fixed according to comments

Author: uri.akavia

src/cobra/core/gene.py

@@ -18,7 +18,7 @@
 from ast import parse as ast_parse
 from copy import deepcopy
 from keyword import kwlist
-from typing import FrozenSet, Iterable, Optional, Set, Tuple, Union
+from typing import TYPE_CHECKING, FrozenSet, Iterable, Optional, Set, Tuple, Union
 from warnings import warn
 
 import sympy.logic.boolalg as spl
@@ -30,6 +30,10 @@
 from cobra.util.util import format_long_string
 
 
+if TYPE_CHECKING:
+    from cobra.core import Reaction
+
+
 # TODO - When https://github.com/symengine/symengine.py/issues/334 is resolved,
 #  change sympy.Symbol (above in imports) to optlang.symbolics.Symbol
 
@@ -246,10 +250,28 @@ def knock_out(self) -> None:
         context.
         """
         self.functional = False
-        for reaction in self.reactions:
+        for reaction in self.reactions:  # type: ignore
             if not reaction.functional:
                 reaction.bounds = (0, 0)
 
+    @property
+    def reactions(self) -> FrozenSet["Reaction"]:
+        """Return a frozenset of reactions.
+
+        If the gene is present in a model, calculates this set by querying
+        the model reactions for this gene.
+        If not, returns the _reaction field, see cobra.Species.
+
+        Returns
+        -------
+        FrozenSet
+            A frozenset that includes the reactions of the gene.
+        """
+        if self.model:
+            return frozenset(self.model.reactions.query(lambda x: self in x, "genes"))
+        else:
+            return frozenset(self._reaction)
+
     def _repr_html_(self):
         return f"""
         <table>

src/cobra/core/metabolite.py

@@ -1,7 +1,7 @@
 """Define the Metabolite class."""
 
 import re
-from typing import TYPE_CHECKING, Dict, Optional, Union
+from typing import TYPE_CHECKING, Dict, FrozenSet, Optional, Union
 from warnings import warn
 
 from ..exceptions import OptimizationError
@@ -15,7 +15,7 @@
     from optlang.interface import Container
     from pandas import DataFrame
 
-    from cobra.core import Solution
+    from cobra.core import Reaction, Solution
     from cobra.summary.metabolite_summary import MetaboliteSummary
 
 # Numbers are not required because of the |(?=[A-Z])? block. See the
@@ -276,6 +276,26 @@ def remove_from_model(self, destructive: bool = False) -> None:
         """
         self._model.remove_metabolites(self, destructive)
 
+    @property
+    def reactions(self) -> FrozenSet["Reaction"]:
+        """Return a frozenset of reactions.
+
+        If the metabolite is present in a model, calculates this set by querying
+        the model reactions for this metabolite.
+        If not, returns the _reaction field, see cobra.Species.
+
+        Returns
+        -------
+        FrozenSet
+            A frozenset that includes the reactions of the metabolite.
+        """
+        if self.model:
+            return frozenset(
+                self.model.reactions.query(lambda x: self in x, "metabolites")
+            )
+        else:
+            return frozenset(self._reaction)
+
     def summary(
         self,
         solution: Optional["Solution"] = None,

src/cobra/core/model.py

@@ -723,34 +723,24 @@ def existing_filter(rxn: Reaction) -> bool:
             return True
 
         # First check whether the reactions exist in the model. Copy reactions that
-        # belong to another model, in order not to remove them (see
-        # https://github.com/opencobra/cobrapy/issues/673#issuecomment-371361476).
-        exist_but_different_stoich = set()
+        # belong to another model, in order not to remove them from the original model.
+        exist_but_different = set()
         other_model = ""
         for reaction in filter(lambda x: not existing_filter(x), reaction_list):
-            met_id_dict = {
-                met.id: stoich for met, stoich in reaction.metabolites.items()
-            }
-            existing_met_id_dict = {
-                met.id: stoich
-                for met, stoich in self.reactions.get_by_id(
-                    reaction.id
-                ).metabolites.items()
-            }
-            if met_id_dict != existing_met_id_dict:
-                exist_but_different_stoich.add(reaction.id)
-                other_model = reaction.model
-        if len(exist_but_different_stoich):
+            if reaction != self.reactions.get_by_id(reaction.id):
+                exist_but_different.add(reaction.id)
+                other_model = other_model or reaction.model
+        if len(exist_but_different):
             logger.warning(
-                f"The reactions {', '.join(exist_but_different_stoich)} exist"
+                f"The reactions {', '.join(exist_but_different)} exist"
                 f" in both {self} and {other_model}, but have different "
-                f"stoichiometries in the two mdoels. Please check to see "
-                f"which stoichiometry you'd like to add."
+                f"properties in the two mdoels. Please check to see "
+                f"which properties are the correct ones you'd like to add."
             )
         pruned = DictList(
             [
                 reaction
-                if not reaction._model or reaction._model == self
+                if not reaction.model or reaction.model == self
                 else reaction.copy()
                 for reaction in filter(existing_filter, reaction_list)
             ]
@@ -763,20 +753,15 @@ def existing_filter(rxn: Reaction) -> bool:
             reaction._model = self
             if context:
                 context(partial(setattr, reaction, "_model", None))
-            met_id_dict = {
-                met.id: stoich for met, stoich in reaction.metabolites.items()
-            }
-            met_dict = {met.id: met for met in reaction.metabolites.keys()}
             mets_to_add = [
-                met_dict[met_id]
-                for met_id in set(met_id_dict.keys()).difference(
-                    self.metabolites.list_attr("id")
-                )
+                met
+                for met in reaction.metabolites
+                if met.id not in self.metabolites.list_attr("id")
             ]
             self.add_metabolites(mets_to_add)
             new_stoich = {
-                self.metabolites.get_by_id(met_id): stoich
-                for met_id, stoich in met_id_dict.items()
+                self.metabolites.get_by_id(met.id): stoich
+                for met, stoich in reaction.metabolites.items()
             }
             reaction.metabolites = new_stoich
             reaction.update_genes_from_gpr()
@@ -846,15 +831,15 @@ def remove_reactions(
                 self.reactions.remove(reaction)
                 reaction._model = None
 
-                for met in reaction.metabolites:
+                for met in reaction._metabolites:
                     if reaction in met._reaction:
-                        met.reaction_remove(reaction, context)
+                        met.remove_reaction(reaction)
                         if remove_orphans and len(met.reactions) == 0:
                             self.remove_metabolites(met)
 
-                for gene in reaction.genes:
+                for gene in reaction._genes:
                     if reaction in gene._reaction:
-                        gene.reaction_remove(reaction, context)
+                        gene.remove_reaction(reaction)
 
                         if remove_orphans and len(gene.reactions) == 0:
                             self.genes.remove(gene)
@@ -1287,13 +1272,13 @@ def repair(
             self.groups._generate_index()
         if rebuild_relationships:
             for met in self.metabolites:
-                met.reaction_clear()
+                met.clear_reaction()
             for gene in self.genes:
-                gene.reaction_clear()
+                gene.clear_reaction()
             for rxn in self.reactions:
                 rxn.update_genes_from_gpr()
                 for met in rxn.metabolites:
-                    met.reaction_add(rxn)
+                    met.add_reaction(rxn)
 
         # point _model to self
         for dict_list in (self.reactions, self.genes, self.metabolites, self.groups):

src/cobra/core/reaction.py

@@ -1,6 +1,7 @@
 """Define the Reaction class."""
 
 import hashlib
+import math
 import re
 from collections import defaultdict
 from copy import copy, deepcopy
@@ -594,7 +595,7 @@ def metabolites(self, value: Dict[Metabolite, float]) -> None:
         self._metabolites = value
         context = get_context(self)
         for met in value.keys():
-            met.reaction_add(self, context)
+            met.add_reaction(self)
 
     @property
     def genes(self) -> FrozenSet:
@@ -858,9 +859,9 @@ def _update_awareness(self) -> None:
             This function is deprecated and shouldn't be used.
         """
         for x in self._metabolites:
-            x.reaction_add(self)
+            x.add_reaction(self)
         for x in self._genes:
-            x.reaction_add(self)
+            x.add_reaction(self)
 
     def remove_from_model(self, remove_orphans: bool = False) -> None:
         """Remove the reaction from a model.
@@ -951,7 +952,7 @@ def __setstate__(self, state: Dict) -> None:
         self.__dict__.update(state)
         for x in set(state["_metabolites"]).union(state["_genes"]):
             x._model = self._model
-            x.reaction_add(self)
+            x.add_reaction(self)
 
     def copy(self) -> "Reaction":
         """Copy a reaction.
@@ -1001,7 +1002,7 @@ def __add__(self, other: "Reaction") -> "Reaction":
 
         """
         new_reaction = self.copy()
-        if other == 0:
+        if isinstance(other, int) and other == 0:
             return new_reaction
         else:
             new_reaction += other
@@ -1285,7 +1286,7 @@ def add_metabolites(
                 self._metabolites[metabolite] = coefficient
                 # make the metabolite aware that it is involved in this
                 # reaction
-                metabolite.reaction_add(self)
+                metabolite.add_reaction(self)
 
         # from cameo ...
         model = self.model
@@ -1304,7 +1305,7 @@ def add_metabolites(
             if the_coefficient == 0:
                 # make the metabolite aware that it no longer participates
                 # in this reaction
-                metabolite.reaction_remove(self)
+                metabolite.remove_reaction(self)
                 self._metabolites.pop(metabolite)
 
         context = get_context(self)
@@ -1504,7 +1505,7 @@ def _associate_gene(self, cobra_gene: Gene) -> None:
 
         """
         self._genes.add(cobra_gene)
-        cobra_gene.reaction_add(self)
+        cobra_gene.add_reaction(self)
         cobra_gene._model = self._model
 
     def _dissociate_gene(self, cobra_gene: Gene) -> None:
@@ -1516,7 +1517,7 @@ def _dissociate_gene(self, cobra_gene: Gene) -> None:
 
         """
         self._genes.discard(cobra_gene)
-        cobra_gene.reaction_remove(self)
+        cobra_gene.remove_reaction(self)
 
     def knock_out(self) -> None:
         """Knockout reaction by setting its bounds to zero."""
@@ -1673,6 +1674,51 @@ def summary(
             fva=fva,
         )
 
+    def __eq__(self, other) -> bool:
+        self_state = self.__getstate__()
+        self_state["_metabolites"] = {
+            met.id: stoic for met, stoic in self.metabolites.items()
+        }
+        self_state["_genes"] = {gene.id for gene in self.genes}
+        self_state.pop("_model")
+        other_state = other.__getstate__()
+        other_state["_metabolites"] = {
+            met.id: stoic for met, stoic in other.metabolites.items()
+        }
+        other_state["_genes"] = {gene.id for gene in other.genes}
+        other_state.pop("_model")
+
+        self_state.pop("_lower_bound")
+        self_state.pop("_upper_bound")
+        other_state.pop("_lower_bound")
+        other_state.pop("_upper_bound")
+
+        _tolerance = 1e-7
+        if self.model:
+            _tolerance = self.model.tolerance
+        elif other.model:
+            _tolerance = other.model.tolerance
+        elif self.model and other.model:
+            _tolerance = min(self.model.tolerance, other.model.tolerance)
+        if not math.isclose(self.lower_bound, other.lower_bound, abs_tol=_tolerance):
+            return False
+        elif not math.isclose(self.upper_bound, other.upper_bound, abs_tol=_tolerance):
+            return False
+        else:
+            return self_state == other_state
+
+    def __hash__(self) -> int:
+        """Define __hash__ explicitly to allow usage of reaction in sets.
+
+        Python objects that define __eq__ MUST define __hash__ explicitly, or they
+        are unhashable. __hash__ is set to the __hash__ function of cobra.Object.
+
+        Returns
+        -------
+        int
+        """
+        return Object.__hash__(self)
+
     def __str__(self) -> str:
         """Return reaction id and reaction as str.