Demographic model recombination rate #2215
Workflow file for this run
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| name: tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # Use a login shell, so that ~/.bash_profile is executed and | |
| # the conda environment gets initialised. | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, macos-12, windows-latest] | |
| python: ["3.8", "3.10"] | |
| env: | |
| CONDA_ENV_NAME: stdpopsim | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - name: cancel previous runs | |
| uses: styfle/cancel-workflow-action@0.6.0 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: checkout | |
| uses: actions/checkout@v2 | |
| - name: find conda | |
| id: find-conda | |
| run: | | |
| echo "CONDA=$CONDA" >> $GITHUB_OUTPUT | |
| - name: fix conda permissions | |
| if: runner.os == 'macOS' | |
| run: | | |
| # Fix incorrect conda permissions on mac that prevent cache restore. | |
| sudo chown -R $USER:staff ${{ steps.find-conda.outputs.CONDA }} | |
| - name: cache conda | |
| id: cache | |
| uses: actions/cache@v3 | |
| env: | |
| # Increase this to reset the cache if the key hasn't changed. | |
| CACHE_NUM: 9 | |
| with: | |
| path: | | |
| ${{ steps.find-conda.outputs.CONDA }}/envs/${{ env.CONDA_ENV_NAME }} | |
| ~/.bash_profile | |
| key: ${{ runner.os }}-${{ matrix.python }}-conda-${{ hashFiles('requirements/CI/*') }}-${{ env.CACHE_NUM }} | |
| - name: install conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| with: | |
| activate-environment: ${{ env.CONDA_ENV_NAME }} | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| channel-priority: strict | |
| auto-update-conda: true | |
| use-only-tar-bz2: true | |
| - name: move profile | |
| if: steps.cache.outputs.cache-hit != 'true' && runner.os != 'Windows' | |
| run: | | |
| # The setup-miniconda action leaves different shell init files for | |
| # different OSes. Bash gives priority to ~/.bash_profile, so here we | |
| # ensure that's used for all platforms. | |
| mv ~/.profile ~/.bash_profile | |
| - name: install dependencies | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| # We install msprime from conda to avoid GSL-related build issues | |
| # when pip installing without binary wheels (on Windows). | |
| conda install --yes --file=requirements/CI/conda.txt | |
| pip install -r requirements/CI/requirements.txt | |
| - name: run test suite | |
| run: | | |
| python -m pytest \ | |
| -n 0 \ | |
| -v \ | |
| --cov=stdpopsim \ | |
| --cov-branch \ | |
| --cov-report=term-missing \ | |
| --cov-report=xml \ | |
| tests | |
| - name: upload coverage report to codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| fail_ci_if_error: true | |
| env_vars: OS,PYTHON | |
| # Use upload token to avoid upload failures. | |
| # https://github.com/codecov/codecov-action/issues/837 | |
| token: 8ae76ade-9d0e-4a2d-b9ef-1180235be07f |