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name: Scaden CI | ||
# This workflow installs Scaden, creates example data and performs all | ||
# steps of the Scaden workflow: simulation, processing, training and prediction | ||
on: [push, pull_request] | ||
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jobs: | ||
run_scaden: | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- uses: actions/checkout@v2 | ||
- name: Set up Python | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: "3.x" | ||
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- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install setuptools wheel twine | ||
- name: Install Scaden | ||
run: | | ||
pip install . | ||
- name: Create example data | ||
run: | | ||
mkdir example_data | ||
scaden example -out example_data | ||
- name: Simulate training data | ||
run: | | ||
scaden simulate -d example_data --pattern '*_counts.txt' | ||
- name: Scaden process | ||
run: | | ||
scaden process data.h5ad example_data/example_bulk_data.txt | ||
- name: Scaden training | ||
run: | | ||
scaden train processed.h5ad --steps 100 --model_dir model | ||
- name: Scaden predict | ||
run: | | ||
scaden predict --model_dir model example_data/example_bulk_data.txt |