quilt_summarize.json editor
#9836
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |