codecov.yml

name: Full spikeinterface tests codecov
on: workflow_dispatch
jobs:
  build-and-test:
    name: Codecov
    runs-on: "ubuntu-latest"
    steps:
      - uses: actions/checkout@v2
        with:
          python-version: 3.8
      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
      - uses: actions/cache@v2
        id: cache-venv
        with:
          path: ~/test_env
          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}${{ hashFiles('**/requirements_full.txt') }}-${{ hashFiles('**/requirements_extractors.txt') }}-${{ hashFiles('**/requirements_test.txt') }}-${{ steps.date.outputs.date }}
      - name: Install dependencies
        run: |
          sudo apt update
          # this is for datalad and download testing datasets
          sudo apt install git 
          # needed for correct operation of git/git-annex/DataLad
          git config --global user.email "CI@example.com"
          git config --global user.name "CI Almighty"
          # this is for spyking circus
          sudo apt install mpich libmpich-dev
          # create an environement (better for cahing)
          python -m venv ~/test_env
          source ~/test_env/bin/activate
          python -m pip install --upgrade pip
          pip install setuptools wheel twine
          ## clean some cache to avoid using old cache
          pip cache remove numpy
          pip cache remove hdbscan
          pip cache remove numba
          # TODO remove it after neo release
          # because it force some version (numpy/numba/dhdbscan...)
          pip install numpy==1.20
          pip install -r requirements_test.txt
          pip install -r requirements.txt
          pip install -r requirements_full.txt
          pip install -r requirements_extractors.txt
          pip install -e .
      - name: git-annex install
        run: |
          wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
          tar xvzf git-annex-standalone-amd64.tar.gz
          echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH
      - name: git-annex version
        run: |
          git-annex version
      - name: pip list
        run: |
          source ~/test_env/bin/activate
          pip list
      - name: Get ephy_testing_data current head hash
        # the key depend on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
        id: vars
        run: |
          echo "HASH_EPHY_DATASET=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
      - uses: actions/cache@v2
        id: cache-datasets
        env:
          # the key depend 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: run tests
        run: |
          source ~/test_env/bin/activate
          pytest --cov=./ --cov-report xml:./coverage.xml
      - uses: codecov/codecov-action@v2
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          version: "v0.1.15"
          fail_ci_if_error: true
          file: ./coverage.xml
          flags: unittests