Simplify var_groups

src/scanpy/neighbors/_connectivity.py

@@ -122,7 +122,7 @@ def umap(
         warnings.filterwarnings("ignore", message=r"Tensorflow not installed")
         from umap.umap_ import fuzzy_simplicial_set
 
-    X = coo_matrix(([], ([], [])), shape=(n_obs, 1))
+    X = coo_matrix((n_obs, 1))
     connectivities, _sigmas, _rhos = fuzzy_simplicial_set(
         X,
         n_neighbors,

src/scanpy/plotting/_baseplot_class.py

@@ -38,6 +38,11 @@ class VBoundNorm(NamedTuple):
     norm: Normalize | None
 
 
+class VarGroups(NamedTuple):
+    labels: Sequence[str]
+    positions: Sequence[tuple[int, int]]
+
+
 doc_common_groupby_plot_args = """\
 title
     Title for the figure
@@ -87,6 +92,8 @@ class BasePlot:
 
     MAX_NUM_CATEGORIES = 500  # maximum number of categories allowed to be plotted
 
+    var_groups: VarGroups | None
+
     @old_positionals(
         "use_raw",
         "log",
@@ -129,18 +136,24 @@ def __init__(
         norm: Normalize | None = None,
         **kwds,
     ):
-        self.var_names = var_names
-        self.var_group_labels = var_group_labels
-        self.var_group_positions = var_group_positions
+        self.var_names, self.var_groups = _var_groups(var_names, ref=adata.var_names)
+        match (var_group_labels, var_group_positions, self.var_groups):
+            case (None, None, _):
+                pass  # inferred from `var_names`
+            case (None, _, _) | (_, None, _):
+                msg = "both or none of var_group_labels and var_group_positions must be set"
+                raise TypeError(msg)
+            case (_, _, None):
+                if len(var_group_labels) != len(var_group_positions):
+                    msg = "var_group_labels and var_group_positions must have the same length"
+                    raise ValueError(msg)
+                self.var_groups = VarGroups(var_group_labels, var_group_positions)
+            case (_, _, _):
+                msg = "var_group_labels and var_group_positions cannot be set if var_names is a dict"
+                raise TypeError(msg)
         self.var_group_rotation = var_group_rotation
         self.width, self.height = figsize if figsize is not None else (None, None)
 
-        self.has_var_groups = (
-            var_group_positions is not None and len(var_group_positions) > 0
-        )
-
-        self._update_var_groups()
-
         self.categories, self.obs_tidy = _prepare_dataframe(
             adata,
             self.var_names,
@@ -702,7 +715,7 @@ def make_figure(self):
             width_ratios=[mainplot_width + self.group_extra_size, self.legends_width],
         )
 
-        if self.has_var_groups:
+        if self.var_groups:
             # add some space in case 'brackets' want to be plotted on top of the image
             if self.are_axes_swapped:
                 var_groups_height = category_height
@@ -754,14 +767,14 @@ def make_figure(self):
             if self.plot_group_extra is not None:
                 group_extra_ax = self.fig.add_subplot(mainplot_gs[2, 1], sharey=main_ax)
                 group_extra_orientation = "right"
-            if self.has_var_groups:
+            if self.var_groups:
                 gene_groups_ax = self.fig.add_subplot(mainplot_gs[1, 0], sharex=main_ax)
                 var_group_orientation = "top"
         else:
             if self.plot_group_extra:
                 group_extra_ax = self.fig.add_subplot(mainplot_gs[1, 0], sharex=main_ax)
                 group_extra_orientation = "top"
-            if self.has_var_groups:
+            if self.var_groups:
                 gene_groups_ax = self.fig.add_subplot(mainplot_gs[2, 1], sharey=main_ax)
                 var_group_orientation = "right"
 
@@ -781,11 +794,11 @@ def make_figure(self):
             return_ax_dict["group_extra_ax"] = group_extra_ax
 
         # plot group legends on top or left of main_ax (if given)
-        if self.has_var_groups:
+        if self.var_groups:
             self._plot_var_groups_brackets(
                 gene_groups_ax,
-                group_positions=self.var_group_positions,
-                group_labels=self.var_group_labels,
+                group_positions=self.var_groups.positions,
+                group_labels=self.var_groups.labels,
                 rotation=self.var_group_rotation,
                 left_adjustment=0.2,
                 right_adjustment=0.7,
@@ -924,31 +937,30 @@ def _format_first_three_categories(_categories):
         if self.var_names is not None:
             var_names_idx_ordered = list(range(len(self.var_names)))
 
-        if self.has_var_groups:
-            if set(self.var_group_labels) == set(self.categories):
+        if self.var_groups:
+            if set(self.var_groups.labels) == set(self.categories):
                 positions_ordered = []
                 labels_ordered = []
                 position_start = 0
                 var_names_idx_ordered = []
                 for cat_name in categories_ordered:
-                    idx = self.var_group_labels.index(cat_name)
-                    position = self.var_group_positions[idx]
+                    idx = self.var_groups.labels.index(cat_name)
+                    position = self.var_groups.positions[idx]
                     _var_names = self.var_names[position[0] : position[1] + 1]
                     var_names_idx_ordered.extend(range(position[0], position[1] + 1))
                     positions_ordered.append(
                         (position_start, position_start + len(_var_names) - 1)
                     )
                     position_start += len(_var_names)
-                    labels_ordered.append(self.var_group_labels[idx])
-                self.var_group_labels = labels_ordered
-                self.var_group_positions = positions_ordered
+                    labels_ordered.append(self.var_groups.labels[idx])
+                self.var_groups = VarGroups(labels_ordered, positions_ordered)
             else:
                 logg.warning(
                     "Groups are not reordered because the `groupby` categories "
                     "and the `var_group_labels` are different.\n"
                     f"categories: {_format_first_three_categories(self.categories)}\n"
                     "var_group_labels: "
-                    f"{_format_first_three_categories(self.var_group_labels)}"
+                    f"{_format_first_three_categories(self.var_groups.labels)}"
                 )
 
         if var_names_idx_ordered is not None:
@@ -1082,35 +1094,30 @@ def _plot_var_groups_brackets(
             axis="x", bottom=False, labelbottom=False, labeltop=False
         )
 
-    def _update_var_groups(self) -> None:
-        """
-        checks if var_names is a dict. Is this is the cases, then set the
-        correct values for var_group_labels and var_group_positions
 
-        updates var_names, var_group_labels, var_group_positions
-        """
-        if isinstance(self.var_names, Mapping):
-            if self.has_var_groups:
-                logg.warning(
-                    "`var_names` is a dictionary. This will reset the current "
-                    "values of `var_group_labels` and `var_group_positions`."
-                )
-            var_group_labels = []
-            _var_names = []
-            var_group_positions = []
-            start = 0
-            for label, vars_list in self.var_names.items():
-                if isinstance(vars_list, str):
-                    vars_list = [vars_list]
-                # use list() in case var_list is a numpy array or pandas series
-                _var_names.extend(list(vars_list))
-                var_group_labels.append(label)
-                var_group_positions.append((start, start + len(vars_list) - 1))
-                start += len(vars_list)
-            self.var_names = _var_names
-            self.var_group_labels = var_group_labels
-            self.var_group_positions = var_group_positions
-            self.has_var_groups = True
-
-        elif isinstance(self.var_names, str):
-            self.var_names = [self.var_names]
+def _var_groups(
+    var_names: _VarNames | Mapping[str, _VarNames], *, ref: pd.Index[str]
+) -> tuple[Sequence[str], VarGroups | None]:
+    """
+    Normalize var_names.
+    If it’s a mapping, also return var_group_labels and var_group_positions.
+    """
+
+    if not isinstance(var_names, Mapping):
+        var_names = [var_names] if isinstance(var_names, str) else var_names
+        return var_names, None
+
+    var_group_labels: list[str] = []
+    var_names_seq: list[str] = []
+    var_group_positions: list[tuple[int, int]] = []
+    for label, vars_list in var_names.items():
+        vars_list = [vars_list] if isinstance(vars_list, str) else vars_list
+        start = len(var_names_seq)
+        # use list() in case var_list is a numpy array or pandas series
+        var_names_seq.extend(list(vars_list))
+        var_group_labels.append(label)
+        var_group_positions.append((start, start + len(vars_list) - 1))
+    if not var_names_seq:
+        msg = "No valid var_names were passed."
+        raise ValueError(msg)
+    return var_names_seq, VarGroups(var_group_labels, var_group_positions)