fix sympy parsing problem

conda-recipe/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = '0.0.8' %}
+{% set version = '0.0.9' %}
 
 package:
   name: optlang_enumerator
@@ -19,6 +19,7 @@ requirements:
     - optlang
     - cobra
     - efmtool_link
+    - sympy>=1.12
 
 
 build:

optlang_enumerator/mcs_computation.py

@@ -155,14 +155,14 @@ def parse_relation(lhs : str, rhs : float, reac_id_symbols=None):
         denominator = lhs[slash+1:]
         numerator = lhs[0:slash]
         denominator = parse_expr(denominator, transformations=transformations, evaluate=False, local_dict=reac_id_symbols)
-        denominator = sympy.collect(denominator, denominator.free_symbols)
+        denominator = sympy.collect(sympy.expand(denominator), denominator.free_symbols)
         numerator = parse_expr(numerator, transformations=transformations, evaluate=False, local_dict=reac_id_symbols)
-        numerator = sympy.collect(numerator, numerator.free_symbols)
+        numerator = sympy.collect(sympy.expand(numerator), numerator.free_symbols)
         lhs = numerator - rhs*denominator
         rhs = 0
     else:
         lhs = parse_expr(lhs, transformations=transformations, evaluate=False, local_dict=reac_id_symbols)
-    lhs = sympy.collect(lhs, lhs.free_symbols, evaluate=False)
+    lhs = sympy.collect(sympy.expand(lhs), lhs.free_symbols, evaluate=False)
 
     return lhs, rhs
 

setup.py

@@ -1,12 +1,12 @@
 from setuptools import setup
 
 setup(name='optlang_enumerator',
-    version='0.0.8',
+    version='0.0.9',
     description='Enumeration of multiple solutions to a MILP with optlang.',
     url='https://github.com/cnapy-org/optlang_enumerator.git',
     author='Axel von Kamp',
     author_email='[email protected]',
     license='Apache License 2.0',
     packages=['optlang_enumerator'],
-    install_requires=['numpy<1.24', 'scipy', 'cobra', 'optlang', 'efmtool_link', 'sympy', 'swiglpk'],
+    install_requires=['numpy<1.24', 'scipy', 'cobra', 'optlang', 'efmtool_link', 'sympy>=1.12', 'swiglpk'],
     zip_safe=False)