Skip to content

coxph_forestplot

coxph_forestplot #3067

Workflow file for this run

name: Run Notebooks
on:
- push
- pull_request
jobs:
run:
runs-on: ubuntu-latest
strategy:
matrix:
notebook: [
"docs/tutorials/notebooks/ehrapy_introduction.ipynb",
"docs/tutorials/notebooks/mimic_2_introduction.ipynb",
"docs/tutorials/notebooks/mimic_2_survival_analysis.ipynb",
# "docs/tutorials/notebooks/mimic_2_fate.ipynb", # https://github.com/theislab/cellrank/issues/1235
"docs/tutorials/notebooks/mimic_2_causal_inference.ipynb",
# "docs/tutorials/notebooks/mimic_3_demo.ipynb",
# "docs/tutorials/notebooks/medcat.ipynb",
]
steps:
- uses: actions/checkout@v4
with:
submodules: "true"
token: "${{ secrets.CT_SYNC_TOKEN }}"
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Install UV
run: pip install uv
- name: Install ehrapy and additional dependencies
run: uv pip install --system . cellrank nbconvert ipykernel graphviz
- name: Install scvelo from Github
run: uv pip install --system git+https://github.com/theislab/scvelo.git
- name: Run ${{ matrix.notebook }} Notebook
run: jupyter nbconvert --to notebook --execute ${{ matrix.notebook }}