From 5149cc3558598bff93bdbe422490f75cb943c01a Mon Sep 17 00:00:00 2001
From: Freiburgermsu_Sequoia <freiburgermsu@aol.com>
Date: Fri, 13 Sep 2024 18:55:02 +0000
Subject: [PATCH] CommScores associated edits

---
 modelseedpy/core/__init__.py       | 2 +-
 modelseedpy/core/fbahelper.py      | 2 +-
 modelseedpy/core/msminimalmedia.py | 2 +-
 modelseedpy/core/msmodelutl.py     | 4 +++-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/modelseedpy/core/__init__.py b/modelseedpy/core/__init__.py
index 59f32bf..f566f92 100755
--- a/modelseedpy/core/__init__.py
+++ b/modelseedpy/core/__init__.py
@@ -11,7 +11,7 @@
 from modelseedpy.core.msatpcorrection import MSATPCorrection
 from modelseedpy.core.msgrowthphenotypes import MSGrowthPhenotypes, MSGrowthPhenotype
 from modelseedpy.core.msmodelutl import MSModelUtil
-from modelseedpy.core.msminimalmedia import MSMinimalMedia
+from modelseedpy.core.msminimalmedia import MSMinimalMedia, minimizeFlux_withGrowth, bioFlux_check
 from modelseedpy.core.optlanghelper import OptlangHelper
 from modelseedpy.core.mstemplate import MSTemplateBuilder
 from modelseedpy.core.msmodelreport import MSModelReport
diff --git a/modelseedpy/core/fbahelper.py b/modelseedpy/core/fbahelper.py
index 1bc1009..0872c2c 100755
--- a/modelseedpy/core/fbahelper.py
+++ b/modelseedpy/core/fbahelper.py
@@ -272,7 +272,7 @@ def IDRxnMets(rxn):
             return {met.id: stoich for met, stoich in rxn.items()}
 
     @staticmethod
-    def convert_kbase_media(kbase_media, uniform_uptake=None):
+    def convert_kbase_media(kbase_media, uniform_uptake=1000):
         if uniform_uptake is None:
             return {"EX_"+exID: -bound[0] for exID, bound in kbase_media.get_media_constraints().items()}
         return {"EX_"+exID: uniform_uptake for exID in kbase_media.get_media_constraints().keys()}
diff --git a/modelseedpy/core/msminimalmedia.py b/modelseedpy/core/msminimalmedia.py
index 1d235b2..be4c529 100644
--- a/modelseedpy/core/msminimalmedia.py
+++ b/modelseedpy/core/msminimalmedia.py
@@ -259,7 +259,7 @@ def _examine_permutations(model, exchange_ids_to_explore, variables, sol_dict, s
 
     @staticmethod
     def determine_min_media(model, minimization_method="minFlux", min_growth=None, environment=None,
-                            interacting=True, solution_limit=5, printing=True):
+                            interacting=True, printing=True):
         if minimization_method == "minFlux":
             return MSMinimalMedia.minimize_flux(model, min_growth, environment, interacting, printing)
         if minimization_method == "minComponents":
diff --git a/modelseedpy/core/msmodelutl.py b/modelseedpy/core/msmodelutl.py
index a454461..f0ca161 100644
--- a/modelseedpy/core/msmodelutl.py
+++ b/modelseedpy/core/msmodelutl.py
@@ -142,6 +142,7 @@ def __init__(self, model, copy=False, environment=None):
         self.test_objective = None
         self.reaction_scores = None
         self.score = None
+        # identify the forward biomass reaction
         try:
             objectiveVars = list(self.model.objective.variables)
             for var in objectiveVars:
@@ -1674,9 +1675,10 @@ def add_kbase_media(self, kbase_media):
 
     def add_medium(self, media, uniform_uptake=None):
         # add the new media and its flux constraints
-        if media is None:  return self.model.medium
         exIDs = [exRXN.id for exRXN in self.exchange_list()]
         if not hasattr(media, "items"):  media = FBAHelper.convert_kbase_media(media)
+        elif not any(["EX_" in x for x in list(media.keys())]):
+            media = {"EX_"+k+"_e0":v for k,v in media.items()}
         self.model.medium = {ex: uptake for ex, uptake in media.items() if ex in exIDs}
         if uniform_uptake is not None:  self.model.medium = dict(zip(
             list(self.model.medium.keys()), [uniform_uptake]*len(self.model.medium)))