Move segment attrs to lineage #2064
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
| 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 |