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try activate conda env in every step
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Original file line number | Diff line number | Diff line change |
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@@ -11,6 +11,9 @@ jobs: | |
test: | ||
runs-on: ubuntu-latest | ||
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env: | ||
CONDA_ENV: test | ||
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steps: | ||
- uses: actions/checkout@v4 | ||
- run: git fetch --prune --unshallow --tags | ||
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@@ -21,38 +24,30 @@ jobs: | |
auto-activate-base: false | ||
python-version: 3.9 | ||
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- name: Activate conda environment | ||
run: echo "conda activate test" >> $GITHUB_ENV | ||
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- name: Global Setup | ||
env: | ||
CONDA_PREFIX: test | ||
run: | | ||
source activate $CONDA_PREFIX | ||
conda activate $CONDA_ENV | ||
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 | ||
env: | ||
CONDA_PREFIX: test | ||
run: | | ||
source activate $CONDA_PREFIX | ||
conda activate $CONDA_ENV | ||
pip install .[test] | ||
pip install -e .[full] | ||
- name: Install BioFormats requirements | ||
env: | ||
CONDA_PREFIX: test | ||
run: | | ||
source activate $CONDA_PREFIX | ||
conda activate $CONDA_ENV | ||
pip install aicsimageio>=4.14.0 | ||
conda install -c conda-forge bioformats_jar | ||
- name: Set JAVA_HOME | ||
run: | | ||
conda activate $CONDA_ENV | ||
if [ -z "${JAVA_HOME}" ]; then | ||
echo "JAVA_HOME=$CONDA_PREFIX" >> $GITHUB_ENV | ||
fi | ||
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@@ -69,8 +64,6 @@ jobs: | |
key: ophys-datasets-042023-${{ runner.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }} | ||
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- name: Run BioFormats tests | ||
env: | ||
CONDA_PREFIX: test | ||
run: | | ||
source activate $CONDA_PREFIX | ||
conda activate $CONDA_ENV | ||
pytest tests/test_cxdimagingextractor.py -n auto --dist loadscope |