build: drop python 3.8, support python 3.13 #379
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name: test dependents | |
on: | |
push: | |
branches: | |
- "main" | |
pull_request: | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
jobs: | |
test-aicsimageio: | |
name: test aicsimageio | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
repository: AllenCellModeling/aicsimageio | |
submodules: true | |
- uses: actions/checkout@v4 | |
with: | |
path: ome-types | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Install aicsimageio | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install .[test] | |
python -m pip install bioformats_jar | |
- uses: actions/cache@v4 | |
id: cache | |
with: | |
path: aicsimageio/tests/resources | |
key: ${{ hashFiles('scripts/TEST_RESOURCES_HASH.txt') }} | |
- name: Download Test Resources | |
if: steps.cache.outputs.cache-hit != 'true' | |
run: python scripts/download_test_resources.py --debug | |
- name: Install ome-types | |
run: pip install . | |
working-directory: ome-types | |
- name: Run Tests | |
run: | | |
pytest --color=yes -k \ | |
"not test_known_errors_without_cleaning and not bad and not Imaris" \ | |
aicsimageio/tests/readers/test_ome_tiff_reader.py \ | |
aicsimageio/tests/writers/test_ome_tiff_writer.py \ | |
aicsimageio/tests/readers/extra_readers/test_bioformats_reader.py \ | |
aicsimageio/tests/readers/extra_readers/test_ome_zarr_reader.py | |
test-paquo: | |
name: test paquo | |
runs-on: ubuntu-latest | |
env: | |
QUPATH_VERSION: 0.4.3 | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
- name: Install dependencies | |
run: | | |
python -m pip install -U pip | |
python -m pip install .[test] | |
python -m pip install paquo | |
- name: Restore qupath cache | |
uses: actions/cache@v4 | |
env: | |
CACHE_NUMBER: 0 | |
with: | |
path: ./qupath/download | |
key: ${{ runner.os }}-qupath-v${{ env.CACHE_NUMBER }} | |
- name: Install qupath and set PAQUO_QUPATH_DIR | |
shell: bash | |
run: | | |
python -c "import os; os.makedirs('qupath/download', exist_ok=True)" | |
python -c "import os; os.makedirs('qupath/apps', exist_ok=True)" | |
python -m paquo get_qupath --install-path ./qupath/apps --download-path ./qupath/download ${{ env.QUPATH_VERSION }} \ | |
| grep -v "^#" | sed "s/^/PAQUO_QUPATH_DIR=/" >> $GITHUB_ENV | |
- name: Test with pytest | |
run: pytest tests/test_paquo.py | |
test-nd2: | |
name: test nd2 | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
repository: tlambert03/nd2 | |
fetch-depth: 0 | |
- uses: actions/checkout@v4 | |
with: | |
path: ome-types | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Install nd2 | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install .[test] | |
- uses: actions/cache@v4 | |
id: cache | |
with: | |
path: tests/data | |
key: ${{ hashFiles('scripts/download_samples.py') }} | |
- name: Download Samples | |
if: steps.cache.outputs.cache-hit != 'true' | |
run: | | |
pip install requests | |
python scripts/download_samples.py | |
- name: Install ome-types | |
run: pip install . | |
working-directory: ome-types | |
- name: Run Tests | |
run: pytest --color=yes -v tests/test_ome.py | |
test_omero_cli: | |
name: test omero-cli-transfer | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.9" | |
- name: Install dependencies | |
run: | | |
python -m pip install -U pip | |
python -m pip install .[test] | |
python -m pip install omero-cli-transfer --no-deps | |
- name: Test | |
run: pytest tests/test_omero_cli.py -v |