Full spikeinterface tests codecov #139
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| name: Full spikeinterface tests codecov | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 12 * * *" # Daily at noon UTC | |
| env: | |
| KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }} | |
| KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }} | |
| jobs: | |
| build-and-test: | |
| name: Codecov in Ubuntu | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # "macos-latest", "windows-latest" | |
| os: ["ubuntu-latest", ] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Get current year-month | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT | |
| - name: Restore cached virtual environment with dependencies | |
| uses: actions/cache/restore@v3 | |
| id: cache-venv | |
| with: | |
| path: ~/test_env | |
| key: ${{ runner.os }}-venv-${{ hashFiles('**/pyproject.toml') }}-${{ steps.date.outputs.date }} | |
| restore-keys: | | |
| ${{ runner.os }}-venv- | |
| - name: Get ephy_testing_data current head hash | |
| # the key depends on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git | |
| id: vars | |
| run: | | |
| echo "HASH_EPHY_DATASET=$(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@v3 | |
| 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: | | |
| ${{ runner.os }}-datasets | |
| - name: Install dependencies | |
| run: | | |
| # this is for datalad and download testing datasets | |
| sudo apt install git | |
| # needed for correct operation of git/git-annex/DataLad | |
| git config --global user.email "CI@example.com" | |
| git config --global user.name "CI Almighty" | |
| python -m venv ~/test_env | |
| python -m pip install -U pip # Official recommended way | |
| source ~/test_env/bin/activate | |
| pip install tabulate # This produces summaries at the end | |
| ## clean some cache to avoid using old cache | |
| pip cache remove numpy | |
| pip cache remove hdbscan | |
| pip cache remove numba | |
| pip install -e .[test,extractors,full] | |
| - name: git-annex install | |
| run: | | |
| wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz | |
| tar xvzf git-annex-standalone-amd64.tar.gz | |
| echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH | |
| - name: git-annex version | |
| run: | | |
| git-annex version | |
| - name: Packages installed | |
| run: | | |
| source ~/test_env/bin/activate | |
| pip list | |
| - name: Check ephy_testing_data files | |
| run: | | |
| if [ -d "$HOME/spikeinterface_datasets" ]; then | |
| find $HOME/spikeinterface_datasets | |
| fi | |
| - name: run tests | |
| run: | | |
| source ~/test_env/bin/activate | |
| pytest -m "not sorters_external" --cov=./ --cov-report xml:./coverage.xml -vv -ra --durations=0 | tee report_full.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1 | |
| echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY | |
| python ./.github/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY | |
| cat $GITHUB_STEP_SUMMARY | |
| rm report_full.txt | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| file: ./coverage.xml | |
| flags: unittests |