Merge pull request #204 from NCAR/main-autopep8

Auto-format code by autopep8

src/acom_music_box/__init__.py

@@ -19,4 +19,4 @@
 
 from .evolving_conditions import EvolvingConditions
 from .music_box import MusicBox
-from .examples import Examples
+from .examples import Examples

src/acom_music_box/examples/__init__.py

@@ -1 +1 @@
-from .examples import Examples
+from .examples import Examples

src/acom_music_box/examples/examples.py

@@ -1,41 +1,43 @@
 import os
 
+
 class Example:
     def __init__(self, name, short_name, description, path):
         self.name = name
         self.short_name = short_name
         self.description = description
         self.path = path
-    
+
     def __str__(self):
         return f'{self.name}: {self.description}'
-    
+
     def __repr__(self):
         return f'{self.name}: {self.description}'
 
     @classmethod
     def from_config(cls, display_name, folder_name, short_name, description):
         path = os.path.join(os.path.dirname(__file__), 'configs', folder_name, 'my_config.json')
-        return cls(name=display_name, short_name = short_name, description=description, path=path)
+        return cls(name=display_name, short_name=short_name, description=description, path=path)
+
 
 class _Examples:
     CarbonBond5 = Example.from_config(
-        display_name='Carbon Bond IV', 
+        display_name='Carbon Bond IV',
         short_name='CB5',
         folder_name='carbon_bond_5',
         description='Carbon bond 5')
     Chapman = Example.from_config(
-        display_name='Chapman', 
+        display_name='Chapman',
         short_name='Chapman',
         folder_name='chapman',
         description='The Chapman cycle with conditions over Boulder, Colorado')
     FlowTube = Example.from_config(
-        display_name='Flow Tube', 
+        display_name='Flow Tube',
         short_name='FlowTube',
         folder_name='flow_tube',
         description='A fictitious flow tube experiment')
     Analytical = Example.from_config(
-        display_name='Analytical', 
+        display_name='Analytical',
         short_name='Analytical',
         folder_name='analytical',
         description='An example of an analytical solution to a simple chemical system')
@@ -52,4 +54,5 @@ def __getattr__(self, item):
             return getattr(self, item)
         raise AttributeError(f"'{self.__class__.__name__}' object has no attribute '{item}'")
 
-Examples = _Examples()
+
+Examples = _Examples()

src/acom_music_box/main.py

@@ -8,9 +8,11 @@
 import subprocess
 import tempfile
 
+
 def format_examples_help(examples):
     return '\n'.join(f"{e.short_name}: {e.description}" for e in examples)
 
+
 def parse_arguments():
     parser = argparse.ArgumentParser(
         description='MusicBox simulation runner.',
@@ -50,6 +52,7 @@ def parse_arguments():
     )
     return parser.parse_args()
 
+
 def setup_logging(verbosity, color_output):
     if verbosity >= 2:
         log_level = logging.DEBUG
@@ -58,9 +61,19 @@ def setup_logging(verbosity, color_output):
     else:
         log_level = logging.CRITICAL
 
-    formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s', datefmt='%Y-%m-%d %H:%M:%S')
+    formatter = logging.Formatter(
+        '%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s',
+        datefmt='%Y-%m-%d %H:%M:%S')
     if color_output:
-        color_formatter = colorlog.ColoredFormatter('%(log_color)s%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s', datefmt='%Y-%m-%d %H:%M:%S', log_colors={'DEBUG': 'green', 'INFO': 'cyan', 'WARNING': 'yellow', 'ERROR': 'red', 'CRITICAL': 'bold_red'})
+        color_formatter = colorlog.ColoredFormatter(
+            '%(log_color)s%(asctime)s - %(levelname)s - %(module)s.%(funcName)s - %(message)s',
+            datefmt='%Y-%m-%d %H:%M:%S',
+            log_colors={
+                'DEBUG': 'green',
+                'INFO': 'cyan',
+                'WARNING': 'yellow',
+                'ERROR': 'red',
+                'CRITICAL': 'bold_red'})
         console_handler = logging.StreamHandler()
         console_handler.setLevel(log_level)
         console_handler.setFormatter(color_formatter)
@@ -71,20 +84,23 @@ def setup_logging(verbosity, color_output):
         console_handler.setFormatter(formatter)
         logging.basicConfig(level=log_level, handlers=[console_handler])
 
+
 def plot_with_gnuplot(data, species_list):
     # Prepare columns and data for plotting
     columns = ['time'] + species_list
     data_to_plot = data[columns]
-    
+
     data_csv = data_to_plot.to_csv(index=False)
-    
+
     try:
         with tempfile.NamedTemporaryFile(delete=False, suffix='.csv') as data_file:
             data_file.write(data_csv.encode())
             data_file_path = data_file.name
-
-        plot_commands = ',\n\t'.join(f"'{data_file_path}' using 1:{i+2} with lines title '{species}'" for i, species in enumerate(species_list))
-
+
+        plot_commands = ',\n\t'.join(
+            f"'{data_file_path}' using 1:{i+2} with lines title '{species}'" for i,
+            species in enumerate(species_list))
+
         gnuplot_command = f"""
         set datafile separator ",";
         set terminal dumb size 120,25;
@@ -93,7 +109,7 @@ def plot_with_gnuplot(data, species_list):
         set title 'Time vs Species';
         plot {plot_commands}
         """
-        
+
         subprocess.run(['gnuplot', '-e', gnuplot_command], check=True)
     except FileNotFoundError:
         logging.critical("gnuplot is not installed. Skipping plotting.")
@@ -104,6 +120,7 @@ def plot_with_gnuplot(data, species_list):
         if data_file_path:
             os.remove(data_file_path)
 
+
 def main():
     start = datetime.datetime.now()
 
@@ -138,10 +155,10 @@ def main():
         myBox.config_file)
     myBox.create_solver(config_path)
     result = myBox.solve(musicBoxOutputPath)
-    
+
     if musicBoxOutputPath is None:
         print(result.to_csv(index=False))
-    
+
     if plot_species_list:
         # Prepare data for plotting
         plot_with_gnuplot(result, plot_species_list)
@@ -152,5 +169,6 @@ def main():
 
     sys.exit(0)
 
+
 if __name__ == "__main__":
     main()

src/acom_music_box/music_box.py

@@ -562,7 +562,7 @@ def solve(self, output_path=None):
                 output_path = os.path.join(os.getcwd(), output_path)
             elif not os.path.basename(output_path):
                 raise ValueError(f"Invalid output path: '{output_path}' does not contain a filename.")
-            
+
             # Ensure the directory exists
             dir_path = os.path.dirname(output_path)
             if dir_path and not os.path.exists(dir_path):

tests/test_analytical.py

@@ -3,6 +3,7 @@
 
 import math
 
+
 class TestAnalytical:
     def test_run(self):
         box_model = MusicBox()