Utilize magic comma in new black update (scverse#1394)

.travis.yml

@@ -1,5 +1,8 @@
 dist: xenial
 language: python
+branches:
+  only:
+    - master  # All other branches should become (draft) PRs and be build that way
 matrix:
   include:
   - name: "static analysis"

docs/extensions/function_images.py

@@ -7,7 +7,7 @@
 
 
 def insert_function_images(
-    app: Sphinx, what: str, name: str, obj: Any, options: Options, lines: List[str],
+    app: Sphinx, what: str, name: str, obj: Any, options: Options, lines: List[str]
 ):
     path = app.config.api_dir / f'{name}.png'
     if what != 'function' or not path.is_file():

docs/extensions/github_links.py

@@ -26,7 +26,7 @@ def __call__(
     ):
         url = self.url_template.format(text)
         title = self.title_template.format(text)
-        options = {**dict(classes=[self.class_name],), **options}
+        options = {**dict(classes=[self.class_name]), **options}
         node = nodes.reference(rawtext, title, refuri=url, **options)
         return [node], []
 

pyproject.toml

@@ -48,7 +48,6 @@ exclude = '''
         |_paga
         |_umap
         |_utils
-        |_leiden
         |_louvain
         |_tsne_fix
         |_top_genes

scanpy/cli.py

@@ -22,9 +22,7 @@
 class _DelegatingSubparsersAction(_SubParsersAction):
     """Like a normal subcommand action, but uses a delegator for more choices"""
 
-    def __init__(
-        self, *args, _command: str, _runargs: Dict[str, Any], **kwargs,
-    ):
+    def __init__(self, *args, _command: str, _runargs: Dict[str, Any], **kwargs):
         super().__init__(*args, **kwargs)
         self.command = _command
         self._name_parser_map = self.choices = _CommandDelegator(
@@ -38,9 +36,7 @@ class _CommandDelegator(cabc.MutableMapping):
     but don’t calculate the whole list until necessary
     """
 
-    def __init__(
-        self, command: str, action: _DelegatingSubparsersAction, **runargs,
-    ):
+    def __init__(self, command: str, action: _DelegatingSubparsersAction, **runargs):
         self.command = command
         self.action = action
         self.parser_map = {}
@@ -120,7 +116,7 @@ def _cmd_settings() -> None:
 
 
 def main(
-    argv: Optional[Sequence[str]] = None, *, check: bool = True, **runargs,
+    argv: Optional[Sequence[str]] = None, *, check: bool = True, **runargs
 ) -> Optional[CompletedProcess]:
     """\
     Run a builtin scanpy command or a scanpy-* subcommand.

scanpy/datasets/_ebi_expression_atlas.py

@@ -43,10 +43,12 @@ def download_experiment(accession: str):
     experiment_dir.mkdir(parents=True, exist_ok=True)
 
     _download(
-        design_url + "experiment-design", experiment_dir / "experimental_design.tsv",
+        design_url + "experiment-design",
+        experiment_dir / "experimental_design.tsv",
     )
     _download(
-        mtx_url + "quantification-raw", experiment_dir / "expression_archive.zip",
+        mtx_url + "quantification-raw",
+        experiment_dir / "expression_archive.zip",
     )
 
 

scanpy/plotting/_anndata.py

@@ -420,7 +420,12 @@ def add_centroid(centroids, name, Y, mask):
             if projection == '3d':
                 data.append(Y[mask_remaining, 2])
             axs[ikey].scatter(
-                *data, marker='.', c='lightgrey', s=size, edgecolors='none', zorder=-1,
+                *data,
+                marker='.',
+                c='lightgrey',
+                s=size,
+                edgecolors='none',
+                zorder=-1,
             )
         legend = None
         if legend_loc.startswith('on data'):
@@ -737,9 +742,7 @@ def violin(
         y = ys[0]
         g = sns.FacetGrid(obs_tidy, col=x, col_order=keys, sharey=False)
         # don't really know why this gives a warning without passing `order`
-        g = g.map(
-            sns.violinplot, y, orient='vertical', scale=scale, order=keys, **kwds,
-        )
+        g = g.map(sns.violinplot, y, orient='vertical', scale=scale, order=keys, **kwds)
         if stripplot:
             g = g.map(
                 sns.stripplot,
@@ -1116,7 +1119,7 @@ def heatmap(
         if dendrogram:
             dendro_ax = fig.add_subplot(axs[1, 2], sharey=heatmap_ax)
             _plot_dendrogram(
-                dendro_ax, adata, groupby, ticks=ticks, dendrogram_key=dendrogram,
+                dendro_ax, adata, groupby, ticks=ticks, dendrogram_key=dendrogram
             )
 
         # plot group legends on top of heatmap_ax (if given)
@@ -1191,7 +1194,7 @@ def heatmap(
         if categorical:
             groupby_ax = fig.add_subplot(axs[2, 0])
             ticks, labels, groupby_cmap, norm = _plot_categories_as_colorblocks(
-                groupby_ax, obs_tidy, colors=groupby_colors, orientation='bottom',
+                groupby_ax, obs_tidy, colors=groupby_colors, orientation='bottom'
             )
             # add lines to main heatmap
             line_positions = (

scanpy/plotting/_baseplot_class.py

@@ -27,7 +27,7 @@
 cmap
     String denoting matplotlib color map.
 standard_scale
-    Whether or not to standardize the given dimension between 0 and 1, meaning for 
+    Whether or not to standardize the given dimension between 0 and 1, meaning for
     each variable or group, subtract the minimum and divide each by its maximum.
 swap_axes
      By default, the x axis contains `var_names` (e.g. genes) and the y axis
@@ -515,7 +515,7 @@ def _plot_legend(self, legend_ax, return_ax_dict, normalize):
             legend_height,
         ]
         fig, legend_gs = make_grid_spec(
-            legend_ax, nrows=2, ncols=1, height_ratios=height_ratios,
+            legend_ax, nrows=2, ncols=1, height_ratios=height_ratios
         )
 
         color_legend_ax = fig.add_subplot(legend_gs[1])
@@ -792,9 +792,7 @@ def savefig(self, filename: str, bbox_inches: Optional[str] = 'tight', **kwargs)
         self.make_figure()
         pl.savefig(filename, bbox_inches=bbox_inches, **kwargs)
 
-    def _reorder_categories_after_dendrogram(
-        self, dendrogram,
-    ):
+    def _reorder_categories_after_dendrogram(self, dendrogram):
         """\
         Function used by plotting functions that need to reorder the the groupby
         observations based on the dendrogram results.

scanpy/plotting/_dotplot.py

@@ -484,7 +484,7 @@ def _plot_legend(self, legend_ax, return_ax_dict, normalize):
             cbar_legend_height,
         ]
         fig, legend_gs = make_grid_spec(
-            legend_ax, nrows=4, ncols=1, height_ratios=height_ratios,
+            legend_ax, nrows=4, ncols=1, height_ratios=height_ratios
         )
 
         if self.show_size_legend:
@@ -943,7 +943,7 @@ def dotplot(
         dot_min=dot_min,
         smallest_dot=smallest_dot,
         dot_edge_lw=kwds.pop('linewidth', DotPlot.DEFAULT_DOT_EDGELW),
-    ).legend(colorbar_title=colorbar_title, size_title=size_title,)
+    ).legend(colorbar_title=colorbar_title, size_title=size_title)
 
     if return_fig:
         return dp

scanpy/plotting/_stacked_violin.py

@@ -524,17 +524,15 @@ def _setup_violin_axes_ticks(self, row_ax, num_cols):
             row_ax.axis('off')
             # remove labels
             row_ax.set_yticklabels([])
-            row_ax.tick_params(
-                axis='y', left=False, right=False,
-            )
+            row_ax.tick_params(axis='y', left=False, right=False)
 
         row_ax.set_ylabel('')
 
         row_ax.set_xlabel('')
 
         row_ax.set_xticklabels([])
         row_ax.tick_params(
-            axis='x', bottom=False, top=False, labeltop=False, labelbottom=False,
+            axis='x', bottom=False, top=False, labeltop=False, labelbottom=False
         )
 
 

scanpy/plotting/_tools/scatterplots.py

@@ -219,9 +219,7 @@ def embedding(
 
         if (
             size is not None
-            and isinstance(
-                size, (cabc.Sequence, pandas.core.series.Series, np.ndarray,)
-            )
+            and isinstance(size, (cabc.Sequence, pandas.core.series.Series, np.ndarray))
             and len(size) == adata.shape[0]
         ):
             size = np.array(size, dtype=float)
@@ -425,7 +423,7 @@ def embedding(
 
         if legend_fontoutline is not None:
             path_effect = [
-                patheffects.withStroke(linewidth=legend_fontoutline, foreground='w',)
+                patheffects.withStroke(linewidth=legend_fontoutline, foreground='w')
             ]
         else:
             path_effect = None
@@ -681,7 +679,7 @@ def diffmap(adata, **kwargs) -> Union[Axes, List[Axes], None]:
     show_save_ax=doc_show_save_ax,
 )
 def draw_graph(
-    adata: AnnData, *, layout: Optional[_IGraphLayout] = None, **kwargs,
+    adata: AnnData, *, layout: Optional[_IGraphLayout] = None, **kwargs
 ) -> Union[Axes, List[Axes], None]:
     """\
     Scatter plot in graph-drawing basis.
@@ -786,7 +784,8 @@ def spatial(
     spatial_data = adata.uns['spatial'][library_id]
     if img_key is _empty:
         img_key = next(
-            (k for k in ['hires', 'lowres'] if k in spatial_data['images']), None,
+            (k for k in ['hires', 'lowres'] if k in spatial_data['images']),
+            None,
         )
 
     if size is None:
@@ -919,7 +918,7 @@ def _get_data_points(
         if f"tissue_{img_key}_scalef" in spatial_data['scalefactors'].keys():
             scalef_key = f"tissue_{img_key}_scalef"
             data_points[0] = np.multiply(
-                data_points[0], spatial_data['scalefactors'][scalef_key],
+                data_points[0], spatial_data['scalefactors'][scalef_key]
             )
         else:
             raise KeyError(
@@ -999,7 +998,7 @@ def _add_categorical_legend(
 
 
 def _get_color_source_vector(
-    adata, value_to_plot, use_raw=False, gene_symbols=None, layer=None, groups=None,
+    adata, value_to_plot, use_raw=False, gene_symbols=None, layer=None, groups=None
 ):
     """
     Get array from adata that colors will be based on.
@@ -1024,7 +1023,7 @@ def _get_color_source_vector(
     else:
         values = adata.obs_vector(value_to_plot, layer=layer)
     if groups and is_categorical_dtype(values):
-        values = values.replace(values.categories.difference(groups), np.nan,)
+        values = values.replace(values.categories.difference(groups), np.nan)
     return values
 
 

scanpy/plotting/_utils.py

@@ -155,7 +155,7 @@ def timeseries_subplot(
 
 
 def timeseries_as_heatmap(
-    X: np.ndarray, var_names: Collection[str] = (), highlights_x=(), color_map=None,
+    X: np.ndarray, var_names: Collection[str] = (), highlights_x=(), color_map=None
 ):
     """\
     Plot timeseries as heatmap.
@@ -357,7 +357,7 @@ def _validate_palette(adata, key):
 
 
 def _set_colors_for_categorical_obs(
-    adata, value_to_plot, palette: Union[str, Sequence[str], Cycler],
+    adata, value_to_plot, palette: Union[str, Sequence[str], Cycler]
 ):
     """
     Sets the adata.uns[value_to_plot + '_colors'] according to the given palette
@@ -541,8 +541,7 @@ def plot_arrows(axs, adata, basis, arrows_kwds=None):
 
 
 def scatter_group(ax, key, imask, adata, Y, projection='2d', size=3, alpha=None):
-    """Scatter of group using representation of data Y.
-    """
+    """Scatter of group using representation of data Y."""
     mask = adata.obs[key].cat.categories[imask] == adata.obs[key].values
     color = adata.uns[key + '_colors'][imask]
     if not isinstance(color[0], str):
@@ -576,8 +575,7 @@ def setup_axes(
     projection: Literal['2d', '3d'] = '2d',
     show_ticks=False,
 ):
-    """Grid of axes for plotting, legends and colorbars.
-    """
+    """Grid of axes for plotting, legends and colorbars."""
     make_projection_available(projection)
     if left_margin is not None:
         raise NotImplementedError('We currently don’t support `left_margin`.')
@@ -738,7 +736,7 @@ def scatter_base(
             fig = pl.gcf()
             ax_cb = fig.add_axes(rectangle)
             cb = pl.colorbar(
-                sct, format=ticker.FuncFormatter(ticks_formatter), cax=ax_cb,
+                sct, format=ticker.FuncFormatter(ticks_formatter), cax=ax_cb
             )
         # set the title
         if title is not None:
@@ -814,9 +812,7 @@ def scatter_single(ax: Axes, Y: np.ndarray, *args, **kwargs):
     ax.set_yticks([])
 
 
-def arrows_transitions(
-    ax: Axes, X: np.ndarray, indices: Sequence[int], weight=None,
-):
+def arrows_transitions(ax: Axes, X: np.ndarray, indices: Sequence[int], weight=None):
     """
     Plot arrows of transitions in data matrix.
 
@@ -876,14 +872,12 @@ def ticks_formatter(x, pos):
 
 
 def pimp_axis(x_or_y_ax):
-    """Remove trailing zeros.
-    """
+    """Remove trailing zeros."""
     x_or_y_ax.set_major_formatter(ticker.FuncFormatter(ticks_formatter))
 
 
 def scale_to_zero_one(x):
-    """Take some 1d data and scale it so that min matches 0 and max 1.
-    """
+    """Take some 1d data and scale it so that min matches 0 and max 1."""
     xscaled = x - np.min(x)
     xscaled /= np.max(xscaled)
     return xscaled
@@ -892,28 +886,27 @@ def scale_to_zero_one(x):
 def hierarchy_pos(G, root, levels=None, width=1.0, height=1.0):
     """Tree layout for networkx graph.
 
-       See https://stackoverflow.com/questions/29586520/can-one-get-hierarchical-graphs-from-networkx-with-python-3
-       answer by burubum.
-
-       If there is a cycle that is reachable from root, then this will see
-       infinite recursion.
-
-       Parameters
-       ----------
-       G: the graph
-       root: the root node
-       levels: a dictionary
-               key: level number (starting from 0)
-               value: number of nodes in this level
-       width: horizontal space allocated for drawing
-       height: vertical space allocated for drawing
+    See https://stackoverflow.com/questions/29586520/can-one-get-hierarchical-graphs-from-networkx-with-python-3
+    answer by burubum.
+
+    If there is a cycle that is reachable from root, then this will see
+    infinite recursion.
+
+    Parameters
+    ----------
+    G: the graph
+    root: the root node
+    levels: a dictionary
+            key: level number (starting from 0)
+            value: number of nodes in this level
+    width: horizontal space allocated for drawing
+    height: vertical space allocated for drawing
     """
     TOTAL = "total"
     CURRENT = "current"
 
     def make_levels(levels, node=root, currentLevel=0, parent=None):
-        """Compute the number of nodes for each level
-        """
+        """Compute the number of nodes for each level"""
         if currentLevel not in levels:
             levels[currentLevel] = {TOTAL: 0, CURRENT: 0}
         levels[currentLevel][TOTAL] += 1