Claude Mosaiq demo #2321
Workflow file for this run
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| name: Library | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| release: | |
| types: | |
| - created | |
| jobs: | |
| # ============================================================================= | |
| PreCommit: | |
| # if: false | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-cache | |
| - name: Run Pre-Commit | |
| run: | | |
| pip install pre-commit | |
| pre-commit run --all-files | |
| - name: Fix any issues | |
| id: fix_issues | |
| if: failure() | |
| run: | | |
| git config --local user.email "pre-commit-bot@pymedphys.com" | |
| git config --local user.name "PyMedPhys Pre-Commit Bot" | |
| git add -A | |
| git stash | |
| git checkout $GITHUB_HEAD_REF | |
| git pull | |
| pre-commit run --all-files || true | |
| git commit -m "Fix pre-commit failures" -a | |
| - name: Get GitHub App token for installation | |
| id: generate-token | |
| if: failure() && steps.fix_issues.outcome == 'success' | |
| uses: tibdex/github-app-token@v2.1.0 | |
| with: | |
| app_id: ${{ secrets.PYMEDPHYS_CI_BOT_ID }} | |
| private_key: ${{ secrets.PYMEDPHYS_CI_BOT_TOKEN }} | |
| - name: Push changes | |
| if: failure() && steps.fix_issues.outcome == 'success' | |
| uses: ad-m/github-push-action@v0.8.0 | |
| with: | |
| github_token: ${{ steps.generate-token.outputs.token }} | |
| branch: ${{ github.event.pull_request.head.ref }} | |
| # ============================================================================= | |
| Tests: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu", "macos", "windows"] | |
| task: | |
| [ | |
| "tests", | |
| "docs", | |
| "stackoverflow", | |
| "updates", | |
| "cypress", | |
| "slow", | |
| "pyright", | |
| "propagate", | |
| ] | |
| exclude: | |
| - os: "windows" | |
| task: "stackoverflow" | |
| - os: "windows" | |
| task: "updates" | |
| - os: "windows" | |
| task: "slow" | |
| - os: "windows" | |
| task: "pyright" | |
| - os: "windows" | |
| task: "propagate" | |
| - os: "windows" | |
| task: "cypress" | |
| - os: "macos" | |
| task: "stackoverflow" | |
| - os: "macos" | |
| task: "updates" | |
| - os: "macos" | |
| task: "cypress" | |
| - os: "macos" | |
| task: "slow" | |
| - os: "macos" | |
| task: "pyright" | |
| - os: "macos" | |
| task: "propagate" | |
| include: | |
| # Spread the below across the range of supported Python versions. | |
| - os: "ubuntu" | |
| python-version: "3.11" # TODO: Upgrade this to 3.12 | |
| - os: "windows" | |
| python-version: "3.10" | |
| - os: "macos" | |
| python-version: "3.9" | |
| runs-on: ${{ matrix.os }}-latest | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| if: matrix.task != 'propagate' | |
| - uses: actions/checkout@v4 | |
| if: matrix.task == 'propagate' | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get full Python version | |
| id: full-python-version | |
| shell: bash | |
| run: | | |
| echo version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") >> $GITHUB_OUTPUT | |
| # ----------------------------------------------------------------------------- | |
| # Set up pip | |
| - name: Get pip cache dir | |
| id: pip-cache | |
| shell: bash | |
| run: | | |
| python -m pip install -U pip # to ensure version > 20 to have cache dir | |
| echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT | |
| - name: Pip Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ steps.pip-cache.outputs.dir }} | |
| key: pip-${{ matrix.task }}-${{ runner.os }}-${{ steps.full-python-version.outputs.version }} | |
| # ----------------------------------------------------------------------------- | |
| # Upgrade pip and setuptools, and install poetry | |
| - name: Upgrade pip and setuptools | |
| run: | | |
| pip install --upgrade pip setuptools | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1.3.4 | |
| with: | |
| version: 1.7.1 | |
| virtualenvs-create: true | |
| - name: Update PATH in Windows | |
| if: matrix.os == 'windows' | |
| run: | | |
| Add-Content -Path $env:GITHUB_PATH -Value "$env:USERPROFILE\.local\bin" | |
| Get-Content -Path $env:GITHUB_PATH | |
| # ----------------------------------------------------------------------------- | |
| # No import and run CLI with no dependencies | |
| - name: Build wheel | |
| if: matrix.task == 'tests' | |
| run: | | |
| poetry build --format wheel | |
| - name: Install wheel | |
| if: matrix.task == 'tests' && matrix.os == 'windows' | |
| run: | | |
| python -m pip install (Get-Item .\dist\*.whl) | |
| - name: Install wheel | |
| if: matrix.task == 'tests' && matrix.os != 'windows' | |
| run: | | |
| python -m pip install ./dist/*.whl | |
| - name: Run clean tests | |
| if: matrix.task == 'tests' | |
| run: | | |
| pymedphys --help | |
| python -c "import pymedphys" | |
| python -c "import pymedphys.beta" | |
| python -c "import pymedphys.experimental" | |
| # Remove confusion for tests down the line | |
| - name: Remove base install of pymedphys | |
| if: matrix.task == 'tests' | |
| run: | | |
| pip uninstall -y pymedphys | |
| # ----------------------------------------------------------------------------- | |
| # Set up Poetry | |
| - name: Configure poetry | |
| run: | | |
| poetry config virtualenvs.in-project true | |
| - name: Poetry Cache | |
| uses: actions/cache@v3 | |
| id: poetry-cache | |
| with: | |
| path: .venv | |
| key: venv-${{ matrix.task }}-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }} | |
| # This is from <https://github.com/python-poetry/poetry/blob/639d5e057/.github/workflows/main.yml#L57-L60> | |
| - name: Ensure cache is healthy | |
| if: steps.poetry-cache.outputs.cache-hit == 'true' | |
| shell: bash | |
| run: | | |
| timeout 10s poetry run pip --version || rm -rf .venv | |
| # Install Node | |
| - uses: actions/setup-node@v3 | |
| if: matrix.task == 'cypress' || matrix.task == 'pyright' || matrix.task == 'build' | |
| with: | |
| node-version: "14" | |
| # cache: "yarn" # TODO: Sort out this cache parameter | |
| # ----------------------------------------------------------------------------- | |
| ## Plain install | |
| - name: Install a plain environment | |
| if: matrix.task == 'stackoverflow' | |
| run: | | |
| poetry install -E user | |
| ## Install with Documentation Environment | |
| - name: Install a docs environment | |
| if: matrix.task == 'docs' | |
| run: | | |
| poetry install -E docs | |
| ## Install with Tests Environment | |
| # TODO: Redesign CI to be more efficient once this issue lands python-poetry/poetry#4842 | |
| - name: Install a tests/doctests environment | |
| if: matrix.task == 'tests' || matrix.task == 'cypress' || matrix.task == 'slow' || matrix.task == 'pyright' | |
| run: | | |
| poetry install -E user -E tests -E doctests | |
| ## Install remaining packages for pyright | |
| - name: Install a propagate environment | |
| if: matrix.task == 'pyright' || matrix.task == 'propagate' | |
| run: | | |
| poetry install -E propagate || poetry lock --no-update && poetry install -E propagate | |
| ## Update all packages and then install with tests environment | |
| - name: Update all packages then install with tests and user environment | |
| if: matrix.task == 'updates' | |
| run: | | |
| poetry install -E user -E tests -E docs | |
| poetry update | |
| poetry install -E user -E tests -E docs | |
| # ----------------------------------------------------------------------------- | |
| # PyMedPhys Data Cache | |
| - name: Get PyMedPhys cache directory | |
| id: pymedphys-cache-location | |
| if: matrix.task != 'pyright' | |
| shell: bash | |
| run: | | |
| echo "dir=$(poetry run python -c 'import pymedphys._config as cf; print(str(cf.get_config_dir()))')" >> $GITHUB_OUTPUT | |
| - name: PyMedPhys Cache | |
| id: pymedphys-cache | |
| if: matrix.task != 'pyright' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ steps.pymedphys-cache-location.outputs.dir }} | |
| key: pymedphys-${{ matrix.task }}-${{ runner.os }}-${{ hashFiles('**/hashes.json') }} | |
| # ----------------------------------------------------------------------------- | |
| # TESTS | |
| ## Propagate | |
| - name: See if propagate is needed | |
| if: matrix.task == 'propagate' | |
| id: propagate-test | |
| shell: bash | |
| run: | | |
| echo "status=before" >> $GITHUB_OUTPUT | |
| poetry check | |
| ## Pyright | |
| - name: Install and run pyright | |
| if: matrix.task == 'pyright' | |
| run: | | |
| npm install -g pyright | |
| poetry run pyright | |
| ## Pytest | |
| - name: Run basic pytest tests | |
| if: matrix.task == 'tests' || matrix.task == 'updates' | |
| run: | | |
| poetry run pymedphys dev tests -v | |
| ## Doctest | |
| - name: Run doctest tests | |
| if: matrix.os == 'ubuntu' && matrix.task == 'tests' | |
| run: | | |
| poetry run pymedphys dev doctests -v | |
| ## Pylint | |
| - name: Run pylint tests | |
| if: matrix.os == 'ubuntu' && ( matrix.task == 'tests' || matrix.task == 'updates' ) | |
| run: | | |
| poetry run pymedphys dev lint | |
| ## Slow | |
| - name: Run slow tests | |
| if: matrix.task == 'slow' | |
| run: | | |
| poetry run pymedphys dev tests -v --slow | |
| ## Docs | |
| - name: Download docs files | |
| if: matrix.task == 'docs' && matrix.os == 'ubuntu' | |
| run: | | |
| poetry run python -c "import pymedphys; pymedphys.data_path('original_dose_beam_4.dcm'); pymedphys.data_path('logfile_dose_beam_4.dcm');" | |
| - name: Build docs | |
| if: matrix.task == 'docs' || matrix.task == 'updates' | |
| run: | | |
| poetry run pymedphys dev docs | |
| - name: Add GitHub Pages Config Files | |
| if: matrix.task == 'docs' && matrix.os == 'ubuntu' && github.event_name == 'push' | |
| run: | | |
| echo docs.pymedphys.com > lib/pymedphys/docs/_build/html/CNAME | |
| touch lib/pymedphys/docs/_build/html/.nojekyll | |
| - name: Deploy docs | |
| if: matrix.task == 'docs' && matrix.os == 'ubuntu' && github.event_name == 'push' | |
| uses: JamesIves/github-pages-deploy-action@4.1.3 | |
| with: | |
| branch: docs | |
| folder: lib/pymedphys/docs/_build/html | |
| ssh-key: ${{ secrets.DEPLOY_KEY }} | |
| ## Stackoverflow | |
| - name: Run stackoverflow example(s) | |
| if: matrix.task == 'stackoverflow' | |
| run: | | |
| poetry run python ./examples/stackoverflow/gamma.py | |
| ## Cypress | |
| - name: Run Cypress tests | |
| if: matrix.task == 'cypress' | |
| run: | | |
| poetry run pymedphys dev tests --cypress | |
| - uses: actions/upload-artifact@v2 | |
| if: failure() && matrix.task == 'cypress' | |
| with: | |
| name: cypress-videos | |
| path: pymedphys/tests/e2e/cypress/videos |