Run notebooks in CI

.github/workflows/test_tutorials.yml

@@ -0,0 +1,94 @@
+name: Test tutorials
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    test:
+        runs-on: ubuntu-latest
+        defaults:
+            run:
+              # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
+              shell: bash -euo pipefail {0}
+
+        env:
+            NOTEBOOK_PATH: docs/tutorials/notebooks
+
+        strategy:
+            fail-fast: false
+            matrix:
+                notebook: [
+                        "augur.ipynb",
+                        "cinemaot.ipynb",
+                        "differential_gene_expression.ipynb",
+                        "distances.ipynb",
+                        "distance_tests.ipynb",
+                        "enrichment.ipynb",
+                        "guide_rna_assignment.ipynb",
+                        "milo.ipynb",
+                        "mixscape.ipynb",
+                        "perturbation_space.ipynb",
+                        "sccoda.ipynb",
+                        # "dialogue.ipynb", takes too long
+                        # "tasccoda.ipynb", a pain to get running because of the required QT dependency. The QT action leads to a dead kernel
+                        # also no use cases yet
+                    ]
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                filter: blob:none
+                fetch-depth: 0
+                submodules: "true"
+
+            - name: Cache .pertpy_cache
+              uses: actions/cache@v4
+              with:
+                path: cache
+                key: ${{ runner.os }}-pertpy-cache-${{ hashFiles('pertpy/metadata/**') }}
+                restore-keys: |
+                  ${{ runner.os }}-pertpy-cache
+
+            - name: Set up Python
+              uses: actions/setup-python@v5
+              with:
+                  python-version: "3.13"
+            - name: Install R
+              uses: r-lib/actions/setup-r@v2
+              with:
+                  r-version: "4.4.3"
+
+            - name: Cache R packages
+              id: r-cache
+              uses: actions/cache@v3
+              with:
+                path: ${{ env.R_LIBS_USER }}
+                key: ${{ runner.os }}-r-${{ hashFiles('**/pertpy/tools/_milo.py') }}
+                restore-keys: ${{ runner.os }}-r-
+
+            - name: Install R dependencies
+              if: steps.r-cache.outputs.cache-hit != 'true'
+              run: |
+                mkdir -p ${{ env.R_LIBS_USER }}
+                Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); BiocManager::install('edgeR', lib='${{ env.R_LIBS_USER }}')"
+
+            - name: Install uv
+              uses: astral-sh/setup-uv@v6
+              with:
+                enable-cache: true
+                cache-dependency-glob: pyproject.toml
+            - name: Install dependencies
+              run: |
+                  uv pip install --system rpy2 decoupler muon
+                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
+                  uv pip install --system nbconvert ipykernel
+
+            - name: Run ${{ matrix.notebook }} Notebook
+              run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }}

pertpy/tools/_coda/_base_coda.py

@@ -1472,6 +1472,7 @@ def plot_effects_barplot(  # pragma: no cover # noqa: D417
         if return_fig and not plot_facets:
             return plt.gcf()
         plt.show()
+
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
@@ -1823,6 +1824,7 @@ def label_point(x, y, val, ax):
         if return_fig:
             return plt.gcf()
         plt.show()
+
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
@@ -1881,7 +1883,7 @@ def plot_draw_tree(  # pragma: no cover # noqa: D417
             from ete4.treeview import CircleFace, NodeStyle, TextFace, TreeStyle, faces
         except ImportError:
             raise ImportError(
-                "To use tasccoda please install additional dependencies with `pip install pertpy[coda]`"
+                "To use tasccoda please install additional dependencies: `pip install pertpy[coda]`"
             ) from None
 
         if isinstance(data, MuData):
@@ -1902,8 +1904,8 @@ def my_layout(node):
             tree.render(save, tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)  # type: ignore
         if return_fig:
             return tree, tree_style
+
         return tree.render("%%inline", tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)  # type: ignore
-        return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
     def plot_draw_effects(  # pragma: no cover # noqa: D417
@@ -1969,7 +1971,7 @@ def plot_draw_effects(  # pragma: no cover # noqa: D417
             from ete4.treeview import CircleFace, NodeStyle, TextFace, TreeStyle, faces
         except ImportError:
             raise ImportError(
-                "To use tasccoda please install additional dependencies as `pip install pertpy[coda]`"
+                "To use tasccoda please install additional dependencies: `pip install pertpy[coda]`"
             ) from None
 
         if isinstance(data, MuData):
@@ -2207,6 +2209,7 @@ def plot_effects_umap(  # pragma: no cover # noqa: D417
         if return_fig:
             return fig
         plt.show()
+
         return None
 
 
@@ -2325,6 +2328,7 @@ def df2newick(df: pd.DataFrame, levels: list[str], inner_label: bool = True) ->
     strs = [traverse(df_tax, a, 0, inner_label) for a in alevel]
 
     newick = f"({','.join(strs)});"
+
     return newick