Add kilosort4 wrapper tests #30
Workflow file for this run
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| name: Testing Kilosort4 | |
| 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: | |
| fetch-versions: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.12 | |
| - name: Install dependencies | |
| run: | | |
| pip install requests | |
| - name: Fetch package versions from PyPI | |
| run: | | |
| python .github/scripts/check_kilosort4_releases.py | |
| echo $(pwd) | |
| pwd | |
| ls .github/scripts | |
| echo ${{ github.workspace }} | |
| shell: bash | |
| - name: Upload versions file | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: versions | |
| path: ${{ github.workspace }}/.github/scripts/kilosort4-latest-version.json | |
| configure: | |
| needs: fetch-versions | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: Checkout to repository | |
| uses: actions/checkout@v2 | |
| - name: Set matrix data | |
| id: set-matrix | |
| run: | | |
| pwd | |
| ls .github/scripts | |
| ls | |
| echo "matrix=$(jq -c . < ${{ github.workspace }}/.github/scripts/kilosort4-latest-version.json)" >> $GITHUB_OUTPUT | |
| test: | |
| needs: configure | |
| name: ${{ matrix.os }} Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12"] # TODO: "3.9", # Lower and higher versions we support | |
| os: [ubuntu-latest] # TODO: macos-13, windows-latest, | |
| ks_version: ${{ fromJson(needs.configure.outputs.matrix) }} # TODO: add / build from pypi based on Christians PR | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install packages | |
| # TODO: maybe dont need full? | |
| run: | | |
| pip install -e .[test] | |
| # git config --global user.email "[email protected]" | |
| # git config --global user.name "CI Almighty" | |
| # pip install tabulate | |
| shell: bash | |
| - name: Install Kilosort | |
| run: | | |
| pip install kilosort==${{ matrix.ks_version }} | |
| shell: bash | |
| - name: Run new kilosort4 tests | |
| # run: chmod +x .github/test_kilosort4.sh | |
| # TODO: figure out the paths to be able to run this by calling the file directly | |
| run: | | |
| pytest -k test_kilosort4_new --durations=0 | |
| shell: bash | |
| # TODO: pip install -e .[full,dev] is failing # | |
| #The conflict is caused by: | |
| # spikeinterface[docs] 0.101.0rc0 depends on datalad==0.16.2; extra == "docs" | |
| # spikeinterface[test] 0.101.0rc0 depends on datalad>=1.0.2; extra == "test" |