Automatic curation with metrics #1281
Workflow file for this run
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| name: Complete tests | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 12 * * 0" # Weekly on Sunday at noon UTC | |
| pull_request: | |
| types: [synchronize, opened, reopened] | |
| branches: | |
| - main | |
| env: | |
| KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }} | |
| KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }} | |
| concurrency: # Cancel previous workflows on the same pull request | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| run: | |
| name: ${{ matrix.os }} Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.12"] # Lower and higher versions we support | |
| os: [macos-13, windows-latest, ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v41 | |
| - name: List all changed files | |
| shell: bash | |
| env: | |
| ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }} | |
| run: | | |
| for file in ${ALL_CHANGED_FILES}; do | |
| echo "$file was changed" | |
| done | |
| - name: Set testing environment # This decides which tests are run and whether to install especial dependencies | |
| shell: bash | |
| run: | | |
| changed_files="${{ steps.changed-files.outputs.all_changed_files }}" | |
| python .github/determine_testing_environment.py $changed_files | |
| - name: Display testing environment | |
| shell: bash | |
| run: | | |
| echo "RUN_EXTRACTORS_TESTS=${RUN_EXTRACTORS_TESTS}" | |
| echo "RUN_PREPROCESSING_TESTS=${RUN_PREPROCESSING_TESTS}" | |
| echo "RUN_POSTPROCESSING_TESTS=${RUN_POSTPROCESSING_TESTS}" | |
| echo "RUN_QUALITYMETRICS_TESTS=${RUN_QUALITYMETRICS_TESTS}" | |
| echo "RUN_CURATION_TESTS=${RUN_CURATION_TESTS}" | |
| echo "RUN_SORTINGCOMPONENTS_TESTS=${RUN_SORTINGCOMPONENTS_TESTS}" | |
| echo "RUN_GENERATION_TESTS=${RUN_GENERATION_TESTS}" | |
| echo "RUN_COMPARISON_TESTS=${RUN_COMPARISON_TESTS}" | |
| echo "RUN_WIDGETS_TESTS=${RUN_WIDGETS_TESTS}" | |
| echo "RUN_EXPORTERS_TESTS=${RUN_EXPORTERS_TESTS}" | |
| echo "RUN_SORTERS_TESTS=${RUN_SORTERS_TESTS}" | |
| echo "RUN_INTERNAL_SORTERS_TESTS=${RUN_INTERNAL_SORTERS_TESTS}" | |
| echo "INSTALL_PLEXON_DEPENDENCIES=${INSTALL_PLEXON_DEPENDENCIES}" | |
| echo "RUN_STREAMING_EXTRACTORS_TESTS=${RUN_STREAMING_EXTRACTORS_TESTS}" | |
| - name: Install packages | |
| run: | | |
| pip install -e .[test_core] | |
| shell: bash | |
| - name: Test core | |
| run: pytest -m "core" | |
| shell: bash | |
| - name: Install Dependencies for Timing Display | |
| run: | | |
| pip install tabulate | |
| pip install pandas | |
| shell: bash | |
| - name: Get current hash (SHA) of the ephy_testing_data repo | |
| shell: bash | |
| id: repo_hash | |
| run: echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT | |
| - name: Cache datasets | |
| if: env.RUN_EXTRACTORS_TESTS == 'true' | |
| id: cache-datasets | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ~/spikeinterface_datasets | |
| key: ${{ runner.os }}-datasets-${{ steps.repo_hash.outputs.dataset_hash }} | |
| restore-keys: ${{ runner.os }}-datasets | |
| - name: Install git-annex | |
| shell: bash | |
| if: env.RUN_EXTRACTORS_TESTS == 'true' | |
| run: | | |
| pip install datalad-installer | |
| if [ ${{ runner.os }} = 'Linux' ]; then | |
| wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz | |
| mkdir /home/runner/work/installation | |
| mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/ | |
| workdir=$(pwd) | |
| cd /home/runner/work/installation | |
| tar xvzf git-annex-standalone-amd64.tar.gz | |
| echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH | |
| cd $workdir | |
| elif [ ${{ runner.os }} = 'macOS' ]; then | |
| datalad-installer --sudo ok git-annex --method brew | |
| elif [ ${{ runner.os }} = 'Windows' ]; then | |
| datalad-installer --sudo ok git-annex --method datalad/git-annex:release | |
| fi | |
| git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency | |
| - name : Install Plexon dependencies | |
| if: env.INSTALL_PLEXON_DEPENDENCIES == 'true' | |
| uses: ./.github/actions/install-wine | |
| - name: Set execute permissions on run_tests.sh | |
| shell: bash | |
| run: chmod +x .github/run_tests.sh | |
| - name: Test extractors | |
| shell: bash | |
| env: | |
| HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell | |
| if: env.RUN_EXTRACTORS_TESTS == 'true' | |
| run: | | |
| pip install -e .[extractors,streaming_extractors,test_extractors] | |
| ./.github/run_tests.sh "extractors and not streaming_extractors" --no-virtual-env | |
| - name: Test streaming extractors | |
| shell: bash | |
| if: env.RUN_STREAMING_EXTRACTORS_TESTS | |
| run: | | |
| pip install -e .[streaming_extractors,test_extractors] | |
| ./.github/run_tests.sh "streaming_extractors" --no-virtual-env | |
| - name: Test preprocessing | |
| shell: bash | |
| if: env.RUN_PREPROCESSING_TESTS == 'true' | |
| run: | | |
| pip install -e .[preprocessing,test_preprocessing] | |
| ./.github/run_tests.sh "preprocessing and not deepinterpolation" --no-virtual-env | |
| - name: Install remaining testing dependencies # TODO: Remove this step once we have better modularization | |
| shell: bash | |
| run: | | |
| pip install -e .[test] | |
| - name: Test postprocessing | |
| shell: bash | |
| if: env.RUN_POSTPROCESSING_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh postprocessing --no-virtual-env | |
| - name: Test quality metrics | |
| shell: bash | |
| if: env.RUN_QUALITYMETRICS_TESTS == 'true' | |
| run: | | |
| pip install -e .[qualitymetrics] | |
| ./.github/run_tests.sh qualitymetrics --no-virtual-env | |
| - name: Test comparison | |
| shell: bash | |
| if: env.RUN_COMPARISON_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh comparison --no-virtual-env | |
| - name: Test core sorters | |
| shell: bash | |
| if: env.RUN_SORTERS_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh sorters --no-virtual-env | |
| - name: Test internal sorters | |
| shell: bash | |
| if: env.RUN_INTERNAL_SORTERS_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh sorters_internal --no-virtual-env | |
| - name: Test curation | |
| shell: bash | |
| if: env.RUN_CURATION_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh curation --no-virtual-env | |
| - name: Test widgets | |
| shell: bash | |
| if: env.RUN_WIDGETS_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh widgets --no-virtual-env | |
| - name: Test exporters | |
| shell: bash | |
| if: env.RUN_EXPORTERS_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh exporters --no-virtual-env | |
| - name: Test sortingcomponents | |
| shell: bash | |
| if: env.RUN_SORTINGCOMPONENTS_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh sortingcomponents --no-virtual-env | |
| - name: Test generation | |
| shell: bash | |
| if: env.RUN_GENERATION_TESTS == 'true' | |
| run: | | |
| pip install -e .[full] | |
| ./.github/run_tests.sh generation --no-virtual-env |