Add changes to achieve progress described #427
Workflow file for this run
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| name: CI | |
| on: | |
| # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | |
| # Existing codes likely still have "master" as the primary branch | |
| # Both are tracked here to keep legacy and new codes working | |
| push: | |
| branches: | |
| - "master" | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "master" | |
| - "main" | |
| # schedule: | |
| # # Nightly tests run on master by default: | |
| # # Scheduled workflows run on the latest commit on the default or base branch. | |
| # # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| # - cron: "0 0 * * *" | |
| jobs: | |
| CI: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.7", "3.8"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Additional info about the build | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # Get date for the cache key | |
| - name: Get current time | |
| uses: josStorer/[email protected] | |
| id: current-time | |
| - name: Cache conda env | |
| uses: actions/cache@v3 | |
| id: cache | |
| env: | |
| # Increase this value to reset cache if mols.yml has not changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| # Key contains current year and month to ensure it is updated once a month | |
| ${{ runner.os }}-py${{ matrix.python-version }}-conda-${{ steps.current-time.outputs.year }}-${{ | |
| steps.current-time.outputs.month }}-${{ hashFiles('devtools/conda-envs/mols.yml') }}-${{ | |
| env.CACHE_NUMBER }} | |
| # More info on the whole conda setup: https://github.com/conda-incubator/setup-miniconda | |
| - name: Setup Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| id: conda-setup | |
| with: | |
| # mamba-version: "*" # uncomment to activate mamba | |
| python-version: ${{ matrix.python-version }} | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,defaults | |
| environment-file: devtools/conda-envs/mols.yml | |
| activate-environment: molsimp | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| - name: Install package | |
| run: | | |
| pip install -e . --no-deps | |
| pip install pytest-cov | |
| conda list | |
| - name: Run tests | |
| run: | | |
| pytest -v --cov=molSimplify --cov-report=xml | |
| - name: Run doctest | |
| # For now still excluding several subfolders and files | |
| run: | | |
| pytest --doctest-modules --ignore=molSimplify/job_manager --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify | |
| - name: Upload coverage report to codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| directory: ./coverage/reports/ | |
| env_vars: OS,PYTHON | |
| files: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| verbose: true | |
| - name: Report Status | |
| # Slack notifications only on the main repo | |
| if: ${{job.status == 'failure' && github.event_name != 'pull_request' && github.repository == 'hjkgrp/molSimplify' }} | |
| #uses: ravsamhq/notify-slack-action@v1 | |
| uses: 8398a7/action-slack@v3 | |
| with: | |
| job_name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| fields: message,commit,author,workflow,job,took | |
| status: ${{ job.status }} | |
| env: | |
| SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}} | |
| #MATRIX_CONTEXT: ${{ toJson(matrix) }} # required |