Unify compute_isi_violation docs and add UltraMegaSort2000 citation #9632

Workflow file for this run

.github/workflows/full-test.yml at d1ea215

	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

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Unify compute_isi_violation docs and add UltraMegaSort2000 citation #9632

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Unify compute_isi_violation docs and add UltraMegaSort2000 citation #9632

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Workflow file for this run