quilt_summarize.json editor
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| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - "*" | |
| pull_request: | |
| merge_group: | |
| jobs: | |
| linter: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install 'pylint==3.2.7' 'pycodestyle>=2.6.1' | |
| - name: Run pylint | |
| run: | | |
| pylint . | |
| - name: Run pycodestyle | |
| run: | | |
| pycodestyle $(find -name '*.py' -not -path './venv/*') | |
| isort: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install isort | |
| - name: Run isort | |
| run: | | |
| isort --check --diff . | |
| test-gendocs: | |
| runs-on: ubuntu-latest | |
| env: | |
| QUILT_DISABLE_USAGE_METRICS: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| # on newer versions it crashes with | |
| # TypeError: <classmethod(<function Package.install at 0x105219f30>)> is not a callable object | |
| python-version: '3.9' | |
| - name: install deps | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install api/python nbconvert git+https://github.com/quiltdata/[email protected]+quilt3.2 | |
| - name: generate docs | |
| run: cd gendocs && python build.py | |
| - name: show invisible changes via cat | |
| run: git diff | cat -A | |
| - name: check there are no changes | |
| run: git diff --exit-code | |
| test-testdocs: | |
| runs-on: ubuntu-latest | |
| env: | |
| QUILT_DISABLE_USAGE_METRICS: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: install poetry | |
| run: python -m pip install poetry | |
| - name: install deps | |
| run: cd testdocs && poetry install | |
| - name: test codeblocks | |
| run: cd testdocs && poetry run pytest --codeblocks ../docs | |
| test-client: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest] | |
| python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| QUILT_DISABLE_USAGE_METRICS: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install -e api/python[tests] | |
| - name: Run Pytest | |
| run: | | |
| pytest --cov=api/python api/python | |
| - uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| OS: ${{ matrix.os }} | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| with: | |
| flags: api-python | |
| name: ${{ github.job }} | |
| env_vars: OS,PYTHON_VERSION | |
| pypi-release-tag-check: | |
| needs: test-client | |
| runs-on: ubuntu-latest | |
| outputs: | |
| check: ${{ steps.check.outputs.check }} | |
| if: github.ref_type == 'tag' | |
| steps: | |
| - name: check git tag | |
| id: check | |
| run: | | |
| if [[ ${{ github.ref_name }} =~ ^[0-9]+(\.[0-9]+)*([abrc]+[0-9]+)?$ ]]; then | |
| echo ::set-output name=check::true | |
| fi | |
| pypi-release: | |
| needs: pypi-release-tag-check | |
| if: github.ref_type == 'tag' && needs.pypi-release-tag-check.outputs.check == 'true' | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: api/python | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| python -m pip install build==1.2.2.post1 twine==5.1.1 | |
| - name: verify git tag vs. version | |
| env: | |
| CIRCLE_TAG: ${{ github.ref_name }} | |
| run: python setup.py verify | |
| - name: build | |
| run: python -m build | |
| - name: upload to PyPI | |
| env: | |
| TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} | |
| TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} | |
| run: twine upload dist/* | |
| test-lambda: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| path: | |
| - access_counts | |
| - indexer | |
| - pkgevents | |
| - pkgpush | |
| - preview | |
| - s3hash | |
| - shared | |
| - status_reports | |
| - tabular_preview | |
| - thumbnail | |
| - transcode | |
| runs-on: ubuntu-latest | |
| env: | |
| QUILT_DISABLE_USAGE_METRICS: true | |
| PYTHONPATH: deps | |
| JUPYTER_PATH: deps/share/jupyter # Jupyter is not smart enough to handle custom Python paths | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version-file: lambdas/${{ matrix.path }}/.python-version | |
| - name: Install dependencies | |
| run: | | |
| if [ ${{ matrix.path }} == "thumbnail" ] | |
| then | |
| # Due to behavior change in pip>=23.1 installing tifffile==0.15.1 | |
| # from thumbnail lambda fails whithout installed wheel. | |
| # See https://github.com/pypa/pip/issues/8559. | |
| # HACK: Pre-install numpy v1 as a build dependency for tifffile to prevent it from using v2 and failing to build | |
| python -m pip install wheel 'numpy<2' | |
| fi | |
| # Try to simulate the lambda .zip file: | |
| # - Use --no-deps to ensure that second-order dependencies are included in the requirements file | |
| # - Remove "tests" directories | |
| # - Run "strip" on shared libraries | |
| python -m pip install -t deps --no-deps -r lambdas/${{ matrix.path }}/requirements.txt lambdas/${{ matrix.path }} | |
| find deps -name tests -type d -exec rm -r \{} \+ | |
| find deps \( -name '*.so.*' -o -name '*.so' \) -type f -exec strip \{} \+ | |
| python -m pip install -r lambdas/${{ matrix.path }}/test-requirements.txt | |
| - name: Pytest | |
| run: | | |
| pytest --cov=lambdas lambdas/${{ matrix.path }} | |
| - uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| LAMBDA: ${{ matrix.path }} | |
| with: | |
| flags: lambda | |
| name: ${{ github.job }} | |
| env_vars: LAMBDA |