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fixed test. had to return figure and axis, so the test can save the i… #3072

fixed test. had to return figure and axis, so the test can save the i…

fixed test. had to return figure and axis, so the test can save the i… #3072

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 }}