Initial steps for internal pedigree samples #2114
Workflow file for this run
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| name: Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| jobs: | |
| pre-commit: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| - name: install clang-format | |
| run: | | |
| pip install clang-format==6.0.1 | |
| - uses: pre-commit/[email protected] | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python: [ 3.9, 3.12 ] | |
| os: [ macos-latest, ubuntu-latest, windows-latest ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Cache conda and dependencies | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v2-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }} | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| with: | |
| activate-environment: anaconda-client-env | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge, anaconda | |
| channel-priority: strict | |
| auto-update-conda: true | |
| - name: Fix windows symlinks | |
| # This is horrible, but the "git config core.symlinks true" didn't work. | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| rm lwt_interface | |
| cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface | |
| - name: Fix windows .profile | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest' | |
| run: | | |
| cp ~/.bash_profile ~/.profile | |
| - name: Install conda deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} #We need a login shell to get conda | |
| run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt | |
| - name: Install pip deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| pip install -r requirements/CI-tests-pip/requirements.txt | |
| pip uninstall -y msprime | |
| - name: Build module | |
| env: | |
| MSP_CONDA_PREFIX: c:\Miniconda\envs\anaconda-client-env | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| python setup.py build_ext --inplace | |
| - name: Run tests | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| pytest -xvs -n0 |