Full spikeinterface tests codecov #109
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |