Update sphinx-rtd-theme requirement from <3.0,>=1.0 to >=1.0,<4.0 #641
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| # Scan the code for security vulnerabilities with CodeQL. | |
| # See https://github.com/github/codeql-action | |
| name: "CodeQL" | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| - "develop" | |
| pull_request: | |
| # The branches below must be a subset of the branches above. | |
| branches: | |
| - "main" | |
| - "develop" | |
| jobs: | |
| scan: | |
| strategy: | |
| matrix: | |
| os: | |
| - "ubuntu-latest" | |
| python-version: | |
| - "3.9" | |
| runs-on: "${{ matrix.os }}" | |
| permissions: | |
| security-events: "write" | |
| steps: | |
| - name: "Checkout repository" | |
| uses: "actions/checkout@v4" | |
| - name: "Set up Python ${{ matrix.python-version }}" | |
| uses: "actions/setup-python@v5" | |
| with: | |
| python-version: "${{ matrix.python-version }}" | |
| - name: "Export ${HOME}/.local/bin to ${PATH}" | |
| # Executable Python binaries are usually stored there. | |
| run: 'echo "${HOME}/.local/bin" >> ${GITHUB_PATH}' | |
| - name: "Get pip cache dir" | |
| # pip's cache path depends on the operating system. See | |
| # https://github.com/actions/cache/blob/main/examples.md#python---pip | |
| # This requires pip >=20.1. | |
| id: "pip-cache" | |
| run: | | |
| python -m pip install --user --upgrade pip | |
| echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT} | |
| - name: "Create/Restore cache" | |
| uses: "actions/cache@v4" | |
| with: | |
| path: "${{ steps.pip-cache.outputs.dir }}/**" | |
| key: | | |
| ${{ runner.os }}-${{ matrix.python-version }}-${{ github.job }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ matrix.python-version }} | |
| ${{ runner.os }} | |
| - name: "Install/Upgrade setuptools and wheel" | |
| # MDAnalysis requires NumPy (>=1.19.2) for setup (see also | |
| # https://github.com/MDAnalysis/mdanalysis/issues/3374#issuecomment-889189979). | |
| # MDAnalysis <3.0 requires Cython <3.0 (see | |
| # https://github.com/MDAnalysis/mdanalysis/pull/4129 and | |
| # https://github.com/cython/cython/issues/3690). | |
| # Strangely, without `python-dev-tools` the installation of | |
| # MDAnalysis might fail while building the wheel. | |
| run: | | |
| python -m pip install --user --upgrade setuptools wheel | |
| python -m pip install --user --upgrade python-dev-tools | |
| python -m pip install --user "Cython <3.0" | |
| python -m pip install --user "numpy >=1.19.2" | |
| - name: "Install/Upgrade requirements of MDTools" | |
| run: | | |
| python -m pip install --user --upgrade -r requirements.txt | |
| # Set the `CODEQL-PYTHON` environment variable to the Python | |
| # executable that includes the dependencies. | |
| echo "CODEQL_PYTHON=$(which python)" >> ${GITHUB_ENV} | |
| - name: "Initialize CodeQL" | |
| uses: "github/codeql-action/init@v3" | |
| with: | |
| languages: "python" | |
| # Override the default behavior so that the action doesn't | |
| # attempt to auto-install Python dependencies. See | |
| # https://docs.github.com/en/code-security/secure-coding/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#analyzing-python-dependencies | |
| setup-python-dependencies: false | |
| - name: "Perform CodeQL Analysis" | |
| uses: "github/codeql-action/analyze@v3" |