MSCompatibility scrubbing to CommScores

modelseedpy/__init__.py

@@ -40,7 +40,7 @@
 from modelseedpy.core.exceptions import *
 
 from modelseedpy.community import (
-    MSCommunity, CommunityMember, MSCompatibility, MSKineticsFBA, CommScores, CommPhitting,
+    MSCommunity, CommunityMember, MSKineticsFBA, CommScores, CommPhitting,
     MSSteadyCom, build_from_species_models, phenotypes)
 
 from modelseedpy.biochem import ModelSEEDBiochem

modelseedpy/community/__init__.py

@@ -9,7 +9,6 @@
 from modelseedpy.community.datastandardization import *
 from modelseedpy.community.mssteadycom import MSSteadyCom
 from modelseedpy.community.commphitting import CommPhitting
-from modelseedpy.community.mscompatibility import MSCompatibility
 from modelseedpy.community.commhelper import build_from_species_models, phenotypes
 from modelseedpy.community.mskineticsfba import MSKineticsFBA
 

modelseedpy/community/commhelper.py

@@ -1,10 +1,10 @@
 from modelseedpy.core.msminimalmedia import minimizeFlux_withGrowth, bioFlux_check
 from modelseedpy.core.exceptions import NoFluxError, ObjectiveError
-from modelseedpy.community.mscompatibility import MSCompatibility
 from modelseedpy.core.msmodelutl import MSModelUtil
 from modelseedpy.core.fbahelper import FBAHelper
 from cobra import Model, Reaction, Metabolite
 from cobra.medium import minimal_medium
+from commscores import GEMCompatibility
 from cobra.flux_analysis import pfba
 from collections import OrderedDict
 from optlang.symbolics import Zero
@@ -55,7 +55,7 @@ def build_from_species_models(org_models, model_id=None, name=None, abundances=N
     ------
     """
     # construct the new model
-    models = org_models if not standardize else MSCompatibility.standardize(
+    models = org_models if not standardize else GEMCompatibility.standardize(
         org_models, exchanges=True, conflicts_file_name='exchanges_conflicts.json')
     biomass_indices = []
     biomass_index = minimal_biomass_index = 2