Allow sets of covariates to be selected (#63) #348
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| # This workflow will install Python dependencies and run tests | |
| # For more information see: | |
| # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: tests | |
| on: # yamllint disable-line rule:truthy | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["main"] | |
| workflow_dispatch: | |
| inputs: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11"] | |
| poetry-version: ["1.8.2"] | |
| node_version: ["lts/*"] | |
| steps: | |
| # Setup | |
| - name: Check out source repository | |
| uses: actions/checkout@v3 | |
| - name: Set up poetry | |
| uses: abatilo/actions-poetry@v2 | |
| with: | |
| poetry-version: ${{ matrix.poetry-version }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'poetry' | |
| - name: Install Python Dependencies | |
| run: poetry install --with daq,web,ana,dev | |
| # File filters | |
| - name: Paths Changes Filter | |
| uses: dorny/paths-filter@v3 | |
| id: filter | |
| with: | |
| list-files: shell | |
| filters: | | |
| poetry: | |
| # Do not run poetry check and lock if just the pyproject.toml file changes | |
| # - added|modified: '**/pyproject.toml' | |
| - added|modified: '**/poetry.lock' | |
| python: | |
| - added|modified: '**.py' | |
| - added|modified: '**.ipynb' | |
| javascript: | |
| - added|modified: '**.js' | |
| html: | |
| - added|modified: '**.html' | |
| prettier: | |
| - added|modified: '**.html' | |
| - added|modified: '**.css' | |
| - added|modified: '**.scss' | |
| - added|modified: '**.json' | |
| # prettier-plugin-toml is not being properly installed on the actions runner, | |
| # lint toml files locally | |
| # - added|modified: '**.toml' | |
| yaml: | |
| - added|modified: '**.yaml' | |
| - added|modified: '**.yml' | |
| makefile: | |
| - added|modified: '**/Makefile' | |
| - added|modified: '**/makefile' | |
| markdown: | |
| - added|modified: '**.md' | |
| tex: | |
| - added|modified: '**.tex' | |
| rst: | |
| - added|modified: '**.rst' | |
| - name: Free Disk Space | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| # This might remove tools that are actually needed, if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| # Does not break anything, and saves a lot of space, but runs slowly, | |
| # do not use unless necessary, i.e. when running poetry checks. | |
| large-packages: ${{steps.filter.outputs.poetry}} | |
| # Needed by any dockerized github action | |
| docker-images: false | |
| # Gets the poetry cache back | |
| swap-storage: false | |
| # These will be cleaned | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| # Filtered setup | |
| - name: Install Node | |
| if: steps.filter.outputs.javascript == 'true' || steps.filter.outputs.prettier == 'true' | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: ${{ matrix.node_version }} | |
| check-latest: true | |
| - name: Install Node Dependencies | |
| if: steps.filter.outputs.javascript == 'true' || steps.filter.outputs.prettier == 'true' | |
| run: sudo npm install --global standard prettier | |
| # All files | |
| - name: detect-secrets | |
| run: poetry run detect-secrets-hook --exclude-lines 'integrity=' | |
| - name: blocklint | |
| run: poetry run blocklint --skip-files=poetry.lock --max-issue-threshold=1 | |
| # poetry | |
| - name: poetry | |
| if: steps.filter.outputs.poetry == 'true' | |
| run: poetry check && poetry lock --no-update | |
| # python | |
| - name: isort | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run isort ${{ steps.filter.outputs.python_files }} | |
| - name: black | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run black --check --diff ${{ steps.filter.outputs.python_files }} | |
| - name: flake8 | |
| if: steps.filter.outputs.python == 'true' | |
| run: | | |
| echo "::group::version and plugins" | |
| poetry run flake8 --version | |
| echo "::endgroup::" | |
| poetry run flake8 ${{ steps.filter.outputs.python_files }} | |
| - name: mypy | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run mypy ${{ steps.filter.outputs.python_files }} | |
| - name: pylint | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run pylint ${{ steps.filter.outputs.python_files }} | |
| - name: bandit | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run bandit -r ${{ steps.filter.outputs.python_files }} | |
| - name: vulture | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run vulture . # Needs to run on whole package | |
| - name: pyupgrade | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run pyupgrade ${{ steps.filter.outputs.python_files }} | |
| - name: deptry | |
| if: steps.filter.outputs.python == 'true' | |
| run: poetry run deptry . # Runs on whole package | |
| # javascript | |
| - name: standard | |
| if: steps.filter.outputs.javascript == 'true' | |
| run: standard ${{ steps.filter.outputs.javascript_files }} | |
| # html | |
| - name: html5validator | |
| if: steps.filter.outputs.html == 'true' | |
| uses: Cyb3r-Jak3/html5validator-action@master # blocklint: pragma | |
| with: | |
| config: .dev_config/.html5validator.yaml | |
| # only configurable to run on paths, so just run on whole package | |
| # prettier: html css scss json | |
| - name: prettier | |
| if: steps.filter.outputs.prettier == 'true' | |
| id: prettier | |
| run: prettier --ignore-path .dev_config/.prettierignore --ignore-path .gitignore --config .dev_config/.prettierrc.yaml --check ${{ steps.filter.outputs.prettier_files }} # yamllint disable-line rule:line-length | |
| # yaml | |
| - name: yamllint | |
| if: steps.filter.outputs.yaml == 'true' | |
| run: poetry run yamllint -c .dev_config/.yamllint.yaml --strict ${{ steps.filter.outputs.yaml_files }} # yamllint disable-line rule:line-length | |
| # makefile | |
| - name: checkmake | |
| if: steps.filter.outputs.makefile == 'true' | |
| uses: Uno-Takashi/checkmake-action@main # Can not pass multiple files | |
| # shell files - no extension to filter on, always run | |
| - name: shellcheck shfmt checkbashisms | |
| uses: luizm/action-sh-checker@master # blocklint: pragma | |
| env: | |
| SHFMT_OPTS: -bn -ci -sr -s -d | |
| with: | |
| sh_checker_checkbashisms_enable: true | |
| # typos - always run | |
| - name: typos | |
| uses: crate-ci/typos@v1.19.0 | |
| with: | |
| config: pyproject.toml | |
| # docs | |
| - name: markdownlint | |
| if: steps.filter.outputs.markdown == 'true' | |
| uses: nosborn/github-action-markdown-cli@v3.3.0 | |
| with: | |
| files: ${{ steps.filter.outputs.markdown_files }} | |
| dot: true | |
| config_file: .dev_config/.markdownlint.yaml | |
| ignore_files: LICENSE.md | |
| - name: blacken-docs | |
| if: steps.filter.outputs.python == 'true' || steps.filter.outputs.markdown == 'true' || steps.filter.outputs.rst == 'true' || steps.filter.outputs.tex == 'true' # yamllint disable-line rule:line-length | |
| run: poetry run blacken-docs --line-length=100 ${{ steps.filter.outputs.python_files }} ${{ steps.filter.outputs.markdown_files }} ${{ steps.filter.outputs.rst_files }} ${{ steps.filter.outputs.tex_files }} # yamllint disable-line rule:line-length |