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refmap-ci.yml
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name: Run tutorials (refmap)
on:
push:
branches:
- main
pull_request:
branches:
- main
env:
debug: 'true'
jobs:
refmap:
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 '.[refmap_old]'
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
# Note: all three files are renamed during the download to trim the "subsample_" prefix
- name: Preparing the data
run: |
mkdir -p reference_mapping && cd reference_mapping
mkdir data.dir && cd data.dir
curl -L -o pancreas_querydata.h5ad https://figshare.com/ndownloader/files/43166068
curl -L -o pancreas_refdata.h5mu https://figshare.com/ndownloader/files/43166074
cd ..
mkdir -p models && cd models
mkdir -p pancreas_model
mkdir -p pancreas_model_scanvi
curl -L -o pancreas_model_scanvi/model.pt https://figshare.com/ndownloader/files/43166410
curl -L -o pancreas_model/model.pt https://figshare.com/ndownloader/files/43166413
- name: Preparing the configuration file
shell: bash -el {0}
run: |
cd reference_mapping
panpipes refmap config
- name: Edit the submission file
run: |
cd reference_mapping
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/refmap_pancreas/pipeline.yml
#scib is not up to date with scanpy
- name: Replace template contents in configuration file
run: |
cd reference_mapping
sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml
sed -i 's+/Users/fabiola.curion/Documents/devel/data_test.dir/data_for_scvi_test/pancreas_model/model.pt+models/pancreas_model/model.pt+g' pipeline.yml
sed -i 's+/Users/fabiola.curion/Documents/devel/data_test.dir/data_for_scvi_test/pancreas_model_scanvi/model.pt+models/pancreas_model_scanvi/model.pt+g' pipeline.yml
sed -i 's+max_epochs: 200+max_epochs: 20+g' pipeline.yml
sed -i 's+run: True+run: False+g' pipeline.yml
- name: File tree
if: env.debug == 'true'
run: tree reference_mapping
- name: Review pipeline tasks
shell: bash -el {0}
run: |
cd reference_mapping
panpipes refmap show full --local
- name: Run pipeline tasks
shell: bash -el {0}
run: |
cd reference_mapping
panpipes refmap make full --local
- name: File tree
if: env.debug == 'true'
run: tree reference_mapping