run_pynwb_tests.yml

name: Run PyNWB tests
on:
  pull_request:
  schedule:
    - cron: '0 5 * * *'  # once per day at midnight ET
  workflow_dispatch:

jobs:
  run-pynwb-tests:
    runs-on: ubuntu-latest
    concurrency:
      group: ${{ github.workflow }}-${{ github.ref }}
      cancel-in-progress: true
    steps:
      - name: Checkout repo with submodules
        uses: actions/checkout@v4
        with:
          submodules: 'recursive'
          fetch-depth: 0  # tags are required to determine the version

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.12'

      - name: Update pip
        run: python -m pip install --upgrade pip

      - name: Clone PyNWB and install dev branch of HDMF
        run: |
          python -m pip list
          git clone https://github.com/NeurodataWithoutBorders/pynwb.git --recurse-submodules
          cd pynwb
          python -m pip install -r requirements-dev.txt  # do not install the pinned install requirements
          # must install in editable mode for coverage to find sources
          python -m pip install -e .  # this will install a different version of hdmf from the current one
          cd ..
          python -m pip uninstall -y hdmf  # uninstall the other version of hdmf
          python -m pip install .  # reinstall current branch of hdmf
          python -m pip list

      - name: Run PyNWB tests on PyNWB dev branch
        run: |
          cd pynwb
          python test.py -v