ete4

Signed-off-by: Lukas Heumos <[email protected]>

Author: Zethson

.github/workflows/test_tutorials.yml

@@ -86,7 +86,7 @@ jobs:
                 cache-dependency-glob: pyproject.toml
             - name: Install dependencies
               run: |
-                  uv pip install --system rpy2 decoupler muon
+                  uv pip install --system rpy2 decoupler muon ete4
                   uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,tcoda,de]"
                   uv pip install --system nbconvert ipykernel
 

docs/tutorials/notebooks

@@ -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)
@@ -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
@@ -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