spikeinterface/.github/workflows/test_kilosort4.yml at main · SpikeInterface/spikeinterface · GitHub

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name: Testing Kilosort4

on:
  workflow_dispatch:
  schedule:
    - cron: "0 12 * * 0" # Weekly on Sunday at noon UTC
  pull_request:
    paths:
      - "**/kilosort4.py"
      - "**/test_kilosort4_ci.py"

jobs:
  versions:
    # Poll Pypi for all released KS4 versions >4.0.16, save to JSON
    # and store them in a matrix for the next job.
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Set up Python
        uses: actions/setup-python@v6
        with:
          python-version: "3.12"
      - uses: astral-sh/setup-uv@v7
        with:
          python-version: "3.12"
          enable-cache: true

      - name: Install dependencies
        run: |
          uv pip install --system requests packaging
          uv pip install --system .

      - name: Fetch package versions from PyPI
        run: |
          python .github/scripts/check_kilosort4_releases.py
        shell: bash

      - name: Set matrix data
        id: set-matrix
        run: |
          echo "matrix=$(jq -c . < .github/scripts/kilosort4-latest-version.json)" >> $GITHUB_OUTPUT

  test:
    needs: versions
    name: ${{ matrix.ks_version }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.12"]
        os: [ubuntu-latest]
        ks_version: ${{ fromJson(needs.versions.outputs.matrix) }}
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Setup Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
      - uses: astral-sh/setup-uv@v7
        with:
          python-version: ${{ matrix.python-version }}
          enable-cache: true

      - name: Install SpikeInterface
        run: |
          uv pip install --system -e .[full] --group test-sorters
        shell: bash

      - name: Install legacy setuptools for KS4 < 4.0.19
        if: matrix.ks_version == '4.0.16' || matrix.ks_version == '4.0.17' || matrix.ks_version == '4.0.18'
        run: uv pip install --system setuptools==78.0.2

      - name: Install legacy numpy for KS4 4.1.1 - 4.1.5
        if: |
          matrix.ks_version == '4.1.1' ||
          matrix.ks_version == '4.1.2' ||
          matrix.ks_version == '4.1.3' ||
          matrix.ks_version == '4.1.4' ||
          matrix.ks_version == '4.1.5' ||
          matrix.ks_version == '4.1.6'
        run: uv pip install --system "numpy<2.4"

      - name: Install Kilosort
        run: |
          uv pip install --system kilosort==${{ matrix.ks_version }}
        shell: bash

      - name: Run new kilosort4 tests
        run: |
          pytest .github/scripts/test_kilosort4_ci.py
        shell: bash