added documentations to missing functions

src/acom_music_box/music_box.py

@@ -601,6 +601,18 @@ def readFromUIJsonString(self, data):
         self.evolving_conditions = EvolvingConditions.from_UI_JSON(data, self.species_list, self.reaction_list)    
 
     def readConditionsFromJson(self, path_to_json):
+        """
+        Reads and parses a JSON file from the CAMP JSON file to set up the box model simulation.
+
+        Args:
+            path_to_json (str): The JSON path to the JSON file.
+
+        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)

src/acom_music_box/music_box_reaction_list.py

@@ -98,6 +98,20 @@ def add_reaction(self, reaction):
 
     @classmethod
     def get_reactants_from_JSON(self, reaction, species_list):
+        """
+        Retrieves reactants from a JSON object.
+
+        This method iterates over the 'reactants' field of the provided JSON object,
+        matches each reactant with a species from the provided species list, and
+        creates a Reactant object for each one.
+
+        Args:
+            reaction (dict): A dictionary representing a reaction, as parsed from JSON.
+            species_list (SpeciesList): A list of all possible species.
+
+        Returns:
+            list: A list of Reactant objects representing the reactants of the reaction.
+        """
         reactants = []
 
         for reactant, reactant_info in reaction['reactants'].items():
@@ -110,6 +124,21 @@ def get_reactants_from_JSON(self, reaction, species_list):
 
     @classmethod
     def get_products_from_JSON(self, reaction, species_list):
+        """
+        Extracts products from a JSON object.
+
+        This method checks if the 'products' field is present in the provided JSON object.
+        If it is, the method iterates over the 'products' field, matches each product with
+        a species from the provided species list, and creates a Product object for each one.
+
+        Args:
+            reaction (dict): A dictionary representing a reaction, as parsed from JSON.
+            species_list (SpeciesList): A list of all possible species.
+
+        Returns:
+            list: A list of Product objects representing the products of the reaction, or
+                an empty list if the 'products' field is not present in the JSON object.
+        """
         products = []
         if 'products' in reaction:
                 for product, product_info in reaction['products'].items():