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Add two function that deal with overlapping atoms #450

Add two function that deal with overlapping atoms

Add two function that deal with overlapping atoms #450

Triggered via pull request April 7, 2026 16:58
@pmrvpmrv
opened #479
geom
Status Success
Total duration 5m 23s
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pipeline.yml

on: pull_request
Matrix: unittest_matrix
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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/
uv_check
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/
minimal
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/
minimal
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'.
pip_check
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/
pip_check
warning libmamba [pymatgen-2026.3.23-py314hc02f841_0] The following files were already present in the environment: - bin/pmg
pip_check
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'.
unittest_matrix (ubuntu-latest, 3.11, linux-64-py-3-11)
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/
unittest_matrix (ubuntu-latest, 3.11, linux-64-py-3-11)
warning libmamba [pymatgen-2026.3.23-py311h0372a8f_0] The following files were already present in the environment: - bin/pmg
unittest_matrix (ubuntu-latest, 3.11, linux-64-py-3-11)
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'.
unittest_old
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/
unittest_old
warning libmamba [mesalib-25.0.5-h57bcd07_2] The following files were already present in the environment: - include/GL/gl.h - include/GL/glcorearb.h - include/GL/glext.h - include/KHR/khrplatform.h
unittest_old
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'.
unittest_matrix (ubuntu-latest, 3.13, linux-64-py-3-13)
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/
unittest_matrix (ubuntu-latest, 3.13, linux-64-py-3-13)
warning libmamba [pymatgen-2026.3.23-py313h29aa505_0] The following files were already present in the environment: - bin/pmg
unittest_matrix (ubuntu-latest, 3.13, linux-64-py-3-13)
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'.
unittest_matrix (ubuntu-latest, 3.12, linux-64-py-3-12)
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/
unittest_matrix (ubuntu-latest, 3.12, linux-64-py-3-12)
warning libmamba [pymatgen-2026.3.23-py312h4f23490_0] The following files were already present in the environment: - bin/pmg
unittest_matrix (ubuntu-latest, 3.12, linux-64-py-3-12)
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'.
unittest_matrix (ubuntu-latest, 3.14, linux-64-py-3-14)
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/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea, 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/
unittest_matrix (ubuntu-latest, 3.14, linux-64-py-3-14)
warning libmamba [pymatgen-2026.3.23-py314hc02f841_0] The following files were already present in the environment: - bin/pmg
unittest_matrix (ubuntu-latest, 3.14, linux-64-py-3-14)
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'.
unittest_matrix (macos-latest, 3.14, osx-64-py-3-14)
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/
unittest_matrix (macos-latest, 3.14, osx-64-py-3-14)
warning libmamba [pymatgen-2026.3.23-py314h2115a04_0] The following files were already present in the environment: - bin/pmg
unittest_matrix (macos-latest, 3.14, osx-64-py-3-14)
warning libmamba [gfortran_osx-arm64-14.3.0-h3c33bd0_0] The following files were already present in the environment: - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/ar - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/as - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/clang - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/ld - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/nm - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/ranlib - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/strip
unittest_matrix (macos-latest, 3.14, osx-64-py-3-14)
warning libmamba [gfortran_impl_osx-arm64-14.3.0-h6d03799_1] The following files were already present in the environment: - lib/gcc/arm64-apple-darwin20.0.0/14.3.0/include/ISO_Fortran_binding.h
unittest_matrix (macos-latest, 3.14, osx-64-py-3-14)
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'.
unittest_matrix (windows-latest, 3.14, win-64-py-3-14)
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/
unittest_matrix (windows-latest, 3.14, win-64-py-3-14)
warning libmamba [pymatgen-2026.3.23-py314h2dcd201_0] The following files were already present in the environment: - Scripts\pmg.exe
unittest_matrix (windows-latest, 3.14, win-64-py-3-14)
ERROR: 'conda activate "test"' exited with code 1.
unittest_matrix (windows-latest, 3.14, win-64-py-3-14)
EnvironmentNameNotFound: Could not find conda environment: test You can list all discoverable environments with `conda info --envs`.
unittest_matrix (windows-latest, 3.14, win-64-py-3-14)
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'.