From MuData to SpatialData #349
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name: Run integration01 | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
env: | |
debug: 'true' | |
jobs: | |
integration: | |
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 | |
# important: this patch is only to test if multivi integration works | |
# pip install -e . #'.[multivipatch]' | |
# issues are not related to panpipes | |
# https://discourse.scverse.org/t/error-when-training-model-on-m3-max-mps/1896/2 | |
# https://discourse.scverse.org/t/macbook-m1-m2-mps-acceleration-with-scvi/2075/4 | |
# now disabling adversarial training for temp fix to ensure running latest multivi | |
# https://github.com/scverse/scvi-tools/issues/2581 | |
- name: Install Panpipes | |
shell: bash -el {0} | |
run: | | |
pip install -e . | |
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 teaseq/integration && cd teaseq/integration | |
curl -L -o teaseq.h5mu https://figshare.com/ndownloader/files/44796985 | |
# Note: we run the following to test that the commands works | |
# However, the following task will replacing the file anyway | |
- name: Preparing the configuration file | |
shell: bash -el {0} | |
run: | | |
cd teaseq/integration | |
panpipes integration config | |
- name: Edit the submission file | |
run: | | |
cd teaseq/integration | |
curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes/main/tests/integration_1/pipeline.yml | |
- name: Replace template contents in configuration file | |
run: | | |
cd teaseq/integration | |
sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree teaseq | |
- name: Review pipeline tasks | |
shell: bash -el {0} | |
run: | | |
cd teaseq/integration | |
panpipes integration show full --local | |
- name: Run pipeline tasks | |
shell: bash -el {0} | |
run: | | |
cd teaseq/integration | |
panpipes integration make full --local | |
- name: File tree | |
if: env.debug == 'true' | |
run: tree teaseq | |
- name: check logs | |
if: always() | |
run: cat teaseq/integration/logs/4_multimodal_multivi.log |