From MuData to SpatialData #354
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name: Run tutorials (spatial deconvolution) | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
env: | |
debug: 'true' | |
jobs: | |
spatial_deconvolution: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" | |
python-version: ["3.10"] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
miniforge-version: latest | |
auto-activate-base: true | |
auto-update-conda: true | |
channels: conda-forge | |
channel-priority: strict | |
activate-environment: pipeline_env | |
environment-file: pipeline_env.yaml | |
- name: Install Panpipes | |
shell: bash -el {0} | |
run: | | |
pip install .[spatial] | |
conda list | |
- name: Conda info | |
if: env.debug == 'true' | |
shell: bash -el {0} | |
run: conda info | |
- name: Conda list | |
if: env.debug == 'true' | |
shell: pwsh | |
run: conda list | |
- name: Preparing the data | |
run: | | |
mkdir deconvolution deconvolution/data deconvolution/data/spatial_data | |
cd deconvolution/data | |
curl -L -o Human_Heart_reference.h5mu https://figshare.com/ndownloader/files/44969677 | |
cd spatial_data | |
curl -L -o Human_Heart.h5mu https://figshare.com/ndownloader/files/44969488 | |
# Note: we run the following to test that the commands works | |
- name: Preparing the configuration file | |
shell: bash -el {0} | |
run: | | |
cd deconvolution | |
panpipes deconvolution_spatial config | |
- name: Edit the submission file | |
run: | | |
cd deconvolution | |
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/deconvolution/pipeline.yml | |
- name: Replace template contents in configuration file | |
run: | | |
cd deconvolution | |
sed -i 's+use_gpu:+use_gpu: False+g' pipeline.yml | |
sed -i 's+max_epochs: 400+max_epochs: 50+g' pipeline.yml | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree deconvolution | |
- name: Review pipeline tasks | |
shell: bash -el {0} | |
run: | | |
cd deconvolution | |
panpipes deconvolution_spatial show full --local | |
- name: Run pipeline tasks | |
shell: bash -el {0} | |
run: | | |
cd deconvolution | |
panpipes deconvolution_spatial make full --local | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree deconvolution |