move ag3/af1 to after species selection #22
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name: notebooks-gambiae | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
jobs: | |
run: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: true | |
matrix: | |
python-version: ['3.8', '3.11'] | |
steps: | |
- name: Checkout source | |
uses: actions/checkout@v3 | |
- name: Install poetry | |
run: pipx install poetry==1.4.2 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: 'poetry' | |
- name: Install dependencies | |
run: | | |
poetry install | |
poetry run python -m ipykernel install --user --name AnoPrimer | |
- name: Run notebooks | |
run: | | |
poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params.json | |
poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR2_run.ipynb -k AnoPrimer -f tests/cDNA_Params_2.json | |
poetry run papermill notebooks/AnoPrimer-long.ipynb gDNA_run.ipynb -k AnoPrimer -f tests/gDNA_probe_Params.json | |
poetry run papermill notebooks/AnoPrimer-long.ipynb probe_run.ipynb -k AnoPrimer -f tests/probe_Params.json | |
poetry run papermill notebooks/AnoPrimer-short.ipynb short_run.ipynb -k AnoPrimer |