diff --git a/.github/workflows/run-bioformats-tests.yml b/.github/workflows/run-bioformats-tests.yml index 969ea69a..a16afe78 100644 --- a/.github/workflows/run-bioformats-tests.yml +++ b/.github/workflows/run-bioformats-tests.yml @@ -21,21 +21,12 @@ jobs: auto-activate-base: false python-version: 3.9 - - name: Create conda environment from file - run: conda env create -f src/roiextractors/extractors/bioformatsimagingextractors/bioformats_env.yml - - name: Activate conda environment - run: echo "conda activate bioformats-environment" >> $GITHUB_ENV - - - name: Set JAVA_HOME - run: | - if [ -z "${JAVA_HOME}" ]; then - echo "JAVA_HOME=$CONDA_PREFIX" >> $GITHUB_ENV - fi + run: echo "conda activate test" >> $GITHUB_ENV - name: Global Setup env: - CONDA_PREFIX: bioformats-environment + CONDA_PREFIX: test run: | source activate $CONDA_PREFIX pip install -U pip @@ -46,12 +37,26 @@ jobs: - name: Install full requirements env: - CONDA_PREFIX: bioformats-environment + CONDA_PREFIX: test run: | source activate $CONDA_PREFIX pip install .[test] pip install -e .[full] + - name: Install BioFormats requirements + env: + CONDA_PREFIX: test + run: | + source activate $CONDA_PREFIX + pip install aicsimageio>=4.14.0 + conda install -c conda-forge bioformats_jar + + - name: Set JAVA_HOME + run: | + if [ -z "${JAVA_HOME}" ]; then + echo "JAVA_HOME=$CONDA_PREFIX" >> $GITHUB_ENV + fi + - name: Get ophys_testing_data current head hash id: ophys run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)" @@ -65,7 +70,7 @@ jobs: - name: Run BioFormats tests env: - CONDA_PREFIX: bioformats-environment + CONDA_PREFIX: test run: | source activate $CONDA_PREFIX pytest tests/test_cxdimagingextractor.py -n auto --dist loadscope