From a5a4ffd8b642dc0d76759ad46ebe9d7a9e049210 Mon Sep 17 00:00:00 2001
From: Bruce Perry <bruce.perry@nrel.gov>
Date: Wed, 18 Oct 2023 16:54:28 -0600
Subject: [PATCH 1/2] updated black formatting

---
 Support/ceptr/ceptr/__init__.py       | 1 +
 Support/ceptr/ceptr/__main__.py       | 1 +
 Support/ceptr/ceptr/ceptr.py          | 1 +
 Support/ceptr/ceptr/ck.py             | 1 +
 Support/ceptr/ceptr/constants.py      | 1 +
 Support/ceptr/ceptr/converter.py      | 1 +
 Support/ceptr/ceptr/formatter.py      | 1 -
 Support/ceptr/ceptr/gjs.py            | 1 +
 Support/ceptr/ceptr/inputs.py         | 1 +
 Support/ceptr/ceptr/jacobian.py       | 1 +
 Support/ceptr/ceptr/production.py     | 5 ++---
 Support/ceptr/ceptr/qssa.py           | 1 +
 Support/ceptr/ceptr/qssa_converter.py | 1 +
 Support/ceptr/ceptr/qssa_graphs.py    | 1 +
 Support/ceptr/ceptr/qssa_info.py      | 1 +
 Support/ceptr/ceptr/qssa_reduction.py | 1 +
 Support/ceptr/ceptr/reaction_info.py  | 1 +
 Support/ceptr/ceptr/sparsity.py       | 1 +
 Support/ceptr/ceptr/species_info.py   | 1 +
 Support/ceptr/ceptr/symbolic_math.py  | 1 +
 Support/ceptr/ceptr/thermo.py         | 1 +
 Support/ceptr/ceptr/transport.py      | 1 +
 Support/ceptr/ceptr/utilities.py      | 1 +
 Support/ceptr/ceptr/writer.py         | 1 -
 Support/ceptr/tests/test_ceptr.py     | 1 +
 25 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/Support/ceptr/ceptr/__init__.py b/Support/ceptr/ceptr/__init__.py
index 9b56d3059..c2367dfb9 100644
--- a/Support/ceptr/ceptr/__init__.py
+++ b/Support/ceptr/ceptr/__init__.py
@@ -1,2 +1,3 @@
 """CEPTR."""
+
 __version__ = "0.1.0"
diff --git a/Support/ceptr/ceptr/__main__.py b/Support/ceptr/ceptr/__main__.py
index d42e3ac2b..68ffa399e 100644
--- a/Support/ceptr/ceptr/__main__.py
+++ b/Support/ceptr/ceptr/__main__.py
@@ -1,4 +1,5 @@
 """Executable for CEPTR package."""
+
 import ceptr.ceptr as cp
 
 if __name__ == "__main__":
diff --git a/Support/ceptr/ceptr/ceptr.py b/Support/ceptr/ceptr/ceptr.py
index ddde831a2..07b366cfa 100644
--- a/Support/ceptr/ceptr/ceptr.py
+++ b/Support/ceptr/ceptr/ceptr.py
@@ -1,4 +1,5 @@
 """Convert cantera mechanism to C++ files."""
+
 import argparse
 import pathlib
 import time
diff --git a/Support/ceptr/ceptr/ck.py b/Support/ceptr/ceptr/ck.py
index e71be20c7..0079b5f28 100644
--- a/Support/ceptr/ceptr/ck.py
+++ b/Support/ceptr/ceptr/ck.py
@@ -1,4 +1,5 @@
 """CK routines."""
+
 import ceptr.constants as cc
 import ceptr.thermo as cth
 import ceptr.writer as cw
diff --git a/Support/ceptr/ceptr/constants.py b/Support/ceptr/ceptr/constants.py
index 5561c12a3..d1683e683 100644
--- a/Support/ceptr/ceptr/constants.py
+++ b/Support/ceptr/ceptr/constants.py
@@ -1,4 +1,5 @@
 """Constants."""
+
 import cantera as ct
 from pint import UnitRegistry
 
diff --git a/Support/ceptr/ceptr/converter.py b/Support/ceptr/ceptr/converter.py
index 572c8780c..04a6fede7 100644
--- a/Support/ceptr/ceptr/converter.py
+++ b/Support/ceptr/ceptr/converter.py
@@ -1,4 +1,5 @@
 """Generate C++ files for a mechanism."""
+
 import pathlib
 import shutil
 import subprocess as spr
diff --git a/Support/ceptr/ceptr/formatter.py b/Support/ceptr/ceptr/formatter.py
index 8fa13931f..c900ea727 100644
--- a/Support/ceptr/ceptr/formatter.py
+++ b/Support/ceptr/ceptr/formatter.py
@@ -1,6 +1,5 @@
 """Helper functions for CPP formatting."""
 
-
 def format_species(species):
     """Remove characters not allowed in preprocessor defines."""
     s = species.strip()
diff --git a/Support/ceptr/ceptr/gjs.py b/Support/ceptr/ceptr/gjs.py
index ef0aaa1bd..5b6eaeecb 100644
--- a/Support/ceptr/ceptr/gjs.py
+++ b/Support/ceptr/ceptr/gjs.py
@@ -1,4 +1,5 @@
 """Gauss-Jordan functions."""
+
 import ceptr.writer as cw
 
 
diff --git a/Support/ceptr/ceptr/inputs.py b/Support/ceptr/ceptr/inputs.py
index 998cedf81..118d6308e 100644
--- a/Support/ceptr/ceptr/inputs.py
+++ b/Support/ceptr/ceptr/inputs.py
@@ -1,4 +1,5 @@
 """Classes for toml input files."""
+
 import sys
 
 import toml
diff --git a/Support/ceptr/ceptr/jacobian.py b/Support/ceptr/ceptr/jacobian.py
index eabc2e6ea..a007435ba 100644
--- a/Support/ceptr/ceptr/jacobian.py
+++ b/Support/ceptr/ceptr/jacobian.py
@@ -1,4 +1,5 @@
 """Write jacobian functions."""
+
 import copy
 import sys
 from collections import Counter, OrderedDict
diff --git a/Support/ceptr/ceptr/production.py b/Support/ceptr/ceptr/production.py
index 2b035abd9..07ebc06ce 100644
--- a/Support/ceptr/ceptr/production.py
+++ b/Support/ceptr/ceptr/production.py
@@ -1,4 +1,5 @@
 """Production functions."""
+
 import sys
 from math import isclose
 
@@ -696,9 +697,7 @@ def production_rate(
                     f" {10 ** (-dim * 6) * low_pef.m * 10 ** 3 ** dim:.15g} ",
                 )
                 redp_smp = (
-                    corr_smp
-                    / k_f_smp
-                    * (10 ** (-dim * 6) * low_pef.m * 10 ** (3**dim))
+                    corr_smp / k_f_smp * (10 ** (-dim * 6) * low_pef.m * 10 ** (3**dim))
                 )
                 if (low_beta == 0) and (low_ae.m == 0):
                     cw.writer(
diff --git a/Support/ceptr/ceptr/qssa.py b/Support/ceptr/ceptr/qssa.py
index d018caa8f..e755f25ef 100644
--- a/Support/ceptr/ceptr/qssa.py
+++ b/Support/ceptr/ceptr/qssa.py
@@ -1,4 +1,5 @@
 """Generate QSSA chemistry file."""
+
 import argparse
 import pathlib
 import sys
diff --git a/Support/ceptr/ceptr/qssa_converter.py b/Support/ceptr/ceptr/qssa_converter.py
index e1e7973cb..91ed79f9b 100644
--- a/Support/ceptr/ceptr/qssa_converter.py
+++ b/Support/ceptr/ceptr/qssa_converter.py
@@ -1,4 +1,5 @@
 """QSSA functions needed for conversion."""
+
 import copy
 import sys
 from collections import Counter, OrderedDict, defaultdict
diff --git a/Support/ceptr/ceptr/qssa_graphs.py b/Support/ceptr/ceptr/qssa_graphs.py
index 627011975..57208f0f2 100644
--- a/Support/ceptr/ceptr/qssa_graphs.py
+++ b/Support/ceptr/ceptr/qssa_graphs.py
@@ -1,4 +1,5 @@
 """Graph utilities for QSSA."""
+
 import pathlib
 
 import matplotlib.pyplot as plt
diff --git a/Support/ceptr/ceptr/qssa_info.py b/Support/ceptr/ceptr/qssa_info.py
index 43f70f295..a8620c511 100644
--- a/Support/ceptr/ceptr/qssa_info.py
+++ b/Support/ceptr/ceptr/qssa_info.py
@@ -1,4 +1,5 @@
 """QSSA information."""
+
 from collections import OrderedDict
 
 
diff --git a/Support/ceptr/ceptr/qssa_reduction.py b/Support/ceptr/ceptr/qssa_reduction.py
index 81cac8938..098bba77e 100644
--- a/Support/ceptr/ceptr/qssa_reduction.py
+++ b/Support/ceptr/ceptr/qssa_reduction.py
@@ -1,4 +1,5 @@
 """QSSA utilities."""
+
 import itertools
 
 import ceptr.qssa_graphs as cqg
diff --git a/Support/ceptr/ceptr/reaction_info.py b/Support/ceptr/ceptr/reaction_info.py
index 5efb7def2..a92575bda 100644
--- a/Support/ceptr/ceptr/reaction_info.py
+++ b/Support/ceptr/ceptr/reaction_info.py
@@ -1,4 +1,5 @@
 """Reaction information."""
+
 from collections import OrderedDict
 
 import ceptr.constants as cc
diff --git a/Support/ceptr/ceptr/sparsity.py b/Support/ceptr/ceptr/sparsity.py
index 0b889e034..254d3ee85 100644
--- a/Support/ceptr/ceptr/sparsity.py
+++ b/Support/ceptr/ceptr/sparsity.py
@@ -1,4 +1,5 @@
 """Sparsity patterns."""
+
 import ceptr.writer as cw
 
 
diff --git a/Support/ceptr/ceptr/species_info.py b/Support/ceptr/ceptr/species_info.py
index c25ba9c2f..e0af9cfb3 100644
--- a/Support/ceptr/ceptr/species_info.py
+++ b/Support/ceptr/ceptr/species_info.py
@@ -1,4 +1,5 @@
 """Species information."""
+
 from collections import OrderedDict
 
 import pandas as pd
diff --git a/Support/ceptr/ceptr/symbolic_math.py b/Support/ceptr/ceptr/symbolic_math.py
index 140a91bb6..35dfe2760 100644
--- a/Support/ceptr/ceptr/symbolic_math.py
+++ b/Support/ceptr/ceptr/symbolic_math.py
@@ -1,4 +1,5 @@
 """Symbolic math for symbolic differentiation."""
+
 import re
 from collections import OrderedDict
 
diff --git a/Support/ceptr/ceptr/thermo.py b/Support/ceptr/ceptr/thermo.py
index 4b7313349..9ed1c517e 100644
--- a/Support/ceptr/ceptr/thermo.py
+++ b/Support/ceptr/ceptr/thermo.py
@@ -1,4 +1,5 @@
 """Thermodynamics functions."""
+
 import io
 import sys
 from collections import OrderedDict
diff --git a/Support/ceptr/ceptr/transport.py b/Support/ceptr/ceptr/transport.py
index 0dfe46a3c..2d2301005 100644
--- a/Support/ceptr/ceptr/transport.py
+++ b/Support/ceptr/ceptr/transport.py
@@ -1,4 +1,5 @@
 """Transport routines."""
+
 import sys
 from collections import OrderedDict
 
diff --git a/Support/ceptr/ceptr/utilities.py b/Support/ceptr/ceptr/utilities.py
index 54d95b414..df5e129a7 100644
--- a/Support/ceptr/ceptr/utilities.py
+++ b/Support/ceptr/ceptr/utilities.py
@@ -1,4 +1,5 @@
 """Utility functions used across ceptr."""
+
 import copy
 import sys
 from collections import Counter
diff --git a/Support/ceptr/ceptr/writer.py b/Support/ceptr/ceptr/writer.py
index 923995705..8401043fc 100644
--- a/Support/ceptr/ceptr/writer.py
+++ b/Support/ceptr/ceptr/writer.py
@@ -1,6 +1,5 @@
 """Helper functions for printing."""
 
-
 def comment(string):
     """Comment a string."""
     return f"""// {string}"""
diff --git a/Support/ceptr/tests/test_ceptr.py b/Support/ceptr/tests/test_ceptr.py
index 724196d81..2c93c196a 100644
--- a/Support/ceptr/tests/test_ceptr.py
+++ b/Support/ceptr/tests/test_ceptr.py
@@ -1,4 +1,5 @@
 """Tests for cepter."""
+
 import pathlib
 
 import cantera as ct

From c89d0730404e13dd500aaa399f2cfb4a47605f84 Mon Sep 17 00:00:00 2001
From: Bruce Perry <bruce.perry@nrel.gov>
Date: Wed, 18 Oct 2023 16:54:51 -0600
Subject: [PATCH 2/2] ignore E302 in flake8 due to updated black formatting

---
 Support/ceptr/.flake8 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Support/ceptr/.flake8 b/Support/ceptr/.flake8
index 1ba999d9f..25f91c596 100644
--- a/Support/ceptr/.flake8
+++ b/Support/ceptr/.flake8
@@ -2,7 +2,7 @@
 max-line-length = 88
 max-complexity = 10
 select = C,E,F,W,B,B950,N,D
-ignore = E203,E501,W503,C901,FS003
+ignore = E203,E302,E501,W503,C901,FS003
 docstring-convention = numpy
 exclude =
     .git,