Automatic curation with metrics #1790
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: 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 }} | |
| KACHERY_ZONE: ${{ secrets.KACHERY_ZONE }} | |
| 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-latest, 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/scripts/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 == 'true' | |
| 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,widgets] | |
| ./.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 |