No-credential data download #1122
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_review: | ||
| - types: [submitted] | ||
| 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: | ||
| if: | # If not PR OR is approved PR. | ||
| github.event_name != 'pull_request_review' | ||
| || github.event.review.state == 'approved' | ||
| 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 | ||
