Auto-format code using Clang-Format (#256)

Co-authored-by: GitHub Actions <[email protected]>
NCAR · Oct 9, 2024 · 3758660 · 3758660
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Showing 6 changed files with 48 additions and 40 deletions.
diff --git a/src/acom_music_box/constants.py b/src/acom_music_box/constants.py
@@ -1,3 +1,3 @@
 BOLTZMANN_CONSTANT = 1.380649e-23       # joules / Kelvin
 AVOGADRO_CONSTANT = 6.02214076e23       # / mole
-GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT   # joules / Kelvin-mole
+GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT   # joules / Kelvin-mole
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
@@ -92,7 +92,7 @@ def check_config(self, boxConfigPath):
 
             if dup_names:
                 raise Exception(f"Error: Duplicate reaction names specified within {boxConfigPath}: {dup_names}. "
-                        "Please remove or rename the duplicates.")
+                                "Please remove or rename the duplicates.")
 
         # look for duplicate reaction names in the initial conditions
         if (self.initial_conditions):

diff --git a/src/acom_music_box/species_list.py b/src/acom_music_box/species_list.py
@@ -80,7 +80,7 @@ def from_config_JSON(cls, path_to_json, config_JSON):
 
             # assumes species file is first in the list
             if (len(config['camp-files']) > 0):
-                species_file_path = os.path.join( os.path.dirname(config_file_path), config['camp-files'][0])
+                species_file_path = os.path.join(os.path.dirname(config_file_path), config['camp-files'][0])
                 with open(species_file_path, 'r') as species_file:
                     species_data = json.load(species_file)
                     # loads species by names from camp files

diff --git a/src/acom_music_box/utils.py b/src/acom_music_box/utils.py
@@ -1,6 +1,7 @@
 import re
 from .constants import GAS_CONSTANT, AVOGADRO_CONSTANT
 
+
 def extract_unit(data, key):
     """Extract the value and unit from the key in data."""
     pattern = re.compile(rf'{key} \[(.+)\]')
@@ -10,6 +11,7 @@ def extract_unit(data, key):
             return float(v), match.group(1)
     return None, None
 
+
 def convert_time(data, key):
     """
     Convert the time from the input data to seconds.
@@ -21,7 +23,7 @@ def convert_time(data, key):
         float: The time in seconds.
     """
     time_value, unit = extract_unit(data, key)
-    
+
     if unit == 'sec':
         return time_value
     elif unit == 'min':
@@ -33,6 +35,7 @@ def convert_time(data, key):
     else:
         raise ValueError(f"Unsupported time unit: {unit}")
 
+
 def convert_pressure(data, key):
     """
     Convert the pressure from the input data to Pascals.
@@ -44,7 +47,7 @@ def convert_pressure(data, key):
         float: The pressure in Pascals.
     """
     pressure_value, unit = extract_unit(data, key)
-    
+
     if unit == 'Pa':
         return pressure_value
     elif unit == 'atm':
@@ -58,6 +61,7 @@ def convert_pressure(data, key):
     else:
         raise ValueError(f"Unsupported pressure unit: {unit}")
 
+
 def convert_temperature(data, key):
     """
     Convert the temperature from the input data to Kelvin.
@@ -69,7 +73,7 @@ def convert_temperature(data, key):
         float: The temperature in Kelvin.
     """
     temperature_value, unit = extract_unit(data, key)
-    
+
     if unit == 'K':
         return temperature_value
     elif unit == 'C':
@@ -79,6 +83,7 @@ def convert_temperature(data, key):
     else:
         raise ValueError(f"Unsupported temperature unit: {unit}")
 
+
 def convert_concentration(data, key, temperature, pressure):
     """
     Convert the concentration from the input data to molecules per cubic meter.
@@ -113,6 +118,7 @@ def convert_concentration(data, key, temperature, pressure):
     else:
         raise ValueError(f"Unsupported concentration unit: {unit}")
 
+
 def calculate_air_density(temperature, pressure):
     """
     Calculate the air density in moles/m^3.

diff --git a/tests/integration/test_mixing_ratios.py b/tests/integration/test_mixing_ratios.py
@@ -84,12 +84,11 @@ def run_example(self, example):
                 rel_tol=1e-8,
             ), f"Arrays differ at index ({i}, 2)"
 
-
     def test_mol_mol_1(self):
         current_dir = os.path.dirname(__file__)
         example = os.path.join(current_dir, "configs", "mixing_ratio", "mol mol-1", "my_config.json")
         self.run_example(example)
-    
+
     def test_ppth(self):
         current_dir = os.path.dirname(__file__)
         example = os.path.join(current_dir, "configs", "mixing_ratio", "ppth", "my_config.json")
@@ -99,7 +98,7 @@ def test_ppm(self):
         current_dir = os.path.dirname(__file__)
         example = os.path.join(current_dir, "configs", "mixing_ratio", "ppm", "my_config.json")
         self.run_example(example)
-    
+
     def test_ppb(self):
         current_dir = os.path.dirname(__file__)
         example = os.path.join(current_dir, "configs", "mixing_ratio", "ppb", "my_config.json")

diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py
@@ -1,57 +1,60 @@
 import pytest
 from acom_music_box.utils import (
-    convert_time, 
-    convert_pressure, 
-    convert_temperature, 
-    convert_concentration, 
+    convert_time,
+    convert_pressure,
+    convert_temperature,
+    convert_concentration,
     calculate_air_density
 )
 import math
 
+
 @pytest.mark.parametrize("data, key, expected", [
-  ({'time [sec]': 60}, 'time', 60),
-  ({'time [min]': 1}, 'time', 60),
-  ({'time [hour]': 1}, 'time', 3600),
-  ({'time [day]': 1}, 'time', 86400),
+    ({'time [sec]': 60}, 'time', 60),
+    ({'time [min]': 1}, 'time', 60),
+    ({'time [hour]': 1}, 'time', 3600),
+    ({'time [day]': 1}, 'time', 86400),
 ])
 def test_convert_time(data, key, expected):
-  assert convert_time(data, key) == expected
+    assert convert_time(data, key) == expected
 
 
 @pytest.mark.parametrize("data, key, expected", [
-  ({'pressure [Pa]': 101325}, 'pressure', 101325),
-  ({'pressure [atm]': 1}, 'pressure', 101325),
-  ({'pressure [bar]': 1}, 'pressure', 100000),
-  ({'pressure [kPa]': 101.325}, 'pressure', 101325),
-  ({'pressure [hPa]': 1013.25}, 'pressure', 101325),
+    ({'pressure [Pa]': 101325}, 'pressure', 101325),
+    ({'pressure [atm]': 1}, 'pressure', 101325),
+    ({'pressure [bar]': 1}, 'pressure', 100000),
+    ({'pressure [kPa]': 101.325}, 'pressure', 101325),
+    ({'pressure [hPa]': 1013.25}, 'pressure', 101325),
 ])
 def test_convert_pressure(data, key, expected):
-  assert convert_pressure(data, key) == expected
+    assert convert_pressure(data, key) == expected
+
 
 @pytest.mark.parametrize("data, key, expected", [
-  ({'temp [K]': 273.15}, 'temp', 273.15),
-  ({'temp [C]': 0}, 'temp', 273.15),
-  ({'temp [F]': 32}, 'temp', 273.15),
+    ({'temp [K]': 273.15}, 'temp', 273.15),
+    ({'temp [C]': 0}, 'temp', 273.15),
+    ({'temp [F]': 32}, 'temp', 273.15),
 ])
 def test_convert_temperature(data, key, expected):
-  assert convert_temperature(data, key) == expected
+    assert convert_temperature(data, key) == expected
 
 
 @pytest.mark.parametrize("data, key, temperature, pressure, expected", [
-  ({'concentration [mol m-3]': 1}, 'concentration', 298.15, 101325, 1),
-  ({'concentration [mol cm-3]': 1e-3}, 'concentration', 298.15, 101325, 1),
-  ({'concentration [molec m-3]': 6.02214076e+23}, 'concentration', 298.15, 101325, 1),
-  ({'concentration [molec cm-3]': 6.02214076e+20}, 'concentration', 298.15, 101325, 1),
-  ({'concentration [molecule m-3]': 6.02214076e+23}, 'concentration', 298.15, 101325, 1),
-  ({'concentration [molecule cm-3]': 6.02214076e+20}, 'concentration', 298.15, 101325, 1),
-  ({'concentration [ppth]': 1e-3}, 'concentration', 298.15, 101325, 1e-6 * calculate_air_density(298.15, 101325)),
-  ({'concentration [ppm]': 1}, 'concentration', 298.15, 101325, 1e-6 * calculate_air_density(298.15, 101325)),
-  ({'concentration [ppb]': 1}, 'concentration', 298.15, 101325, 1e-9 * calculate_air_density(298.15, 101325)),
-  ({'concentration [ppt]': 1}, 'concentration', 298.15, 101325, 1e-12 * calculate_air_density(298.15, 101325)),
-  ({'concentration [mol mol-1]': 1}, 'concentration', 298.15, 101325, 1 * calculate_air_density(298.15, 101325)),
+    ({'concentration [mol m-3]': 1}, 'concentration', 298.15, 101325, 1),
+    ({'concentration [mol cm-3]': 1e-3}, 'concentration', 298.15, 101325, 1),
+    ({'concentration [molec m-3]': 6.02214076e+23}, 'concentration', 298.15, 101325, 1),
+    ({'concentration [molec cm-3]': 6.02214076e+20}, 'concentration', 298.15, 101325, 1),
+    ({'concentration [molecule m-3]': 6.02214076e+23}, 'concentration', 298.15, 101325, 1),
+    ({'concentration [molecule cm-3]': 6.02214076e+20}, 'concentration', 298.15, 101325, 1),
+    ({'concentration [ppth]': 1e-3}, 'concentration', 298.15, 101325, 1e-6 * calculate_air_density(298.15, 101325)),
+    ({'concentration [ppm]': 1}, 'concentration', 298.15, 101325, 1e-6 * calculate_air_density(298.15, 101325)),
+    ({'concentration [ppb]': 1}, 'concentration', 298.15, 101325, 1e-9 * calculate_air_density(298.15, 101325)),
+    ({'concentration [ppt]': 1}, 'concentration', 298.15, 101325, 1e-12 * calculate_air_density(298.15, 101325)),
+    ({'concentration [mol mol-1]': 1}, 'concentration', 298.15, 101325, 1 * calculate_air_density(298.15, 101325)),
 ])
 def test_convert_concentration(data, key, temperature, pressure, expected):
-  assert math.isclose(convert_concentration(data, key, temperature, pressure), expected)
+    assert math.isclose(convert_concentration(data, key, temperature, pressure), expected)
+
 
 def test_invalid_concentration():
     data = {'invalid_concentration': 100}