fix: simplify keyword argument passing

cobra/flux_analysis/deletion.py

@@ -94,13 +94,8 @@ def _multi_deletion(model, entity, element_lists, method="fba",
         The number of parallel processes to run. Can speed up the computations
         if the number of knockouts to perform is large. If not passed,
         will be set to the number of CPUs found.
-    **kwargs:
-        delta: float
-            The relative tolerance for ROOM.
-            Default is 0.03.
-        epsilon: float
-            The absolute tolerance for ROOM.
-            Default is 0.001.
+    kwargs :
+        Passed on to underlying simulation functions.
 
     Returns
     -------
@@ -189,7 +184,7 @@ def _element_lists(entities, *ids):
 
 
 def single_reaction_deletion(model, reaction_list=None, method="fba",
-                             solution=None, processes=None):
+                             solution=None, processes=None, **kwargs):
     """
     Knock out each reaction from a given list.
 
@@ -208,6 +203,9 @@ def single_reaction_deletion(model, reaction_list=None, method="fba",
         The number of parallel processes to run. Can speed up the computations
         if the number of knockouts to perform is large. If not passed,
         will be set to the number of CPUs found.
+    kwargs :
+        Keyword arguments are passed on to underlying simulation functions
+        such as ``add_room``.
 
     Returns
     -------
@@ -226,11 +224,11 @@ def single_reaction_deletion(model, reaction_list=None, method="fba",
     return _multi_deletion(
         model, 'reaction',
         element_lists=_element_lists(model.reactions, reaction_list),
-        method=method, solution=solution, processes=processes)
+        method=method, solution=solution, processes=processes, **kwargs)
 
 
 def single_gene_deletion(model, gene_list=None, method="fba", solution=None,
-                         processes=None):
+                         processes=None, **kwargs):
     """
     Knock out each gene from a given list.
 
@@ -249,6 +247,9 @@ def single_gene_deletion(model, gene_list=None, method="fba", solution=None,
         The number of parallel processes to run. Can speed up the computations
         if the number of knockouts to perform is large. If not passed,
         will be set to the number of CPUs found.
+    kwargs :
+        Keyword arguments are passed on to underlying simulation functions
+        such as ``add_room``.
 
     Returns
     -------
@@ -266,11 +267,12 @@ def single_gene_deletion(model, gene_list=None, method="fba", solution=None,
     """
     return _multi_deletion(
         model, 'gene', element_lists=_element_lists(model.genes, gene_list),
-        method=method, solution=solution, processes=processes)
+        method=method, solution=solution, processes=processes, **kwargs)
 
 
 def double_reaction_deletion(model, reaction_list1=None, reaction_list2=None,
-                             method="fba", solution=None, processes=None):
+                             method="fba", solution=None, processes=None,
+                             **kwargs):
     """
     Knock out each reaction pair from the combinations of two given lists.
 
@@ -294,6 +296,9 @@ def double_reaction_deletion(model, reaction_list1=None, reaction_list2=None,
         The number of parallel processes to run. Can speed up the computations
         if the number of knockouts to perform is large. If not passed,
         will be set to the number of CPUs found.
+    kwargs :
+        Keyword arguments are passed on to underlying simulation functions
+        such as ``add_room``.
 
     Returns
     -------
@@ -315,11 +320,11 @@ def double_reaction_deletion(model, reaction_list1=None, reaction_list2=None,
                                                     reaction_list2)
     return _multi_deletion(
         model, 'reaction', element_lists=[reaction_list1, reaction_list2],
-        method=method, solution=solution, processes=processes)
+        method=method, solution=solution, processes=processes, **kwargs)
 
 
-def double_gene_deletion(model, gene_list1=None, gene_list2=None,
-                         method="fba", solution=None, processes=None):
+def double_gene_deletion(model, gene_list1=None, gene_list2=None, method="fba",
+                         solution=None, processes=None, **kwargs):
     """
     Knock out each gene pair from the combination of two given lists.
 
@@ -343,6 +348,9 @@ def double_gene_deletion(model, gene_list1=None, gene_list2=None,
         The number of parallel processes to run. Can speed up the computations
         if the number of knockouts to perform is large. If not passed,
         will be set to the number of CPUs found.
+    kwargs :
+        Keyword arguments are passed on to underlying simulation functions
+        such as ``add_room``.
 
     Returns
     -------
@@ -363,4 +371,4 @@ def double_gene_deletion(model, gene_list1=None, gene_list2=None,
                                             gene_list2)
     return _multi_deletion(
         model, 'gene', element_lists=[gene_list1, gene_list2],
-        method=method, solution=solution, processes=processes)
+        method=method, solution=solution, processes=processes, **kwargs)

cobra/flux_analysis/room.py

@@ -7,8 +7,9 @@
 from optlang.symbolics import Zero, NegativeOne, Add, Mul
 
 
-def add_room(model, solution=None, linear=False, **kwargs):
-    """Add constraints and objective for ROOM.
+def add_room(model, solution=None, linear=False, delta=0.03, epsilon=1E-03):
+    """
+    Add constraints and objective for ROOM.
 
     This function adds variables and constraints for applying regulatory
     on/off minimization (ROOM) to the model.
@@ -22,13 +23,12 @@ def add_room(model, solution=None, linear=False, **kwargs):
     linear : bool
         Whether to use the linear ROOM formulation or not.
         Default is False.
-    **kwargs:
-        delta: float
-            Relative range of tolerance; is additive in nature.
-            Default is 0.03.
-        epsilon: float
-            Absolute range of tolerance; is multiplicative in nature.
-            Default is 0.001.
+    delta: float
+        The relative tolerance range which is additive in nature
+        (default 0.03).
+    epsilon: float
+        The absolute range of tolerance which is multiplicative
+        (default 0.001).
 
     Notes
     -----
@@ -58,13 +58,6 @@ def add_room(model, solution=None, linear=False, **kwargs):
 
     """
 
-    if kwargs:
-        delta = float(kwargs['delta'])
-        epsilon = float(kwargs['epsilon'])
-    else:
-        delta = 0.03
-        epsilon = 0.001
-
     if 'room_old_objective' in model.solver.variables:
         raise ValueError('model is already adjusted for ROOM')
 
@@ -87,11 +80,11 @@ def add_room(model, solution=None, linear=False, **kwargs):
     for rxn in model.reactions:
         flux = solution.fluxes[rxn.id]
 
-        if linear is False:
-            y = problem.Variable("y_" + rxn.id, type="binary")
-        else:
+        if linear:
             y = problem.Variable("y_" + rxn.id, lb=0, ub=1)
             delta = epsilon = Zero
+        else:
+            y = problem.Variable("y_" + rxn.id, type="binary")
 
         # upper constraint
         w_u = flux + (delta * abs(flux)) + epsilon

cobra/test/test_flux_analysis.py

@@ -380,7 +380,7 @@ def test_room_sanity(self, solver):
             room_ref_sol = model.optimize()
             room_ref_ssq = (room_ref_sol.fluxes - sol.fluxes).pow(2).sum()
 
-        assert room_ssq == ssq
+        assert numpy.isclose(room_ssq, ssq, atol=1E-06)
         assert room_ssq > room_ref_ssq
 
     @pytest.mark.parametrize("solver", optlang_solvers)