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full-test.yml
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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: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
# "macos-latest", "windows-latest"
os: ["ubuntu-latest", ]
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Get current year-month
id: date
run: echo "date=$(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