Skip to content

From MuData to SpatialData #354

From MuData to SpatialData

From MuData to SpatialData #354

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