fixed docs

docs/api.md

@@ -2,28 +2,8 @@
 
 ## Preprocessing
 
-```{eval-rst}
-.. module:: pycea.pp
-.. currentmodule:: pycea
-
-.. autosummary::
-    :toctree: generated
-
-    pp.basic_preproc
-```
-
 ## Tools
 
-```{eval-rst}
-.. module:: pycea.tl
-.. currentmodule:: pycea
-
-.. autosummary::
-    :toctree: generated
-
-    tl.basic_tool
-```
-
 ## Plotting
 
 ```{eval-rst}
@@ -34,4 +14,5 @@
     :toctree: generated
 
     pl.branches
+    pl.annotation
 ```

docs/conf.py

@@ -91,10 +91,16 @@
 }
 
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+    "cycler": ("https://matplotlib.org/cycler/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "python": ("https://docs.python.org/3", None),
+    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+    "squidpy": ("https://squidpy.readthedocs.io/en/stable/", None),
     "treedata": ("https://treedata.readthedocs.io/en/stable/", None),
 }
 

src/pycea/pl/tree.py

@@ -10,16 +10,21 @@
 import treedata as td
 from matplotlib.axes import Axes
 from matplotlib.collections import LineCollection
+from scanpy._utils import _doc_params
 
 from pycea.utils import get_keyed_edge_data, get_keyed_obs_data
 
+from ._docs import doc_common_plot_args
 from ._utils import (
     _get_categorical_colors,
     _series_to_rgb_array,
     layout_tree,
 )
 
 
+@_doc_params(
+    common_plot_args=doc_common_plot_args,
+)
 def branches(
     tdata: td.TreeData,
     key: str = None,
@@ -57,7 +62,7 @@ def branches(
         Either an numeric width, or a key for an attribute of the edges to set the linewidth.
     na_linewidth
         The linewidth to use for edges with missing data.
-    {doc_common_plot_args}
+    {common_plot_args}
     kwargs
         Additional keyword arguments passed to `matplotlib.collections.LineCollection`.
 
@@ -158,7 +163,7 @@ def annotation(
         The minimum value for the colormap.
     na_color
         The color to use for annotations with missing data.
-    {doc_common_plot_args}
+    {common_plot_args}
     kwargs
         Additional keyword arguments passed to `matplotlib.pyplot.pcolormesh`.
 
@@ -209,14 +214,14 @@ def annotation(
             end_lat = start_lat + attrs["depth"] + 2 * np.pi
             lats = np.linspace(start_lat, end_lat, data.shape[1] + 1)
         for col in data.columns:
-            rgb_array.append(_series_to_rgb_array(data[col], cmap, vmin=vmin, vmax=vmax, na_color = na_color))
+            rgb_array.append(_series_to_rgb_array(data[col], cmap, vmin=vmin, vmax=vmax, na_color=na_color))
     else:
         for key in keys:
             if data[key].dtype == "category":
                 colors = _get_categorical_colors(tdata, key, data[key], palette)
-                rgb_array.append(_series_to_rgb_array(data[key], colors, na_color = na_color))
+                rgb_array.append(_series_to_rgb_array(data[key], colors, na_color=na_color))
             else:
-                rgb_array.append(_series_to_rgb_array(data[key], cmap, vmin=vmin, vmax=vmax, na_color = na_color))
+                rgb_array.append(_series_to_rgb_array(data[key], cmap, vmin=vmin, vmax=vmax, na_color=na_color))
     rgb_array = np.stack(rgb_array, axis=1)
     # Plot
     if attrs["polar"]:

src/pycea/pp/__init__.py

@@ -1 +0,0 @@
-from .basic import basic_preproc

src/pycea/tl/__init__.py

@@ -1 +0,0 @@
-from .basic import basic_tool