-latest Build and Test with RMS
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.11 macos-latest Build and Test with RMS
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.11 macos-latest Build and Test
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.11 macos-latest Build and Test
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.9 macos-latest Build and Test with RMS
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520
Python 3.9 macos-latest Build and Test with RMS
The macos-latest label will migrate to macOS 15 beginning August 4, 2025. For more information see https://github.com/actions/runner-images/issues/12520

Artifacts

Produced during runtime
Name Size Digest
dynamic_regression_results
5.94 MB
sha256:db2e453430c94c6758081a63b71761c8270a0bd9d2e9f7b5712e077da49d02eb
regression_summary
8.25 KB
sha256:b8437bb3109b2ae354199a0641b60e5da7e43540f6c744005e674766beb8c2a1
regression_test_comparison_results
8.2 KB
sha256:1e8f590b48724f0279c21476b5c02ce973197309c7500908eaf87e87df1075a7