Massive reformatting and style checks

.gitignore

@@ -149,4 +149,4 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/

docs/create_class_page.py

@@ -1,69 +1,111 @@
 # -*- coding: utf-8 -*-
-"""
-Created on Thu Feb  2 10:37:05 2023
+"""Created on Thu Feb  2 10:37:05 2023.
 
 @author: Barney
+
 """
 
+import os
+
+import pandas as pd
+
 from wsimod.core.core import WSIObj
-from wsimod import nodes
 from wsimod.nodes.nutrient_pool import NutrientPool
-import pandas as pd
-import os
+
 
 def get_classes():
-    #Function to return all loaded subclasses of WSIObj (import arcs to include that)
+    """
+
+    Returns:
+
+    """
+
+    # Function to return all loaded subclasses of WSIObj (import arcs to include that)
     def all_subclasses(cls):
-        return set(cls.__subclasses__()).union([s for c in cls.__subclasses__() for s in all_subclasses(c)])
+        """
+
+        Args:
+            cls:
+
+        Returns:
+
+        """
+        return set(cls.__subclasses__()).union(
+            [s for c in cls.__subclasses__() for s in all_subclasses(c)]
+        )
+
     subclasses = all_subclasses(WSIObj)
-    subclasses = {repr(x).split('.')[-1].replace("'>","") : x for x in subclasses}
+    subclasses = {repr(x).split(".")[-1].replace("'>", ""): x for x in subclasses}
     return subclasses
 
 
 def format_text(text):
-    #Convert docstring to a tidy format
-    lines = text.strip().split('\n')
-    lines = [line.strip().lstrip(' ') for line in lines]
-    lines = [' - ' + x.rstrip(' ') for x in ' '.join(lines).split('- ') if len(x) > 0]
-    return '<br>'.join(lines)
+    """
+
+    Args:
+        text:
+
+    Returns:
 
-#Identify which reference file to link modules to
+    """
+    # Convert docstring to a tidy format
+    lines = text.strip().split("\n")
+    lines = [line.strip().lstrip(" ") for line in lines]
+    lines = [" - " + x.rstrip(" ") for x in " ".join(lines).split("- ") if len(x) > 0]
+    return "<br>".join(lines)
+
+
+# Identify which reference file to link modules to
 reference_lookup = {}
 for file in os.listdir(os.getcwd()):
-    if 'reference-' in file:
+    if "reference-" in file:
         with open(file) as f:
             for line in f:
-                if ':::' in line:
-                    reference_lookup[line.replace('::: ','').replace('\n','')] = file.replace('.md','')
+                if ":::" in line:
+                    reference_lookup[
+                        line.replace("::: ", "").replace("\n", "")
+                    ] = file.replace(".md", "")
 
-#Iterate over classes
+# Iterate over classes
 subclasses = get_classes()
-subclasses['NutrientPool'] = NutrientPool
+subclasses["NutrientPool"] = NutrientPool
 mytable = []
 for subclass, obj in subclasses.items():
-    #Get docstring
+    # Get docstring
     otext = obj.__init__.__doc__
     if otext:
-        #Only include docstrings with Key assumptions
-        if 'Key assumptions:' in otext:
-            #Format reference
-            rclass = '.'.join(repr(obj).replace("<class '",'').replace("'>",'').split('.'))
-            module = '.'.join(rclass.split('.')[0:-1])
-            subclass = '[`{0}`](./../{1}/#{2})'.format(subclass, reference_lookup[module], rclass)
-
-            #Format assumptions
-            assum = format_text(otext.split('Key assumptions:')[1].split('Input data and parameter requirements:')[0])
-
-            #Format inputs
-            inputs = format_text(otext.split('Input data and parameter requirements:')[1])
-
-            #Append to table
-            mytable.append({'Component' : subclass, 'Assumptions' : assum, 'Data' : inputs})
-
-#Convert to table
-mytable = pd.DataFrame(mytable).sort_values(by = 'Component')
-mytable['Assumptions'] = mytable['Assumptions'].str.replace('\n', '\n - ')
-mytable['Component'] = mytable['Component'].str.replace('\n', '\n - ')
+        # Only include docstrings with Key assumptions
+        if "Key assumptions:" in otext:
+            # Format reference
+            rclass = ".".join(
+                repr(obj).replace("<class '", "").replace("'>", "").split(".")
+            )
+            module = ".".join(rclass.split(".")[0:-1])
+            subclass = "[`{0}`](./../{1}/#{2})".format(
+                subclass, reference_lookup[module], rclass
+            )
+
+            # Format assumptions
+            assum = format_text(
+                otext.split("Key assumptions:")[1].split(
+                    "Input data and parameter requirements:"
+                )[0]
+            )
+
+            # Format inputs
+            inputs = format_text(
+                otext.split("Input data and parameter requirements:")[1]
+            )
+
+            # Append to table
+            mytable.append(
+                {"Component": subclass, "Assumptions": assum, "Data": inputs}
+            )
+
+# Convert to table
+mytable = pd.DataFrame(mytable).sort_values(by="Component")
+mytable["Assumptions"] = mytable["Assumptions"].str.replace("\n", "\n - ")
+mytable["Component"] = mytable["Component"].str.replace("\n", "\n - ")
 front_text = """
 ## Introduction\n
 WSIMOD contains a variety of components to represent physical processes.
@@ -75,7 +117,7 @@ def format_text(text):
 ## Component Library
 """
 
-#Write
-with open('component-library.md', 'w') as f:
+# Write
+with open("component-library.md", "w") as f:
     f.write(front_text)
-    f.write(mytable.to_markdown(index = False)) 
+    f.write(mytable.to_markdown(index=False))