diff --git a/.github/workflows/ci-test.yml b/.github/workflows/ci-test.yml new file mode 100644 index 0000000..5793457 --- /dev/null +++ b/.github/workflows/ci-test.yml @@ -0,0 +1,45 @@ +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