Merge pull request #76 from moshi4/develop

Bump to v1.7.1

Author: moshi4

src/pycirclize/__init__.py

@@ -1,6 +1,6 @@
 from pycirclize.circos import Circos
 
-__version__ = "1.7.0"
+__version__ = "1.7.1"
 
 __all__ = [
     "Circos",

src/pycirclize/circos.py

@@ -426,7 +426,7 @@ def initialize_from_matrix(
             colors = utils.ColorCycler.get_color_list(len(names))
             name2color = dict(zip(names, colors))
         else:
-            if type(cmap) == defaultdict:
+            if isinstance(cmap, defaultdict):
                 name2color = cmap
             else:
                 name2color: dict[str, str] = defaultdict(lambda: "grey")
@@ -444,10 +444,10 @@ def initialize_from_matrix(
                 outer_track.xticks_by_interval(ticks_interval, **ticks_kws)
 
         # Plot links
-        fromto_label2color = {f"{t[0]}{t[1]}": t[2] for t in link_cmap}
+        fromto_label2color = {f"{t[0]}--->{t[1]}": t[2] for t in link_cmap}
         for link in matrix.to_links():
             from_label, to_label = link[0][0], link[1][0]
-            fromto_label = f"{from_label}{to_label}"
+            fromto_label = f"{from_label}--->{to_label}"
             # Set link color
             if fromto_label in fromto_label2color:
                 color = fromto_label2color[fromto_label]
@@ -1061,7 +1061,7 @@ def plotfig(
         for plot_func in self._get_all_plot_funcs():
             plot_func(ax)
 
-        return fig
+        return fig  # type: ignore
 
     def savefig(
         self,
@@ -1164,7 +1164,7 @@ def _initialize_figure(
         """
         fig = plt.figure(figsize=figsize, dpi=dpi, tight_layout=True)
         ax = fig.add_subplot(projection="polar")
-        return fig, ax
+        return fig, ax  # type: ignore
 
     def _initialize_polar_axes(self, ax: PolarAxes) -> None:
         """Initialize polar axes params

src/pycirclize/parser/matrix.py

@@ -103,7 +103,7 @@ def parse_fromto_table(
         for row in fromto_table.itertuples():
             from_label, to_label, value = str(row[1]), str(row[2]), row[3]
             if float(value) > 0:
-                fromto = f"{from_label}{to_label}"
+                fromto = f"{from_label}-->{to_label}"
                 fromto2value[fromto] = value
                 label2value_sum[from_label] += value
                 label2value_sum[to_label] += value
@@ -134,7 +134,7 @@ def parse_fromto_table(
         for row_label in all_labels:
             row_data = []
             for col_label in all_labels:
-                row_data.append(fromto2value[f"{row_label}{col_label}"])
+                row_data.append(fromto2value[f"{row_label}-->{col_label}"])
             matrix_data.append(row_data)
         matrix_df = pd.DataFrame(matrix_data, index=all_labels, columns=all_labels)
 

src/pycirclize/patches.py

@@ -241,7 +241,7 @@ def __init__(
 
         def arc_paths(
             rad1: float, rad2: float, r: float
-        ) -> list[tuple[Path.code_type, tuple[float, float]]]:
+        ) -> list[tuple[np.uint8, tuple[float, float]]]:
             # If rad1 == rad2, return blank list
             arc_paths = []
             step = config.ARC_RADIAN_STEP if rad1 <= rad2 else -config.ARC_RADIAN_STEP
@@ -251,7 +251,7 @@ def arc_paths(
 
         def arrow_paths(
             rad1: float, rad2: float, r_side: float, r_top: float
-        ) -> list[tuple[Path.code_type, tuple[float, float]]]:
+        ) -> list[tuple[np.uint8, tuple[float, float]]]:
             return [
                 (Path.LINETO, (rad1, r_side)),
                 (Path.LINETO, ((rad1 + rad2) / 2, r_top)),
@@ -260,7 +260,7 @@ def arrow_paths(
 
         def bezier_paths(
             rad1: float, rad2: float, r1: float, r2: float, height_ratio: float = 0.5
-        ) -> list[tuple[Path.code_type, tuple[float, float]]]:
+        ) -> list[tuple[np.uint8, tuple[float, float]]]:
             if height_ratio >= 0.5:
                 # Example1: height_ratio: 0.50 => r_ctl_pos: 0
                 # Example2: height_ratio: 0.75 => r_ctl_pos: 25
@@ -389,7 +389,7 @@ def bezier_paths(
             r1: float,
             r2: float,
             height_ratio: float = 0.5,
-        ) -> list[tuple[Path.code_type, tuple[float, float]]]:
+        ) -> list[tuple[np.uint8, tuple[float, float]]]:
             if height_ratio >= 0.5:
                 # Example1: height_ratio: 0.50 => r_ctl_pos: 0
                 # Example2: height_ratio: 0.75 => r_ctl_pos: 25
@@ -412,7 +412,7 @@ def arrow_line_paths(
             r_pos: float,
             arrow_rad_width: float,
             arrow_r_height: float,
-        ) -> list[tuple[Path.code_type, tuple[float, float]]]:
+        ) -> list[tuple[np.uint8, tuple[float, float]]]:
             arrow_r_pos = r_pos - arrow_r_height
             return [
                 (Path.MOVETO, (rad_pos + (arrow_rad_width / 2), arrow_r_pos)),
@@ -421,7 +421,7 @@ def arrow_line_paths(
             ]
 
         arrow_rad_width = np.radians(arrow_width)
-        path_data: list[tuple[Path.code_type, tuple[float, float]]] = []
+        path_data: list[tuple[np.uint8, tuple[float, float]]] = []
         if direction in (config.Direction.REVERSE, config.Direction.BIDIRECTIONAL):
             path_data.extend(arrow_line_paths(rad1, r1, arrow_rad_width, arrow_height))
         path_data.append((Path.MOVETO, (rad1, r1)))

src/pycirclize/sector.py

@@ -449,8 +449,8 @@ def raster(
 
         # Calculate x, y image set position
         max_r_lim = config.MAX_R + config.R_PLOT_MARGIN
-        im_x = np.cos((np.pi / 2) - rad) * (r / max_r_lim)
-        im_y = np.sin((np.pi / 2) - rad) * (r / max_r_lim)
+        im_x: float = np.cos((np.pi / 2) - rad) * (r / max_r_lim)
+        im_y: float = np.sin((np.pi / 2) - rad) * (r / max_r_lim)
         # Normalize (-1, 1) to (0, 1) axis range
         im_x = (im_x + 1) / 2
         im_y = (im_y + 1) / 2
@@ -463,7 +463,7 @@ def raster(
 
         def plot_raster(ax: PolarAxes) -> None:
             # Set inset axes & plot raster image
-            bounds = [im_x - (size / 2), im_y - (size / 2), size, size]
+            bounds = (im_x - (size / 2), im_y - (size / 2), size, size)
             axin = ax.inset_axes(bounds, transform=ax.transAxes)
             axin.axis("off")
             axin.imshow(im, **imshow_kws)  # type: ignore