Merge pull request #129 from NCAR/127-pep8

Auto format python code using pep8

.github/workflows/pep8.yml

@@ -0,0 +1,45 @@
+name: Pep8
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  autopep8:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: autopep8
+        uses: peter-evans/autopep8@v2
+        with:
+          args: --recursive --in-place --aggressive --aggressive .
+
+      - name: Check for changes
+        id: check-changes
+        run: git diff --exit-code
+        continue-on-error: true
+
+      - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+
+      - name: Push changes to main-autopep8 branch
+        if: steps.check-changes.outcome != 'success'
+        run: git push origin HEAD:main-autopep8
+
+      - name: Create Pull Request
+        if: steps.check-changes.outcome != 'success'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using autopep8"
+          title: "Auto-format code by autopep8"
+          body: "This is an auto-generated PR with fixes by autopep8."
+          branch: main-autopep8

docs/source/conf.py

@@ -22,7 +22,8 @@
 author = 'NCAR/UCAR'
 
 suffix = ''
-# the suffix is required. This is controlled by the dockerfile that builds the docs
+# the suffix is required. This is controlled by the dockerfile that builds
+# the docs
 release = f'0.0.0'
 
 # -- General configuration ---------------------------------------------------
@@ -31,9 +32,9 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-  'sphinx_copybutton',
-  'sphinx_design',
-  'sphinxcontrib.bibtex',
+    'sphinx_copybutton',
+    'sphinx_design',
+    'sphinxcontrib.bibtex',
 ]
 
 bibtex_bibfiles = ['references.bib']
@@ -59,8 +60,8 @@
     "external_links": [],
     "github_url": "https://github.com/NCAR/musica",
     "navbar_end": ["version-switcher", "navbar-icon-links"],
-   "pygment_light_style": "tango",
-   "pygment_dark_style": "monokai"
+    "pygment_light_style": "tango",
+    "pygment_dark_style": "monokai"
 }
 
 html_css_files = [

python/test/analytical.py

@@ -2,13 +2,14 @@
 import numpy as np
 import musica
 
+
 class TestAnalyticalSimulation(unittest.TestCase):
     def test_simulation(self):
         time_step = 200.0
         temperature = 272.5
         pressure = 101253.3
 
-        solver = musica.create_micm("configs/analytical")  
+        solver = musica.create_micm("configs/analytical")
 
         rates = musica.user_defined_reaction_rates(solver)
         ordering = musica.species_ordering(solver)
@@ -18,14 +19,15 @@ def test_simulation(self):
         self.assertEqual(ordering['B'], 1)
         self.assertEqual(ordering['C'], 2)
 
-        # Initalizes concentrations 
+        # Initalizes concentrations
         initial_concentrations = [1, 0, 0]
 
         model_concentrations = [initial_concentrations[:]]
         analytical_concentrations = [initial_concentrations[:]]
 
         k1 = 4.0e-3 * np.exp(50 / temperature)
-        k2 = 1.2e-4 * np.exp(75 / temperature) * (temperature / 50)**7* (1.0 + 0.5 * pressure)
+        k2 = 1.2e-4 * np.exp(75 / temperature) * \
+            (temperature / 50)**7 * (1.0 + 0.5 * pressure)
 
         time_step = 1
         sim_length = 100
@@ -38,23 +40,41 @@ def test_simulation(self):
 
         concentrations = initial_concentrations
 
-        # Gets analytical concentrations 
+        # Gets analytical concentrations
         while curr_time <= sim_length:
-            musica.micm_solve(solver, time_step, temperature, pressure, concentrations, None)
+            musica.micm_solve(
+                solver,
+                time_step,
+                temperature,
+                pressure,
+                concentrations,
+                None)
             model_concentrations.append(concentrations[:])
 
             initial_A = analytical_concentrations[0][idx_A]
-            A_conc = initial_A * np.exp(-(k1)* curr_time)
-            B_conc = initial_A * (k1 / (k2 - k1)) * (np.exp(-k1 * curr_time) - np.exp(-k2 * curr_time))
-            C_conc =  initial_A * (1.0 + (k1 * np.exp(-k2 * curr_time) - k2 * np.exp(-k1 * curr_time)) / (k2 - k1))
+            A_conc = initial_A * np.exp(-(k1) * curr_time)
+            B_conc = initial_A * \
+                (k1 / (k2 - k1)) * (np.exp(-k1 * curr_time) - np.exp(-k2 * curr_time))
+            C_conc = initial_A * \
+                (1.0 + (k1 * np.exp(-k2 * curr_time) - k2 * np.exp(-k1 * curr_time)) / (k2 - k1))
 
             analytical_concentrations.append([A_conc, B_conc, C_conc])
             curr_time += time_step
 
         for i in range(len(model_concentrations)):
-            self.assertAlmostEqual(model_concentrations[i][idx_A], analytical_concentrations[i][idx_A], places=8)
-            self.assertAlmostEqual(model_concentrations[i][idx_B], analytical_concentrations[i][idx_B], places=8)
-            self.assertAlmostEqual(model_concentrations[i][idx_C], analytical_concentrations[i][idx_C], places=8)
+            self.assertAlmostEqual(
+                model_concentrations[i][idx_A],
+                analytical_concentrations[i][idx_A],
+                places=8)
+            self.assertAlmostEqual(
+                model_concentrations[i][idx_B],
+                analytical_concentrations[i][idx_B],
+                places=8)
+            self.assertAlmostEqual(
+                model_concentrations[i][idx_C],
+                analytical_concentrations[i][idx_C],
+                places=8)
+
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main()

python/test/chapman.py

@@ -1,38 +1,50 @@
 import unittest
 import musica
 
+
 class TestChapman(unittest.TestCase):
     def test_micm_solve(self):
         time_step = 200.0
         temperature = 272.5
         pressure = 101253.3
         concentrations = [0.75, 0.4, 0.8, 0.01, 0.02]
 
-        solver = musica.create_micm("configs/chapman")  
+        solver = musica.create_micm("configs/chapman")
         rate_constant_ordering = musica.user_defined_reaction_rates(solver)
         ordering = musica.species_ordering(solver)
 
         rate_constants = {
-            "PHOTO.R1" : 2.42e-17,
-            "PHOTO.R3" : 1.15e-5,
-            "PHOTO.R5" : 6.61e-9
+            "PHOTO.R1": 2.42e-17,
+            "PHOTO.R3": 1.15e-5,
+            "PHOTO.R5": 6.61e-9
         }
 
         ordered_rate_constants = len(rate_constants.keys()) * [0.0]
 
         for key, value in rate_constants.items():
             ordered_rate_constants[rate_constant_ordering[key]] = value
-
-        musica.micm_solve(solver, time_step, temperature, pressure, concentrations, ordered_rate_constants)
 
-        self.assertEqual(ordering, {'M': 0, 'O': 2, 'O1D': 1, 'O2': 3, 'O3': 4})
-        self.assertEqual(rate_constant_ordering, {'PHOTO.R1': 0, 'PHOTO.R3': 1, 'PHOTO.R5': 2})
+        musica.micm_solve(
+            solver,
+            time_step,
+            temperature,
+            pressure,
+            concentrations,
+            ordered_rate_constants)
+
+        self.assertEqual(
+            ordering, {
+                'M': 0, 'O': 2, 'O1D': 1, 'O2': 3, 'O3': 4})
+        self.assertEqual(
+            rate_constant_ordering, {
+                'PHOTO.R1': 0, 'PHOTO.R3': 1, 'PHOTO.R5': 2})
 
         self.assertEqual(concentrations[0], 0.75)
         self.assertNotEqual(concentrations[1], 0.4)
         self.assertNotEqual(concentrations[2], 0.8)
         self.assertNotEqual(concentrations[3], 0.01)
         self.assertNotEqual(concentrations[4], 0.02)
 
+
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main()