Make binary recording memmap efficient III (Avoiding spikes by only reserving memory equal to the trace) #9581
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: 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: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # "macos-latest", "windows-latest" | |
| os: ["ubuntu-latest", ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Get current year-month | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT | |
| - name: Get ephy_testing_data current head hash | |
| # the key depends on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git | |
| id: vars | |
| run: | | |
| echo "HASH_EPHY_DATASET=$(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@v4 | |
| 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: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v41 | |
| - 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 |