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added CI workflow
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KevinMenden committed Dec 19, 2020
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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]

jobs:
run_scaden:
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"

- 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

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