Fix conversion of Zarr string dataset to HDF5 #1834
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name: Run HDMF-Zarr tests | |
on: | |
pull_request: | |
schedule: | |
- cron: '0 5 * * *' # once per day at midnight ET | |
workflow_dispatch: | |
jobs: | |
run-hdmf-zarr-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: '3.10' # use 3.10 until hdmf-zarr updates versioneer.py which breaks on newer python | |
- name: Update pip | |
run: python -m pip install --upgrade pip | |
- name: Clone HDMF-Zarr and install dev branch of HDMF | |
run: | | |
python -m pip list | |
git clone https://github.com/hdmf-dev/hdmf-zarr.git --recurse-submodules | |
cd hdmf-zarr | |
python -m pip install -r requirements-dev.txt # do not install the pinned install requirements | |
python -m pip install . # 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 HDMF-Zarr tests on HDMF-Zarr dev branch | |
run: | | |
cd hdmf-zarr | |
pytest |