Moseq Pipeline #1228
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: 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/ |