From 26a417a729b69a9c91806b43e0325f0913210301 Mon Sep 17 00:00:00 2001
From: Andrew Freiburger <freiburgermsu@aol.com>
Date: Wed, 26 Aug 2026 14:49:02 -0500
Subject: [PATCH] Sync modelseedpy/fbapkg/totalfluxpkg.py from freiburgermsu
 fork

File-level sync to the state of this file in
freiburgermsu/ModelSEEDpy@971df5d, submitted as an individual PR so each
module's divergence can be reviewed independently.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017rcBA87xipNeaukuFW8N2G
---
 modelseedpy/fbapkg/totalfluxpkg.py | 81 ++++++++++++++----------------
 1 file changed, 37 insertions(+), 44 deletions(-)

diff --git a/modelseedpy/fbapkg/totalfluxpkg.py b/modelseedpy/fbapkg/totalfluxpkg.py
index b8eb87c8..a85a7cdd 100644
--- a/modelseedpy/fbapkg/totalfluxpkg.py
+++ b/modelseedpy/fbapkg/totalfluxpkg.py
@@ -1,44 +1,37 @@
-# -*- coding: utf-8 -*-
-
-from __future__ import absolute_import
-
-import logging
-import re
-from optlang.symbolics import Zero, add
-import json as _json
-from cobra.core import Gene, Metabolite, Model, Reaction
-from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
-
-# Adding a few exception classes to handle different types of errors
-class FeasibilityError(Exception):
-    """Error in FBA formulation"""
-
-    pass
-
-
-# Base class for FBA packages
-class TotalFluxPkg(BaseFBAPkg):
-    def __init__(self, model):
-        BaseFBAPkg.__init__(
-            self, model, "totalflux", {"tf": "reaction"}, {"tf": "reaction"}
-        )
-
-    def build_package(self, reaction_filter=None, upper_bound=100):
-        for reaction in self.model.reactions:
-            # Checking that variable has not yet been created
-            if reaction.id not in self.variables["tf"]:
-                # Checking that reaction passes input filter if one is provided
-                if reaction_filter == None or reaction.id in reaction_filter:
-                    self.variables["tf"][reaction.id] = self.model.problem.Variable(
-                        reaction.id + "_tf", lb=0, ub=upper_bound
-                    )
-                    self.model.add_cons_vars(self.variables["tf"][reaction.id])
-                    self.constraints["tf"][reaction.id] = self.model.problem.Constraint(
-                        reaction.forward_variable
-                        + reaction.reverse_variable
-                        - self.variables["tf"][reaction.id],
-                        lb=0,
-                        ub=0,
-                        name=reaction.id + "_tf",
-                    )
-                    self.model.add_cons_vars(self.constraints["tf"][reaction.id])
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+
+import logging
+import re
+from optlang.symbolics import Zero, add
+import json as _json
+from cobra.core import Gene, Metabolite, Model, Reaction
+from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
+from modelseedpy.core.exceptions import FeasibilityError
+
+
+# Base class for FBA packages
+class TotalFluxPkg(BaseFBAPkg):
+    def __init__(self, model):
+        BaseFBAPkg.__init__(
+            self, model, "totalflux", {"tf": "reaction"}, {"tf": "reaction"}
+        )
+
+    def build_package(self, reaction_filter=None, upper_bound=100):
+        for reaction in self.model.reactions:
+            # Checking that variable has not yet been created
+            if reaction.id not in self.variables["tf"]:
+                # Checking that reaction passes input filter if one is provided
+                if reaction_filter == None or reaction.id in reaction_filter:
+                    self.variables["tf"][reaction.id] = self.model.problem.Variable(
+                        reaction.id + "_tf", lb=0, ub=upper_bound
+                    )
+                    self.model.add_cons_vars(self.variables["tf"][reaction.id])
+                    self.constraints["tf"][reaction.id] = self.model.problem.Constraint(
+                        reaction.forward_variable + reaction.reverse_variable - self.variables["tf"][reaction.id],
+                        lb=0,
+                        ub=0,
+                        name=reaction.id + "_tf",
+                    )
+                    self.model.add_cons_vars(self.constraints["tf"][reaction.id])