V2: Make CI complain when notebook tests fail #469
Workflow file for this run
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| # ci.yml | |
| # | |
| # Continuous Integration for Chemprop - checks build, code formatting, and runs tests for all | |
| # proposed changes and on a regular schedule | |
| # | |
| # Note: this file contains extensive inline documentation to aid with knowledge transfer. | |
| name: Continuous Integration | |
| on: | |
| # run on pushes/pull requests to/against main | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| # run this in the morning on weekdays to catch dependency issues | |
| schedule: | |
| - cron: "0 8 * * 1-5" | |
| # allow manual runs | |
| workflow_dispatch: | |
| # cancel previously running tests if new commits are made | |
| # https://docs.github.com/en/actions/examples/using-concurrency-expressions-and-a-test-matrix | |
| concurrency: | |
| group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| name: Check Build | |
| runs-on: ubuntu-latest | |
| steps: | |
| # clone the repo, attempt to build | |
| - uses: actions/checkout@v4 | |
| - run: python -m pip install build | |
| - run: python -m build . | |
| lint: | |
| name: Check Formatting | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| # clone the repo, run black and flake8 on it | |
| - uses: actions/checkout@v4 | |
| - run: python -m pip install black==23.* flake8 | |
| - run: black --check . | |
| - run: flake8 . | |
| test: | |
| name: Execute Tests | |
| needs: lint | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # run with a login shell (so that the conda environment is activated) | |
| # and echo the commands we run as we do them (for debugging purposes) | |
| shell: bash -el {0} | |
| strategy: | |
| # if one platform/python version fails, continue testing the others | |
| fail-fast: false | |
| matrix: | |
| # test on all platforms with both supported versions of Python | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: [3.11, 3.12] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # use a version of the conda virtual environment manager to set up an | |
| # isolated environment with the Python version we want | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-name: temp | |
| condarc: | | |
| channels: | |
| - defaults | |
| - conda-forge | |
| channel_priority: flexible | |
| create-args: | | |
| python=${{ matrix.python-version }} | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install nbmake | |
| python -m pip install ".[dev,docs,test]" | |
| - name: Install hyperopt optional dependencies (Python 3.11 only) | |
| if: ${{ matrix.python-version == '3.11' }} | |
| run: | | |
| python -m pip install ".[hpopt]" | |
| # - name: Test with pytest | |
| # shell: bash -l {0} | |
| # run: | | |
| # pytest -v tests | |
| - name: Test notebooks | |
| shell: bash -l {0} | |
| run: | | |
| pytest --no-cov --nbmake examples/*.ipynb | |
| conda-test: | |
| name: Execute Tests with Conda-based Install | |
| needs: lint | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # run with a login shell (so that the conda environment is activated) | |
| # and echo the commands we run as we do them (for debugging purposes) | |
| shell: bash -el {0} | |
| strategy: | |
| # if one platform/python version fails, continue testing the others | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.11, 3.12] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # use a version of the conda virtual environment manager to set up an | |
| # isolated environment with the Python version we want | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: environment.yml | |
| condarc: | | |
| channels: | |
| - defaults | |
| - conda-forge | |
| - pytorch | |
| channel_priority: flexible | |
| create-args: | | |
| python=${{ matrix.python-version }} | |
| - name: Install Testing Dependencies | |
| run: conda install -c conda-forge pytest>=6.2 pytest-cov | |
| - name: Install Chemprop | |
| run: python -m pip install . --no-deps | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| pytest -v tests | |
| # GitHub allows you to set checks as required before PRs can be merged, which is annoying to do | |
| # for matrix jobs like the one above which have six actual jobs. Instead we have a summary job | |
| # like this, which we mark as required. | |
| # Copied in part from: | |
| # https://github.com/orgs/community/discussions/26822#discussioncomment-3305794 | |
| ci-report-status: | |
| name: report CI status | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: | | |
| result="${{ needs.test.result }}" | |
| if test $result == "success"; then | |
| exit 0 | |
| else | |
| exit 1 | |
| fi | |