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try activate conda env in every step
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weiglszonja committed Jun 5, 2024
1 parent 376a3ef commit d3c5d14
Showing 1 changed file with 8 additions and 15 deletions.
23 changes: 8 additions & 15 deletions .github/workflows/run-bioformats-tests.yml
Original file line number Diff line number Diff line change
@@ -11,6 +11,9 @@ jobs:
test:
runs-on: ubuntu-latest

env:
CONDA_ENV: test

steps:
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow --tags
@@ -21,38 +24,30 @@ jobs:
auto-activate-base: false
python-version: 3.9

- name: Activate conda environment
run: echo "conda activate test" >> $GITHUB_ENV

- 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" >> $GITHUB_ENV
fi
@@ -69,8 +64,6 @@ jobs:
key: ophys-datasets-042023-${{ runner.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}

- 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

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