More formatting wtih black

Author: cshenry

modelseedpy/biochem/modelseed_biochem.py

@@ -179,6 +179,7 @@ def load_metabolites_from_df(
             logger.error("failed to read compound at Index: %s. %s", t[0], e)
     return compounds
 
+
 def _load_aliases_df(df_aliases, seed_index=1, source_index=3, alias_id_index=2):
     aliases = {}
     for i in df_aliases.itertuples():
@@ -319,6 +320,7 @@ def _load_reactions(
 
     return reactions, metabolites_indexed
 
+
 def load_reactions_from_df(
     df: pd.DataFrame,
     database_metabolites: dict,

modelseedpy/biochem/modelseed_compound.py

@@ -149,4 +149,4 @@ def is_obsolete(self):
                 return False
             else:
                 return True
-        return False
+        return False

modelseedpy/community/mscommunity.py

@@ -33,7 +33,7 @@ def __init__(
         biomass_cpd,  # metabolite in the biomass reaction
         names=[],  # names of the community species #TODO - look into whether there should be a names field
         name=None,  # the name of a species
-        index=None  # the index of the species
+        index=None,  # the index of the species
     ):
         self.community, self.biomass_cpd = community, biomass_cpd
         print(self.biomass_cpd.compartment)

modelseedpy/core/biolog.py

@@ -171,4 +171,4 @@ def run_plates(self, model, biomass=None, cmp="e"):  # !!! biomass is never used
                 plate.wells[well_id]["growth"] = ovalue
                 # print(well_id, solution)
                 # print(well_id, media)
-        return prev_medium
+        return prev_medium

modelseedpy/core/fbahelper.py

@@ -287,7 +287,6 @@ def validate_dictionary(dictionary, required_keys, optional_keys={}):
         return dictionary
 
     @staticmethod
-
     def parse_media(media):
         return [cpd.id for cpd in media.data["mediacompounds"]]
 

modelseedpy/core/msatpcorrection.py

@@ -60,7 +60,7 @@ def __init__(
         atp_hydrolysis_id=None,
         load_default_medias=True,
         forced_media=[],
-        default_media_path=None
+        default_media_path=None,
     ):
         """
         :param model:
@@ -285,7 +285,7 @@ def evaluate_growth_media(self):
                 )
                 self.media_gapfill_stats[media] = None
                 output[media.id] = solution.objective_value
-                
+
                 if (
                     solution.objective_value < minimum_obj
                     or solution.status != "optimal"
@@ -345,6 +345,7 @@ def determine_growth_media2(self, max_gapfilling=None):
         Decides which of the test media to use as growth conditions for this model
         :return:
         """
+
         def scoring_function(media):
             return len(self.media_gapfill_stats[media]["new"].keys()) + 0.5 * len(
                 self.media_gapfill_stats[media]["reversed"].keys()

modelseedpy/core/msbuilder.py

@@ -179,7 +179,7 @@
     "cpd15352_c0": -0.00719527989638797,
     "cpd11463_c0": -0.5,
     "cpd11461_c0": -0.1,
-    "cpd11462_c0": -0.2
+    "cpd11462_c0": -0.2,
 }
 
 
@@ -778,6 +778,7 @@ def gapfill_model(original_mdl, target_reaction, template, media):
                 rxn.lower_bound = -100
         return original_mdl
 
+
 def build_metabolic_model(
     genome,
     media=None,

modelseedpy/core/msgapfill.py

@@ -48,7 +48,7 @@ def __init__(
             "cpd02701",
             "cpd11416",
             "cpd15302",
-            "cpd03091"
+            "cpd03091",
         ]  # the cpd11416 compound is filtered during model extension with templates
         self.gfmodel = self.lp_filename = self.last_solution = None
         self.model_penalty = 1

modelseedpy/core/msgenome.py

@@ -18,6 +18,7 @@ def read_fasta(f, split=DEFAULT_SPLIT, h_func=None):
     with open(f, "r") as fh:
         return parse_fasta_str(fh.read(), split, h_func)
 
+
 def parse_fasta_str(faa_str, split=DEFAULT_SPLIT, h_func=None):
     features = []
     seq = None
@@ -36,7 +37,7 @@ def parse_fasta_str(faa_str, split=DEFAULT_SPLIT, h_func=None):
                     desc = header_data[
                         1
                     ]  # The unit test throws an error when this is commented
-                    
+
             seq = MSFeature(seq_id, "", desc)
         else:
             if seq:

modelseedpy/fbapkg/basefbapkg.py

@@ -21,8 +21,10 @@
 # Adding a few exception classes to handle different types of errors
 class FeasibilityError(Exception):
     """Error in FBA formulation"""
+
     pass
 
+
 class BaseFBAPkg:
     """
     Base class for FBA packages

modelseedpy/fbapkg/flexiblebiomasspkg.py

@@ -313,7 +313,7 @@ def build_constraint(self, cobra_obj, obj_type):
                 else:
                     const = BaseFBAPkg.build_constraint(
                         self,
-                       "f" + obj_type,
+                        "f" + obj_type,
                         0,
                         None,
                         {biovar: second_entry, object.forward_variable: -1},

modelseedpy/fbapkg/reactionusepkg.py

@@ -24,7 +24,7 @@ def __init__(self, model):
             },
         )
 
-   def build_package(self, rxn_filter=None, reversibility=False):
+    def build_package(self, rxn_filter=None, reversibility=False):
         for rxn in self.model.reactions:
             # Checking that reaction passes input filter if one is provided
             if rxn_filter == None: