Integrate conda #13
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| --- | |
| name: test workflow with wet run | |
| on: | |
| pull_request: | |
| jobs: | |
| wetrun_test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge and mamba | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: latest | |
| mamba-version: '*' | |
| use-mamba: true | |
| conda-solver: libmamba | |
| auto-activate-base: true | |
| - name: Create environment with snakebids | |
| run: | | |
| mamba create -n snakebids-env snakebids scikit-learn pandas -c bioconda -c conda-forge -y | |
| - name: Cache Snakemake Conda environments | |
| uses: actions/cache@v4 | |
| with: | |
| path: test_data/labelmerge_cache_dir/conda | |
| key: conda-env-${{ hashFiles('labelmerge/workflow/envs/*.yaml') }} | |
| restore-keys: | | |
| conda-env- | |
| - name: Set LABELMERGE_CACHE_DIR | |
| run: | | |
| echo "LABELMERGE_CACHE_DIR=`pwd`/test_data/labelmerge_cache_dir" >> $GITHUB_ENV | |
| - name: Run wet-run test for cortical and subcortical files | |
| shell: bash -l {0} | |
| run: |- | |
| conda activate snakebids-env | |
| ./labelmerge/run.py test_data/bids_wetrun_testing/tpl-MNI152NLin2009cAsym test_out participant \ | |
| --base-desc 100Parcels7Networks --overlay_bids_dir test_data/bids_wetrun_testing/tpl-MNI152NLin2009cAsym \ | |
| --overlay_desc tn --cores all --force-output --conda-frontend mamba | tee labelmerge_output.log |