NeoPlexon2Test #16
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| name: NeoPlexon2Test | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 12 * * 0" # weekly at noon UTC on Sundays | |
| jobs: | |
| build-and-test: | |
| name: Test on (${{ matrix.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.9', '3.12'] | |
| numpy-version: ['1.26', '2.0'] | |
| defaults: | |
| # by default run in bash mode (required for conda usage) | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Get current year-month | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT | |
| - name: Get ephy_testing_data current head hash | |
| # the key depend on the last commit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git | |
| id: ephy_testing_data | |
| run: | | |
| echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT | |
| - uses: actions/cache/restore@v4 | |
| # Loading cache of ephys_testing_dataset | |
| id: cache-datasets | |
| with: | |
| path: ~/ephy_testing_data | |
| key: ${{ runner.os }}-datasets-${{ steps.ephy_testing_data.outputs.dataset_hash }} | |
| restore-keys: ${{ runner.os }}-datasets- | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: neo-test-env-${{ matrix.python-version }} | |
| python-version: "${{ matrix.python-version }}" | |
| - name: Install testing dependencies | |
| # testing environment is only created from yml if no cache was found | |
| # restore-key hits should result in `cache-hit` == 'false' | |
| #if: steps.cache-conda-env.outputs.cache-hit != 'true' | |
| run: | | |
| conda install pip numpy=${{ matrix.numpy-version }} -c conda-forge | |
| # this command is for updating cache. We are resting removal. | |
| # conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune | |
| - name: Install git-annex | |
| # this is the trick from the spikeinterface repo for getting git-annex to work with datalad | |
| # see https://github.com/SpikeInterface/spikeinterface/pull/3877 for more info | |
| shell: bash | |
| run: | | |
| pip install datalad-installer | |
| datalad-installer --sudo ok git-annex --method datalad/packages | |
| git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency | |
| - name: Configure git | |
| run: | | |
| git config --global user.email "neo_ci@fake_mail.com" | |
| git config --global user.name "neo CI" | |
| - name: Python version | |
| run: | | |
| which python | |
| python --version | |
| - name: Install neo including dependencies | |
| # installation with dependencies is only required if no cache was found | |
| # restore-key hits should result in `cache-hit` == 'false' | |
| # if: steps.cache-conda-env.outputs.cache-hit != 'true' | |
| run: | | |
| pip install --upgrade -e . | |
| pip install .[test] | |
| - name: Install wine | |
| run: | | |
| sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list | |
| sudo dpkg --add-architecture i386 | |
| sudo apt-get update -qq | |
| sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine | |
| - name: Pip list | |
| run: | | |
| pip list | |
| - name: Conda list | |
| run: | | |
| conda list | |
| - name: Test with pytest | |
| env: | |
| HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_local_plugin_path | |
| PLEXON2_TEST: true | |
| run: | | |
| # only neo.rawio and neo.io | |
| pytest --cov=neo neo/test/rawiotest | |
| pytest --cov=neo neo/test/iotest |