all-tests.yml

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 }}

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-13, 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 }}
          # cache: 'pip' # caching pip dependencies

      - name: Get current hash (SHA) of the ephy_testing_data repo
        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
        shell: bash
      - name: Cache datasets
        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 packages
        run: |
          git config --global user.email "CI@example.com"
          git config --global user.name "CI Almighty"
          pip install -e .[test,extractors,streaming_extractors,full]
          pip install tabulate
        shell: bash

      - name: Installad datalad
        run: |
          pip install datalad-installer
          if [ ${{ runner.os }} = 'Linux' ]; then
            datalad-installer --sudo ok git-annex --method datalad/packages
          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
          pip install datalad
          git config --global filter.annex.process "git-annex filter-process"  # recommended for efficiency
        shell: bash

      - name: Get changed files
        id: changed-files
        uses: tj-actions/changed-files@v41

      - name: Set environment variables based on changed files
        run: |
          declare -A changes
          changes=(
            ["pyproject.toml"]="CORE_CHANGED"
            ["/core/"]="CORE_CHANGED"
            ["/extractors/neoextractors/neobaseextractor.py"]="CORE_CHANGED"
            ["/extractors/"]="EXTRACTORS_CHANGED"
            ["plexon2"]="PLEXON2_CHANGED"
            ["/preprocessing/"]="PREPROCESSING_CHANGED"
            ["/postprocessing/"]="POSTPROCESSING_CHANGED"
            ["/qualitymetrics/"]="QUALITYMETRICS_CHANGED"
            ["/sorters/"]="SORTERS_CHANGED"
            ["/sorters/external"]="SORTERS_EXTERNAL_CHANGED"
            ["/sorters/internal"]="SORTERS_INTERNAL_CHANGED"
            ["/comparison/"]="COMPARISON_CHANGED"
            ["/curation/"]="CURATION_CHANGED"
            ["/widgets/"]="WIDGETS_CHANGED"
            ["/exporters/"]="EXPORTERS_CHANGED"
            ["/sortingcomponents/"]="SORTINGCOMPONENTS_CHANGED"
            ["/generation/"]="GENERATION_CHANGED"
          )

          for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
            for pattern in "${!changes[@]}"; do
              if [[ $file == *$pattern* ]]; then
                echo "${changes[$pattern]}=true" >> $GITHUB_ENV
              fi
            done
          done

      - name: Set execute permissions on run_tests.sh
        run: chmod +x .github/run_tests.sh
        shell: bash

      - name: Test core
        run: pytest -m "core"
        shell: bash

      - name: Test extractors
        env:
          HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell
        if: env.EXTRACTORS_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: pytest -m "extractors"
        shell: bash

      - name: Test preprocessing
        if: env.PREPROCESSING_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh "preprocessing and not deepinterpolation" --no-virtual-env
        shell: bash

      - name: Test postprocessing
        if: env.POSTPROCESSING_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh postprocessing --no-virtual-env
        shell: bash

      - name: Test quality metrics
        if: env.QUALITYMETRICS_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh qualitymetrics --no-virtual-env
        shell: bash

      - name: Test comparison
        if: env.COMPARISON_CHANGED == 'true' || env.GENERATION_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh comparison --no-virtual-env
        shell: bash

      - name: Test core sorters
        if: env.SORTERS_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh sorters --no-virtual-env
        shell: bash

      - name: Test internal sorters
        if: env.SORTERS_INTERNAL_CHANGED == 'true' || env.SORTINGCOMPONENTS_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh sorters_internal --no-virtual-env
        shell: bash

      - name: Test curation
        if: env.CURATION_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh curation --no-virtual-env
        shell: bash

      - name: Test widgets
        if: env.WIDGETS_CHANGED == 'true' || env.CORE_CHANGED == 'true' || env.QUALITYMETRICS_CHANGED == 'true' || env.PREPROCESSING_CHANGED == 'true'
        run: ./.github/run_tests.sh widgets --no-virtual-env
        shell: bash

      - name: Test exporters
        if: env.EXPORTERS_CHANGED == 'true' || env.CORE_CHANGED == 'true' || env.WIDGETS_CHANGED == 'true'
        run: ./.github/run_tests.sh exporters --no-virtual-env
        shell: bash

      - name: Test sortingcomponents
        if: env.SORTINGCOMPONENTS_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh sortingcomponents --no-virtual-env
        shell: bash

      - name: Test generation
        if: env.GENERATION_CHANGED == 'true' || env.CORE_CHANGED == 'true'
        run: ./.github/run_tests.sh generation --no-virtual-env
        shell: bash