Initial implementation of stripepy plot #168
Workflow file for this run
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
| # Copyright (C) 2024 Roberto Rossini <roberros@uio.no> | |
| # | |
| # SPDX-License-Identifier: MIT | |
| name: CI | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - ".github/workflows/ci.yml" | |
| - "src/**" | |
| - "test/**" | |
| - ".gitignore" | |
| - "pyproject.toml" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/ci.yml" | |
| - "src/**" | |
| - "test/**" | |
| - ".gitignore" | |
| - "pyproject.toml" | |
| # https://stackoverflow.com/a/72408109 | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| matrix-factory: | |
| name: Generate job matrix | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-result.outputs.result }} | |
| steps: | |
| - name: Generate matrix | |
| uses: actions/github-script@v7 | |
| id: set-result | |
| with: | |
| script: | | |
| // Documentation | |
| // https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson | |
| // https://github.com/actions/runner/issues/982#issuecomment-809360765 | |
| const platforms = ["windows-latest", "macos-latest", "ubuntu-latest"] | |
| var python_versions = ["3.9", "3.13"] | |
| if ("${{github.event_name}}" != "pull_request") { | |
| python_versions = python_versions.concat(["3.10", "3.11", "3.12"]) | |
| } | |
| var includes = [] | |
| for (const plat of platforms) { | |
| for (const ver of python_versions) { | |
| includes.push({os: plat, python_version: ver}) | |
| } | |
| } | |
| return { include: includes } | |
| ci: | |
| name: CI | |
| needs: [matrix-factory] | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.matrix-factory.outputs.matrix) }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| TEST_DATASET_ID: 4DNFI9GMP2J8 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python_version }} | |
| cache: pip | |
| cache-dependency-path: pyproject.toml | |
| - name: Install package | |
| run: pip install --verbose '.[test]' | |
| - name: Run simple CLI tests | |
| run: | | |
| stripepy --help | |
| stripepy --version | |
| - name: Cache test dataset | |
| id: cache-dset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: test-dataset | |
| path: | | |
| test/data/${{env.TEST_DATASET_ID }}.mcool | |
| test/data/results*.hdf5 | |
| - name: Download test dataset | |
| if: steps.cache-dset.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir test/data/ | |
| stripepy download \ | |
| --name ${{ env.TEST_DATASET_ID }} \ | |
| --output test/data/${{ env.TEST_DATASET_ID }}.mcool | |
| stripepy download \ | |
| --name __results_v1 \ | |
| --output test/data/results_4DNFI9GMP2J8_v1.hdf5 | |
| - name: Save test dataset | |
| if: steps.cache-dset.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v4 | |
| with: | |
| key: test-dataset | |
| path: | | |
| test/data/${{env.TEST_DATASET_ID }}.mcool | |
| test/data/results*.hdf5 | |
| - name: Run unit tests | |
| run: | | |
| python -m pytest \ | |
| --cov=stripepy \ | |
| --verbose \ | |
| --cov-report=xml \ | |
| --cov-report=term \ | |
| test/ \ | |
| -m unit | |
| - name: Upload unit test coverage report to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| flags: "tests | unit | python-${{ matrix.python_version }}" | |
| disable_search: true | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| - name: Run integration tests | |
| run: | | |
| rm -f coverage.xml | |
| python -m pytest \ | |
| --cov=stripepy \ | |
| --verbose \ | |
| --cov-report=xml \ | |
| --cov-report=term \ | |
| test/ \ | |
| -m end2end | |
| - name: Upload end2end test coverage report to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| flags: "tests | integration | python-${{ matrix.python_version }}" | |
| disable_search: true | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| ci-status-check: | |
| name: Status Check (CI) | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - ci | |
| steps: | |
| - name: Collect job results | |
| if: needs.ci.result != 'success' | |
| run: exit 1 |