Tests #2422
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| name: Tests | |
| permissions: | |
| contents: read | |
| on: | |
| push: | |
| branches: | |
| - '!test_branch' | |
| - '!documentation' | |
| schedule: # once a day at midnight UTC | |
| - cron: '0 0 * * *' | |
| pull_request: # requires approval for first-time contributors | |
| types: [synchronize, opened, reopened, labeled, closed] | |
| workflow_dispatch: # Manually trigger with 'Run workflow' button | |
| inputs: | |
| test_mode: | |
| description: 'Test mode (fast or full)' | |
| required: false | |
| default: 'full' | |
| type: choice | |
| options: | |
| - fast | |
| - full | |
| concurrency: # Replace Cancel Workflow Action | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| run-tests: | |
| # Skip if PR is closed but not merged | |
| if: |- | |
| github.event_name != 'pull_request' || | |
| github.event.action != 'closed' || | |
| github.event.pull_request.merged == true | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| OS: ubuntu-latest | |
| PYTHON: '3.9' | |
| services: | |
| mysql: | |
| image: datajoint/mysql:8.0 | |
| # args: mysql -h 127.0.0.1 -P 3308 -uroot -ptutorial -e "CMD;" | |
| env: | |
| MYSQL_DATABASE: localhost | |
| MYSQL_ROOT_PASSWORD: tutorial | |
| ports: | |
| - 3308:3306 | |
| options: >- | |
| --health-cmd="mysqladmin ping" | |
| --health-interval=10s | |
| --health-timeout=5s | |
| --health-retries=3 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON }} | |
| - name: Set up conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: spyglass | |
| environment-file: environment.yml | |
| miniforge-version: latest | |
| use-mamba: true | |
| - name: Install apt dependencies | |
| run: | | |
| sudo apt-get update # First mysql options | |
| # non-dlc position deps | |
| sudo apt-get install \ | |
| mysql-client libmysqlclient-dev libgirepository1.0-dev -y | |
| sudo apt-get install ffmpeg libsm6 libxext6 -y | |
| - name: Run pip install for test deps | |
| run: | | |
| pip install --quiet .[test] | |
| - name: Cache test data | |
| id: cache-test-data | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| tests/_data/raw/ | |
| tests/_data/video/ | |
| key: |- | |
| test-data-${{ hashFiles('.github/workflows/test-conda.yml') }}-v1 | |
| restore-keys: | | |
| test-data- | |
| - name: Download data | |
| if: steps.cache-test-data.outputs.cache-hit != 'true' | |
| env: | |
| BASEURL: https://ucsf.box.com/shared/static/ | |
| NWB_URL: k3sgql6z475oia848q1rgms4zdh4rkjn.nwb | |
| VID1URL: ykep8ek4ogad20wz4p0vuyuqfo60cv3w.h264 | |
| VID2URL: d2jjk0y565ru75xqojio3hymmehzr5he.h264 | |
| NWBFILE: minirec20230622.nwb | |
| VID_ONE: 20230622_minirec_01_s1.1.h264 | |
| VID_TWO: 20230622_minirec_02_s2.1.h264 | |
| RAW_DIR: /home/runner/work/spyglass/spyglass/tests/_data/raw/ | |
| VID_DIR: /home/runner/work/spyglass/spyglass/tests/_data/video/ | |
| run: | | |
| mkdir -p $RAW_DIR $VID_DIR | |
| curl_opts() { # Declare func with download options | |
| curl -L --output "$1""$2" "$BASEURL""$3" | |
| } | |
| curl_opts $RAW_DIR $NWBFILE $NWB_URL | |
| curl_opts $VID_DIR $VID_ONE $VID1URL | |
| curl_opts $VID_DIR $VID_TWO $VID2URL | |
| - name: Move actions coveragerc | |
| run: mv tests/.coveragerc .coveragerc | |
| - name: Determine test mode | |
| id: test_mode | |
| run: | | |
| # Determine which tests to run based on trigger | |
| if [[ "${{ github.event_name }}" == "push" ]]; then | |
| # Fast tests on push | |
| echo "mode=fast" >> $GITHUB_OUTPUT | |
| echo "marker_args=-m 'not slow and not very_slow'" \ | |
| >> $GITHUB_OUTPUT | |
| echo "description=Fast tests" >> $GITHUB_OUTPUT | |
| elif [[ "${{ github.event_name }}" == "pull_request" ]] \ | |
| && [[ "${{ github.event.action }}" == "closed" ]] \ | |
| && [[ "${{ github.event.pull_request.merged }}" == "true" ]]; then | |
| # Full suite on PR merge | |
| echo "mode=full" >> $GITHUB_OUTPUT | |
| echo "marker_args=" >> $GITHUB_OUTPUT | |
| echo "description=Full test suite" >> $GITHUB_OUTPUT | |
| elif [[ "${{ github.event_name }}" == "workflow_dispatch" ]]; then | |
| # Manual trigger - use input | |
| if [[ "${{ github.event.inputs.test_mode }}" == "fast" ]]; then | |
| echo "mode=fast" >> $GITHUB_OUTPUT | |
| echo "marker_args=-m 'not slow and not very_slow'" \ | |
| >> $GITHUB_OUTPUT | |
| echo "description=Fast tests (manual)" >> $GITHUB_OUTPUT | |
| else | |
| echo "mode=full" >> $GITHUB_OUTPUT | |
| echo "marker_args=" >> $GITHUB_OUTPUT | |
| echo "description=Full suite (manual)" >> $GITHUB_OUTPUT | |
| fi | |
| else | |
| # Full suite for schedule and other PR events | |
| # (synchronize, opened, etc.) | |
| echo "mode=full" >> $GITHUB_OUTPUT | |
| echo "marker_args=" >> $GITHUB_OUTPUT | |
| echo "description=Full test suite" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Run tests (${{ steps.test_mode.outputs.description }}) | |
| run: | | |
| pytest --no-docker --no-dlc \ | |
| --cov-config=.coveragerc --cov=spyglass-neuro --cov-report=xml \ | |
| ${{ steps.test_mode.outputs.marker_args }} \ | |
| tests/ | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: ${{ steps.test_mode.outputs.mode }}-tests | |
| name: ${{ steps.test_mode.outputs.description }} |