Add delete_atoms method and use bonding info for add_hatoms SO107 #343
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| name: CI | |
| on: | |
| # Run on creating or updating a PR | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| # And pushing to the trunk or fix branches | |
| push: | |
| branches: | |
| - trunk | |
| - 'fix*' | |
| # And pushing new version tags e.g. 2024.103 | |
| tags: | |
| - '20[0-9]{2}\.[0-9]{3}' | |
| jobs: | |
| unit-test: | |
| # Run on ubuntu, mac and windows for python 3.8 (in AMS python stack) up to 3.12 | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set Up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build package | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build | |
| python -m build | |
| - name: Install package and dependencies | |
| run: | | |
| pip install dist/plams-*.whl | |
| pip install ".[chem,ams,analysis,dev]" | |
| - name: Run Unit Tests | |
| run: | | |
| coverage run --source='scm.plams' -m pytest unit_tests | |
| # ToDo: Bump the fail-under threshold over time until acceptable level is reached | |
| - name: Evaluate Coverage | |
| run: | | |
| coverage report --omit="*/unit_tests/*" -i --fail-under=35 | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| - name: Set Up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.x" | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ".[dev]" | |
| - name: Run Black | |
| run: | | |
| black --check -t py38 -l 120 . | |
| - name: Run Flake8 | |
| run: | | |
| flake8 --color never --count --config .flake8 . | |
| - name: Run MyPy | |
| run: | | |
| mypy | |
| build-docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| - name: Set Up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.x" | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ".[docs]" | |
| - name: Build Sphinx Docs | |
| working-directory: doc | |
| env: | |
| IGNORE_IMPORT_ERRORS: true | |
| run: | | |
| python build_plams_doc |