some static typing fixes

Author: richardjgowers

cinnabar/plotlying.py

@@ -1,4 +1,4 @@
-from typing import Union
+from typing import Optional
 
 import numpy as np
 import pandas as pd
@@ -16,7 +16,7 @@ def plot_bar(
     exp_error_col: str = "dexp",
     name_col: str = "edge",
     title: str = "",
-    filename: Union[str, None] = None,
+    filename: Optional[str] = None,
 ):
     """
     Creates a plotly barplot. It takes a pandas.Dataframe df as input and plots
@@ -149,15 +149,15 @@ def _master_plot(
     x: np.ndarray,
     y: np.ndarray,
     title: str = "",
-    xerr: Union[list, None] = None,
-    yerr: Union[list, None] = None,
+    xerr: Optional[np.ndarray] = None,
+    yerr: Optional[np.ndarray] = None,
     method_name: str = "",
     target_name: str = "",
     plot_type: str = "",
     guidelines: bool = True,
     origins: bool = True,
     statistics: list = ["RMSE", "MUE"],
-    filename: Union[str, None] = None,
+    filename: Optional[str] = None,
 ):
     nsamples = len(x)
     ax_min = min(min(x), min(y)) - 0.5

cinnabar/plotting.py

@@ -1,5 +1,5 @@
 import itertools
-from typing import Union
+from typing import Union, Optional
 import matplotlib.pylab as plt
 import numpy as np
 import networkx as nx
@@ -11,8 +11,8 @@ def _master_plot(
     x: np.ndarray,
     y: np.ndarray,
     title: str = "",
-    xerr: Union[list, None] = None,
-    yerr: Union[list, None] = None,
+    xerr: Optional[np.ndarray] = None,
+    yerr: Optional[np.ndarray] = None,
     method_name: str = "",
     target_name: str = "",
     quantity: str = r"$\Delta \Delta$ G",
@@ -21,13 +21,13 @@ def _master_plot(
     units: str = r"$\mathrm{kcal\,mol^{-1}}$",
     guidelines: bool = True,
     origins: bool = True,
-    color: Union[str, None] = None,
+    color: Optional[str] = None,
     statistics: list = ["RMSE", "MUE"],
-    filename: Union[str, None] = None,
+    filename: Optional[str] = None,
     centralizing: bool = True,
     shift: float = 0.0,
     figsize: float = 3.25,
-    dpi: float = "figure",
+    dpi: Union[float, str] = "figure",
     data_labels: list = [],
     axis_padding: float = 0.5,
     xy_lim: list = [],
@@ -37,15 +37,15 @@ def _master_plot(
 
     Parameters
     ----------
-    x : list
+    x : np.ndarray
         Values to plot on the x axis
-    y : list
+    y : np.ndarray
         Values to plot on the y axis
     title : string, default = ''
         Title for the plot
-    xerr : list , default = None
+    xerr : np.ndarray , default = None
         Error bars for x values
-    yerr : list , default = None
+    yerr : np.ndarray , default = None
         Error bars for y values
     method_name : string, optional
         name of method associated with results, e.g. 'perses'
@@ -194,7 +194,7 @@ def plot_DDGs(
     target_name: str = "",
     title: str = "",
     map_positive: bool = False,
-    filename: Union[list, None] = None,
+    filename: Optional[str] = None,
     symmetrise: bool = False,
     plotly: bool = False,
     data_label_type: str = None,
@@ -238,7 +238,7 @@ def plot_DDGs(
 
     Returns
     -------
-
+    Nothing
     """
 
     assert (
@@ -332,15 +332,13 @@ def plot_DDGs(
             **kwargs,
         )
 
-    return
-
 
 def plot_DGs(
     graph: nx.DiGraph,
     method_name: str = "",
     target_name: str = "",
     title: str = "",
-    filename: Union[str, None] = None,
+    filename: Optional[str] = None,
     plotly: bool = False,
     centralizing: bool = True,
     shift: float = 0.0,
@@ -409,15 +407,13 @@ def plot_DGs(
             **kwargs,
         )
 
-    return
-
 
 def plot_all_DDGs(
     graph: nx.DiGraph,
     method_name: str = "",
     target_name: str = "",
     title: str = "",
-    filename: Union[str, None] = None,
+    filename: Optional[str] = None,
     plotly: bool = False,
     shift: float = 0.0,
     **kwargs,
@@ -471,15 +467,17 @@ def plot_all_DDGs(
         err = (yabserr[a] ** 2 + yabserr[b] ** 2) ** 0.5
         yerr.append(err)
         yerr.append(err)
-    x_data = np.asarray(x_data)
-    y_data = np.asarray(y_data)
+    x_data_ = np.array(x_data)
+    y_data_ = np.array(y_data)
+    xerr_ = np.array(xerr)
+    yerr_ = np.array(yerr)
 
     if plotly:
         plotlying._master_plot(
-            x_data,
-            y_data,
-            xerr=xerr,
-            yerr=yerr,
+            x_data_,
+            y_data_,
+            xerr=xerr_,
+            yerr=yerr_,
             title=title,
             method_name=method_name,
             plot_type="ΔΔG",
@@ -490,10 +488,10 @@ def plot_all_DDGs(
 
     else:
         _master_plot(
-            x_data,
-            y_data,
-            xerr=xerr,
-            yerr=yerr,
+            x_data_,
+            y_data_,
+            xerr=xerr_,
+            yerr=yerr_,
             title=title,
             method_name=method_name,
             filename=filename,