Fix for Silence periods (saving noise levels) #7056
Workflow file for this run
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| name: Full spikeinterface tests | |
| on: | |
| pull_request: | |
| types: [synchronize, opened, reopened] | |
| branches: | |
| - main | |
| concurrency: # Cancel previous workflows on the same pull request | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: # For the sortingview backend | |
| KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }} | |
| KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }} | |
| jobs: | |
| full-tests-depending-on-changed-files: | |
| name: Test on (${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # "macos-latest", "windows-latest" | |
| os: ["ubuntu-latest", ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Get current year-month | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT | |
| - name: Restore cached virtual environment with dependencies | |
| uses: actions/cache/restore@v3 | |
| id: cache-venv | |
| with: | |
| path: ${{ github.workspace }}/test_env | |
| key: ${{ runner.os }}-venv-${{ hashFiles('**/pyproject.toml') }}-${{ steps.date.outputs.date }} | |
| - name: Get ephy_testing_data current head hash | |
| # the key depends on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git | |
| id: vars | |
| run: | | |
| echo "HASH_EPHY_DATASET=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT | |
| - name: Restore cached gin data for extractors tests | |
| uses: actions/cache/restore@v3 | |
| id: cache-datasets | |
| env: | |
| # the key depends on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git | |
| HASH_EPHY_DATASET: git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1 | |
| with: | |
| path: ~/spikeinterface_datasets | |
| key: ${{ runner.os }}-datasets-${{ steps.vars.outputs.HASH_EPHY_DATASET }} | |
| restore-keys: ${{ runner.os }}-datasets | |
| - name: Install packages | |
| uses: ./.github/actions/build-test-environment | |
| - name: Shows installed packages by pip, git-annex and cached testing files | |
| uses: ./.github/actions/show-test-environment | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v35 | |
| - name: Module changes | |
| id: modules-changed | |
| run: | | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| if [[ $file == *"pyproject.toml" ]]; then | |
| echo "pyproject.toml changed" | |
| echo "CORE_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/core/"* || $file == *"/extractors/neoextractors/neobaseextractor.py" ]]; then | |
| echo "Core changed" | |
| echo "CORE_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/extractors/"* ]]; then | |
| echo "Extractors changed" | |
| echo "EXTRACTORS_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"plexon2"* ]]; then | |
| echo "Plexon2 changed" | |
| echo "PLEXON2_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/preprocessing/"* ]]; then | |
| echo "Preprocessing changed" | |
| echo "PREPROCESSING_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/postprocessing/"* ]]; then | |
| echo "Postprocessing changed" | |
| echo "POSTPROCESSING_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/qualitymetrics/"* ]]; then | |
| echo "Quality metrics changed" | |
| echo "QUALITYMETRICS_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/sorters/"* && $file != *"/sorters/internal/"* && $file != *"/sorters/external/"* ]]; then | |
| echo "Sorters changed" | |
| echo "SORTERS_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/sorters/external"* ]]; then | |
| echo "External sorters changed" | |
| echo "SORTERS_EXTERNAL_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/sorters/internal"* ]]; then | |
| echo "Internal sorters changed" | |
| echo "SORTERS_INTERNAL_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/comparison/"* ]]; then | |
| echo "Comparison changed" | |
| echo "COMPARISON_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/curation/"* ]]; then | |
| echo "Curation changed" | |
| echo "CURATION_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/widgets/"* ]]; then | |
| echo "Widgets changed" | |
| echo "WIDGETS_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/exporters/"* ]]; then | |
| echo "Exporters changed" | |
| echo "EXPORTERS_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/sortingcomponents/"* ]]; then | |
| echo "Sortingcomponents changed" | |
| echo "SORTINGCOMPONENTS_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| if [[ $file == *"/generation/"* ]]; then | |
| echo "Generation changed" | |
| echo "GENERATION_CHANGED=true" >> $GITHUB_OUTPUT | |
| fi | |
| done | |
| - name: Set execute permissions on run_tests.sh | |
| run: chmod +x .github/run_tests.sh | |
| - name: Install Wine (Plexon2) | |
| if: ${{ steps.modules-changed.outputs.PLEXON2_CHANGED == 'true' }} | |
| uses: ./.github/actions/install-wine | |
| - name: Test core | |
| run: ./.github/run_tests.sh core | |
| - name: Test extractors | |
| env: | |
| HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell | |
| if: ${{ steps.modules-changed.outputs.EXTRACTORS_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh "extractors and not streaming_extractors" | |
| - name: Test preprocessing | |
| if: ${{ steps.modules-changed.outputs.PREPROCESSING_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh "preprocessing and not deepinterpolation" | |
| - name: Test postprocessing | |
| if: ${{ steps.modules-changed.outputs.POSTPROCESSING_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh postprocessing | |
| - name: Test quality metrics | |
| if: ${{ steps.modules-changed.outputs.QUALITYMETRICS_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh qualitymetrics | |
| - name: Test core sorters | |
| if: ${{ steps.modules-changed.outputs.SORTERS_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh sorters | |
| - name: Test comparison | |
| if: ${{ steps.modules-changed.outputs.COMPARISON_CHANGED == 'true' || steps.modules-changed.outputs.GENERATION_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh comparison | |
| - name: Test curation | |
| if: ${{ steps.modules-changed.outputs.CURATION_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh curation | |
| - name: Test widgets | |
| if: ${{ steps.modules-changed.outputs.WIDGETS_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' || steps.modules-changed.outputs.QUALITYMETRICS_CHANGED == 'true' || steps.modules-changed.outputs.PREPROCESSING_CHANGED == 'true'}} | |
| run: ./.github/run_tests.sh widgets | |
| - name: Test exporters | |
| if: ${{ steps.modules-changed.outputs.EXPORTERS_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' || steps.modules-changed.outputs.WIDGETS_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh exporters | |
| - name: Test sortingcomponents | |
| if: ${{ steps.modules-changed.outputs.SORTINGCOMPONENTS_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh sortingcomponents | |
| - name: Test internal sorters | |
| if: ${{ steps.modules-changed.outputs.SORTERS_INTERNAL_CHANGED == 'true' || steps.modules-changed.outputs.SORTINGCOMPONENTS_CHANGED || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh sorters_internal | |
| - name: Test generation | |
| if: ${{ steps.modules-changed.outputs.GENERATION_CHANGED == 'true' || steps.modules-changed.outputs.CORE_CHANGED == 'true' }} | |
| run: ./.github/run_tests.sh generation |