ran black

src/cobra/core/reaction.py

@@ -581,7 +581,7 @@ def metabolites(self) -> Dict[Metabolite, float]:
 
     @metabolites.setter
     @resettable
-    def metabolites(self, value:  Dict[Metabolite, float]) -> None:
+    def metabolites(self, value: Dict[Metabolite, float]) -> None:
         """Set metabolites to a dictionary of metabolites and coefficients.
 
         Parameters
@@ -1228,8 +1228,10 @@ def add_metabolites(
             # Make sure metabolites being added belong to the same model, or
             # else copy them.
             if isinstance(metabolite, Metabolite):
-                if (metabolite.model is not None) and self.model and (
-                    metabolite.model is not self._model
+                if (
+                    (metabolite.model is not None)
+                    and self.model
+                    and (metabolite.model is not self._model)
                 ):
                     metabolite = metabolite.copy()
 

src/cobra/core/species.py

@@ -8,6 +8,7 @@
 from ..core.object import Object
 from ..util import HistoryManager
 
+
 if TYPE_CHECKING:
     from .. import Model, Reaction
 
@@ -57,12 +58,14 @@ def reactions(self) -> FrozenSet:
             A frozenset that includes the reactions of the species.
         """
         if self.model and self.__class__.__name__ == "Gene":
-            return self.model.reactions.query(lambda x: self in x, 'genes')
+            return self.model.reactions.query(lambda x: self in x, "genes")
         elif self.model and self.__class__.__name__ == "Metabolite":
-            return self.model.reactions.query(lambda x: self in x, 'metabolites')
+            return self.model.reactions.query(lambda x: self in x, "metabolites")
         return frozenset(self._reaction)
 
-    def reaction_add(self, reaction: Reaction, context: Optional[HistoryManager] = None) -> None:
+    def reaction_add(
+        self, reaction: Reaction, context: Optional[HistoryManager] = None
+    ) -> None:
         """Add reaction to .reaction field, with context.
 
         If this is called with a context, will be reversed when exiting the context.
@@ -77,7 +80,9 @@ def reaction_add(self, reaction: Reaction, context: Optional[HistoryManager] = N
         if context:
             context(partial(self._reaction.remove, reaction))
 
-    def reaction_remove(self, reaction: Reaction, context: Optional[HistoryManager] = None) -> None:
+    def reaction_remove(
+        self, reaction: Reaction, context: Optional[HistoryManager] = None
+    ) -> None:
         """Remove reaction from .reaction field, with context.
 
         If this is called with a context, will be reversed when exiting the context.

tests/test_core/test_model.py

@@ -1020,10 +1020,9 @@ def test_add_reactions_from_another_model(model: Model, data_directory: Path) ->
     data_directory: Path
         Directory where mini_cobra.xml is found.
     """
-    mini = read_sbml_model(data_directory / 'mini_cobra.xml')
-    mini.add_reactions([model.reactions.get_by_id('ACALD')])
-    assert len(mini.metabolites.get_by_id('acald_c').reactions) == 1
-
+    mini = read_sbml_model(data_directory / "mini_cobra.xml")
+    mini.add_reactions([model.reactions.get_by_id("ACALD")])
+    assert len(mini.metabolites.get_by_id("acald_c").reactions) == 1
 
 
 def test_add_reactions_single_existing(model: Model) -> None: