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Add extractor for BioFormats (CXD) #168

Add extractor for BioFormats (CXD)

Add extractor for BioFormats (CXD) #168

Workflow file for this run

name: Dev Testing
on:
pull_request:
workflow_dispatch:
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
run:
name: Ubuntu tests with Python ${{ matrix.python-version }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow --tags
- name: Setup Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Global Setup
run: |
pip install -U pip
pip install pytest-xdist
git config --global user.email "[email protected]"
git config --global user.name "CI Almighty"
pip install wheel==0.41.2 # needed for scanimage
- name: Install full requirements
run: |
pip install .[test]
pip install .[full]
- name: Clone and Install NeuroConv
run: |
git clone https://github.com/catalystneuro/neuroconv.git
cd neuroconv
pip install --no-cache-dir .[full,test]
cd ../
- name: Get ophys_testing_data current head hash
id: ophys
run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
- name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
uses: actions/cache@v2
id: cache-ophys-datasets
with:
path: ./ophys_testing_data
key: ophys-datasets-042023-ubuntu-latest-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
- name: Run NeuroConv tests
run: |
pytest -n auto --dist loadscope neuroconv/tests/test_ophys neuroconv/tests/test_on_data/test_imaging_interfaces.py neuroconv/tests/test_on_data/test_segmentation_interfaces.py