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build: drop python 3.8, support python 3.13 #378

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build: drop python 3.8, support python 3.13

build: drop python 3.8, support python 3.13 #378

Workflow file for this run

.github/workflows/test_dependents.yml at a133b7a
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