create a new hostname #17
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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 | ||
| <<<<<<< chain-multiple-labels | ||
| - name: Run wet-run test for merging 3 labels | ||
| 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 --overlay2_bids_dir test_data/bids_wetrun_testing/tpl-MNI152NLin2009cAsym/ --overlay2_desc carpet --cores all --force-output --conda-frontend mamba | tee labelmerge_output.log | ||
| ======= | ||
| >>>>>>> integrate-conda | ||
