Update tutorial for new VariantData format #1534
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/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: install clang-format | |
| if: steps.clang_format.outputs.cache-hit != 'true' | |
| run: | | |
| sudo pip install clang-format==6.0.1 | |
| sudo ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-6.0 | |
| - uses: pre-commit/action@v3.0.0 | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: [ 3.9, "3.12" ] | |
| os: [ macos-latest, ubuntu-latest, windows-latest ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Cache conda and dependancies | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v5-${{ hashFiles('requirements/CI-tests-conda/requirements.txt')}} | |
| - name: Install Miniconda with Mamba | |
| 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 | |
| # channel-priority: strict | |
| auto-update-conda: true | |
| # mamba-version: "*" | |
| # use-mamba: true | |
| - name: Fix windows .profile | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest' | |
| run: | | |
| cp ~/.bash_profile ~/.profile | |
| # Work around weird issues on OSX possibly caused by mixed compilers | |
| # https://github.com/tskit-dev/tsinfer/issues/376 | |
| - name: Install compiler from conda | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} #We need a login shell to get conda | |
| run: conda install --yes c-compiler | |
| - 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 cyvcf2 #Fails if done via conda due to no windows support. | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest' | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| #Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12 | |
| pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3 | |
| - name: Install sgkit only on windows | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest' | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| #Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12 | |
| pip install sgkit==0.9.0 | |
| - name: Build module | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| # Use numpy2 to build the module | |
| pip install "numpy>=2" | |
| python setup.py build_ext --inplace | |
| - name: Run tests | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| # Test with numpy<2 for numba | |
| pip install "numpy<2" | |
| python -m pytest -xv |