Fix docstrings

src/pycirclize/circos.py

@@ -353,7 +353,7 @@ def initialize_from_tree(
         Returns
         -------
         circos, tv : tuple[Circos, TreeViz]
-            Circos instance initialized from tree, TreeViz instance
+            Circos & TreeViz instances initialized from tree
         """
         # Initialize circos sector with tree size
         tree = TreeViz.load_tree(tree_data, format=format)
@@ -575,9 +575,9 @@ def line(
 
         Parameters
         ----------
-        r : float, tuple[float, float]
+        r : float | tuple[float, float]
             Line radius position (0 - 100). If r is float, (r, r) is set.
-        deg_lim : tuple[float, float]
+        deg_lim : tuple[float, float] | None, optional
             Degree limit region (-360 - 360). If None, `circos.deg_lim` is set.
         arc : bool, optional
             If True, plot arc style line for polar projection.

src/pycirclize/parser/genbank.py

@@ -31,7 +31,7 @@ def __init__(
         gbk_source : str | Path | TextIOWrapper
             Genbank file or source
             (`*.gz`, `*.bz2`, `*.zip` compressed file can be readable)
-        name : str | None
+        name : str | None, optional
             name (If None, `file name` or `record name` is set)
         reverse : bool, optional
             If True, reverse complement genome is used

src/pycirclize/parser/matrix.py

@@ -164,7 +164,7 @@ def sort(self, order: str | list[str] = "asc") -> Matrix:
 
         Parameters
         ----------
-        order : str | list[str] | None, optional
+        order : str | list[str], optional
             Sort order of matrix for plotting Chord Diagram.
             If `asc`|`desc`, sort in ascending(or descending) order by node size.
             If node name list is set, sort in user specified node order.

src/pycirclize/sector.py

@@ -252,7 +252,7 @@ def text(
         ----------
         text : str
             Text content
-        x: float, optional
+        x: float | None, optional
             X position. If None, sector center x is set.
         r : float, optional
             Radius position. By default, outer position `r=105` is set.
@@ -299,11 +299,11 @@ def line(
 
         Parameters
         ----------
-        r : float, tuple[float, float]
+        r : float | tuple[float, float]
             Line radius position (0 - 100). If r is float, (r, r) is set.
-        start : float, optional
+        start : float | None, optional
             Start position (x coordinate). If None, `sector.start` is set.
-        end : float, optional
+        end : float | None, optional
             End position (x coordinate). If None, `sector.end` is set.
         arc : bool, optional
             If True, plot arc style line for polar projection.
@@ -330,11 +330,11 @@ def rect(
 
         Parameters
         ----------
-        start : float, optional
+        start : float | None, optional
             Start position (x coordinate). If None, `sector.start` is set.
-        end : float, optional
+        end : float | None, optional
             End position (x coordinate). If None, `sector.end` is set.
-        r_lim : tuple[float, float] | None
+        r_lim : tuple[float, float] | None, optional
             Radius limit region. If None, (0, 100) is set.
         **kwargs : dict, optional
             Patch properties (e.g. `fc="red", ec="blue", lw=1.0, ...`)

src/pycirclize/track.py

@@ -209,9 +209,9 @@ def text(
         ----------
         text : str
             Text content
-        x : float | None
+        x : float | None, optional
             X position. If None, track center x position is set.
-        r : float | None
+        r : float | None, optional
             Radius position. If None, track center radius position is set.
         adjust_rotation : bool, optional
             If True, text rotation is auto set based on `x` and `orientation` params.
@@ -1149,6 +1149,11 @@ def tree(
         align_line_kws : dict[str, Any] | None, optional
             Patch properties (e.g. `dict(lw=1, ls="dotted", alpha=1.0, ...)`)
             <https://matplotlib.org/stable/api/_as_gen/matplotlib.patches.Patch.html>
+
+        Returns
+        -------
+        tv : TreeViz
+            TreeViz instance
         """
         tv = TreeViz(
             tree_data,

src/pycirclize/tree.py

@@ -204,7 +204,7 @@ def highlight(
         query : str | list[str] | tuple[str]
             Search query node name(s) for highlight. If multiple node names are set,
             MRCA(Most Recent Common Ancester) node is set.
-        color : str | None, optional
+        color : str, optional
             Highlight color
         alpha : float, optional
             Highlight color alpha(transparancy) value