No transactions v0 spikesorting pipeline #1140
Workflow file for this run
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| name: Tests | |
| 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] | |
| workflow_dispatch: # Manually trigger with 'Run workflow' button | |
| concurrency: # Replace Cancel Workflow Action | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| run-tests: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| OS: ubuntu-latest | |
| PYTHON: '3.9' | |
| services: | |
| mysql: | |
| image: datajoint/mysql:8.0 | |
| env: # args: mysql -h 127.0.0.1 -P 3308 -uroot -ptutorial -e "CMD;" | |
| 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 | |
| sudo apt-get install mysql-client libmysqlclient-dev libgirepository1.0-dev -y | |
| sudo apt-get install ffmpeg libsm6 libxext6 -y # non-dlc position deps | |
| - name: Run pip install for test deps | |
| run: | | |
| pip install --quiet .[test] | |
| - name: Download data | |
| 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: Run tests | |
| run: | | |
| pytest --no-docker --no-dlc tests/ |