Auto-format code using pep8 (#302)

Co-authored-by: GitHub Actions <actions@github.com>

src/acom_music_box/conditions.py

@@ -106,7 +106,6 @@ def from_UI_JSON(self, UI_JSON, species_list, reaction_list):
             species_concentrations,
             reaction_rates)
 
-
     @classmethod
     def retrieve_initial_conditions_from_JSON(
             cls,
@@ -133,9 +132,9 @@ def retrieve_initial_conditions_from_JSON(
 
         # look for that JSON section
         if (not 'initial conditions' in json_object):
-            return({})
+            return ({})
         if (len(list(json_object['initial conditions'].keys())) == 0):
-            return({})
+            return ({})
 
         # retrieve initial conditions from CSV and JSON
         initial_csv = {}
@@ -163,7 +162,7 @@ def retrieve_initial_conditions_from_JSON(
                         logger.warning(
                             "Value {}:{} in file {} will override prior value {}"
                             .format(one_csv, file_initial_csv[one_csv],
-                            initial_conditions_path, initial_csv[one_csv]))
+                                    initial_conditions_path, initial_csv[one_csv]))
 
                     initial_csv[one_csv] = file_initial_csv[one_csv]
 
@@ -173,7 +172,7 @@ def retrieve_initial_conditions_from_JSON(
             # read initial conditions from in-place CSV (list of headers and list of values)
             dataConditions = initCond['data']
             initial_data = Conditions.read_data_values_from_table(dataConditions,
-                reaction_types)
+                                                                  reaction_types)
             logger.debug(f"initial_data = {initial_data}")
 
         # override the CSV species initial values with JSON data
@@ -183,13 +182,12 @@ def retrieve_initial_conditions_from_JSON(
             logger.warning(f"Initial data values ({numData}) from JSON will override initial values ({numCSV}) from CSV.")
         for one_data in initial_data:
             chem_name_alone = one_data.split(".")[1]        # remove reaction type
-            chem_name_alone = chem_name_alone.split(" ")[0] # remove units
+            chem_name_alone = chem_name_alone.split(" ")[0]  # remove units
             initial_csv[chem_name_alone] = initial_data[one_data]
 
         logger.debug(f"Overridden initial_csv = {initial_csv}")
 
-        return(initial_csv)
-
+        return (initial_csv)
 
     @classmethod
     def from_config_JSON(
@@ -242,7 +240,6 @@ def from_config_JSON(
             species_concentrations,
             reaction_rates)
 
-
     @classmethod
     def read_initial_conditions_from_file(cls, file_path, react_types=None):
         """
@@ -291,7 +288,7 @@ def read_initial_conditions_from_file(cls, file_path, react_types=None):
             chem_name_alone = f"{reaction_type}.{label}"    # reaction
             if len(parts) == 2:
                 chem_name_alone = label.split(' ')[0]       # strip off [units] to get chemical
-            reaction_rates[chem_name_alone] = df.at[0, key] # retrieve (row, column)
+            reaction_rates[chem_name_alone] = df.at[0, key]  # retrieve (row, column)
 
         return reaction_rates
 
@@ -326,7 +323,7 @@ def read_data_values_from_table(cls, data_json, react_types=None):
         header_row = data_json[0]
         value_row = data_json[1]
         data_values = {key: float(value) for key, value in zip(header_row, value_row)
-            if key.split('.')[0] in react_types}
+                       if key.split('.')[0] in react_types}
         logger.debug(f"For {react_types} data_values = {data_values}")
 
         return data_values

src/acom_music_box/evolving_conditions.py

@@ -125,9 +125,9 @@ def from_config_JSON(
 
         # Check if 'evolving conditions' is a key in the JSON config
         if (not 'evolving conditions' in config_JSON):
-            return(evolving_conditions)
+            return (evolving_conditions)
         if (len(list(config_JSON['evolving conditions'].keys())) == 0):
-            return(evolving_conditions)
+            return (evolving_conditions)
 
         evolveCond = config_JSON['evolving conditions']
         logger.debug(f"evolveCond: {evolveCond}")
@@ -150,7 +150,7 @@ def from_config_JSON(
                 overrideSet = allReactions.intersection(fileReactions)
                 if (len(overrideSet) > 0):
                     logger.warning("File {} will override earlier conditions {}"
-                        .format(file_path, sorted(overrideSet)))
+                                   .format(file_path, sorted(overrideSet)))
                 allReactions = allReactions.union(fileReactions)
 
         return evolving_conditions
@@ -168,7 +168,7 @@ def add_condition(self, time_point, conditions):
         # Work backward from end of list, looking for first time <= this new time.
         timeIndex = len(self.times)
         while (timeIndex > 0
-            and self.times[timeIndex - 1] > time_point):
+               and self.times[timeIndex - 1] > time_point):
             timeIndex -= 1
 
         self.times.insert(timeIndex, time_point)
@@ -226,15 +226,15 @@ def read_conditions_from_file(self, file_path):
                     reaction_rates[f'{condition_type}.{label}'] = row[key]
 
             self.add_condition(time,
-                Conditions(
-                    pressure,
-                    temperature,
-                    species_concentrations,
-                    reaction_rates
-                )
-            )
-
-        return(header_set)
+                               Conditions(
+                                   pressure,
+                                   temperature,
+                                   species_concentrations,
+                                   reaction_rates
+                               )
+                               )
+
+        return (header_set)
 
     # allows len overload for this class
 

src/acom_music_box/tools/waccmToMusicBox.py

@@ -270,9 +270,9 @@ def convertWaccm(varDict):
 # return True for temperature, pressure, ...
 def isEnvironment(varName):
     if (varName.lower() in {"temperature", "pressure"}):
-        return(True)
+        return (True)
 
-    return(False)
+    return (False)
 
 
 # Write CSV file suitable for initial_conditions.csv in MusicBox.
@@ -291,7 +291,7 @@ def writeInitCSV(initValues, filename):
         reaction_type = "CONC"
         if isEnvironment(key):
             reaction_type = "ENV"
-            
+
         fp.write("{}.{} [{}]".format(reaction_type, key, value[unitIndex]))
     fp.write("\n")
 

tests/integration/test_analytical.py

@@ -118,4 +118,3 @@ def test_run(self):
     logging.basicConfig(level=logging.DEBUG)
     test = TestAnalytical()
     test.test_run()
-

tests/integration/test_mixing_ratios.py

@@ -136,4 +136,3 @@ def test_ppt(self):
 if __name__ == "__main__":
     test = TestAnalytical()
     test.test_run()
-

tests/integration/test_waccm_conversion.py

@@ -49,4 +49,3 @@ def test_waccm_to_music_box_conversion(temp_dir):
     assert os.path.exists(os.path.join(os.path.dirname(Examples.WACCM.path), "initial_conditions.csv"))
     assert os.path.exists(os.path.join(os.path.dirname(Examples.WACCM.path), "initial_config.json"))
     assert os.path.exists(os.path.join(temp_dir, "config.zip"))
-