add fix_charged_molecule function
#3
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| name: Continuous Integration | |
| on: | |
| schedule: | |
| # * is a special character in YAML so you have to quote this string | |
| - cron: "0 8 * * *" | |
| push: | |
| pull_request: | |
| workflow_dispatch: | |
| concurrency: | |
| group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| check-formatting: | |
| name: Check Formatting Errors | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install pycodestyle | |
| - name: Run pycodestyle | |
| run: | | |
| pycodestyle --statistics \ | |
| --count \ | |
| --max-line-length 150 \ | |
| --max-doc-length 200 \ | |
| --ignore=E266,E501,W503,W505 \ | |
| --show-source \ | |
| . | |
| build-and-test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| name: ${{ matrix.os }} Python ${{ matrix.python-version }} Subtest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: rdmc_env | |
| environment-file: environment.yml | |
| miniforge-variant: mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: true | |
| use-mamba: true | |
| - name: Install RDMC | |
| run: python -m pip install --no-deps -vv ./ | |
| - name: Install Pytest | |
| run: mamba install -y pytest pytest-cov # temporarily remove "pytest-check" | |
| - name: Mamba info | |
| run: | | |
| mamba info | |
| mamba list | |
| - name: Run Unit Tests | |
| run: pytest | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11' }} | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| directory: ./coverage |