Fix indentation

README.md

@@ -11,7 +11,7 @@ MusicBox: A MUSICA model for boxes and columns.
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14008358.svg)](https://doi.org/10.5281/zenodo.14008358)
 
 
-Copyright (C) 2020 National Center for Atmospheric Research
+Copyright (C) 2020 National Science Foundation - National Center for Atmospheric Research
 
 # Installation
 ```

src/acom_music_box/connections/electron_configuration_reader.py

@@ -10,73 +10,41 @@ class ElectronConfiguraitonReader:
     """ Reads configuration information from the electron applicant to create a box model simulation.
     """
 
-       def __init__(self):
-            self.box_model_options = None
-            self.species_list = None
-            self.reaction_list = None
-            self.initial_conditions = None
-            self.evolving_conditions = None
+    def __init__(self):
+        self.box_model_options = None
+        self.species_list = None
+        self.reaction_list = None
+        self.initial_conditions = None
+        self.evolving_conditions = None
 
-        def read_electron_configuration(self):
-            with open(self.electron_configuration_file_path, 'r') as file:
-                for line in file:
-                    element, configuration = line.strip().split(' ')
-                    self.electron_configuration[element] = configuration
+    def read_electron_configuration(self):
+        with open(self.electron_configuration_file_path, 'r') as file:
+            for line in file:
+                element, configuration = line.strip().split(' ')
+                self.electron_configuration[element] = configuration
 
-        def get_electron_configuration(self, element):
-            return self.electron_configuration[element]
+    def get_electron_configuration(self, element):
+        return self.electron_configuration[element]
 
-        def readFromUIJson(self, path_to_json):
-            """
-            Reads and parses a JSON file from the MusicBox Interactive UI to set up the box model simulation.
+    def readFromUIJson(self, path_to_json):
+        """
+        Reads and parses a JSON file from the MusicBox Interactive UI to set up the box model simulation.
 
-            This function takes the path to a JSON file, reads the file, and parses the JSON
-            to set up the box model simulation.
+        This function takes the path to a JSON file, reads the file, and parses the JSON
+        to set up the box model simulation.
 
-            Args:
-                path_to_json (str): The path to the JSON file from the UI.
+        Args:
+            path_to_json (str): The path to the JSON file from the UI.
 
-            Returns:
-                None
+        Returns:
+            None
 
-            Raises:
-                ValueError: If the JSON file cannot be read or parsed.
-            """
+        Raises:
+            ValueError: If the JSON file cannot be read or parsed.
+        """
 
-            with open(path_to_json, 'r') as json_file:
-                data = json.load(json_file)
-
-                # Set box model options
-                self.box_model_options = BoxModelOptions.from_UI_JSON(data)
-
-                # Set species list
-                self.species_list = SpeciesList.from_UI_JSON(data)
-
-                # Set reaction list
-                self.reaction_list = ReactionList.from_UI_JSON(
-                    data, self.species_list)
-
-                # Set initial conditions
-                self.initial_conditions = Conditions.from_UI_JSON(
-                    data, self.species_list, self.reaction_list)
-
-                # Set evolving conditions
-                self.evolving_conditions = EvolvingConditions.from_UI_JSON(
-                    data, self.species_list, self.reaction_list)
-
-        def readFromUIJsonString(self, data):
-            """
-            Reads and parses a JSON string from the MusicBox Interactive UI to set up the box model simulation.
-
-            Args:
-                json_string (str): The JSON string from the UI.
-
-            Returns:
-                None
-
-            Raises:
-                ValueError: If the JSON string cannot be parsed.
-            """
+        with open(path_to_json, 'r') as json_file:
+            data = json.load(json_file)
 
             # Set box model options
             self.box_model_options = BoxModelOptions.from_UI_JSON(data)
@@ -85,7 +53,8 @@ def readFromUIJsonString(self, data):
             self.species_list = SpeciesList.from_UI_JSON(data)
 
             # Set reaction list
-            self.reaction_list = ReactionList.from_UI_JSON(data, self.species_list)
+            self.reaction_list = ReactionList.from_UI_JSON(
+                data, self.species_list)
 
             # Set initial conditions
             self.initial_conditions = Conditions.from_UI_JSON(
@@ -94,3 +63,34 @@ def readFromUIJsonString(self, data):
             # Set evolving conditions
             self.evolving_conditions = EvolvingConditions.from_UI_JSON(
                 data, self.species_list, self.reaction_list)
+
+    def readFromUIJsonString(self, data):
+        """
+        Reads and parses a JSON string from the MusicBox Interactive UI to set up the box model simulation.
+
+        Args:
+            json_string (str): The JSON string from the UI.
+
+        Returns:
+            None
+
+        Raises:
+            ValueError: If the JSON string cannot be parsed.
+        """
+
+        # Set box model options
+        self.box_model_options = BoxModelOptions.from_UI_JSON(data)
+
+        # Set species list
+        self.species_list = SpeciesList.from_UI_JSON(data)
+
+        # Set reaction list
+        self.reaction_list = ReactionList.from_UI_JSON(data, self.species_list)
+
+        # Set initial conditions
+        self.initial_conditions = Conditions.from_UI_JSON(
+            data, self.species_list, self.reaction_list)
+
+        # Set evolving conditions
+        self.evolving_conditions = EvolvingConditions.from_UI_JSON(
+            data, self.species_list, self.reaction_list)

src/acom_music_box/tools/waccmToMusicBox.py

@@ -4,7 +4,7 @@
 # and convert to initial conditions for MusicBox (case TS1).
 #
 # Author: Carl Drews
-# Copyright 2024 by Atomospheric Chemistry Observations & Modeling (UCAR/ACOM)
+# Copyright 2024 by Atmospheric Chemistry Observations & Modeling (UCAR/ACOM)
 
 # import os
 import argparse