use pyasp-1.3.1

CHANGES.txt

+1.2.1
+----------
+use pyasp-1.3.1
 1.2
 ----------
 use pyasp-1.3

setup.py

@@ -33,7 +33,7 @@ class install(_install):
                          
 setup(cmdclass={'install': install},
       name='precursor',
-      version='1.2',
+      version='1.2.1',
       url='http://pypi.python.org/pypi/precursor/',
       license='GPLv3+',
       description='Compute minimal metabolic precursors sets that enable the production of target metabolites.',
@@ -45,6 +45,6 @@ setup(cmdclass={'install': install},
       package_data = {'__precursor__' : ['encodings/*.lp']},
       scripts = ['precursor.py'],
       install_requires=[
-        "pyasp == 1.3"
+        "pyasp == 1.3.1"
       ]
 )
\ No newline at end of file

src/query.py

@@ -36,7 +36,7 @@ def satcheck(net, pseeds, targets):
     target_f = targets.to_file()
     prg = [satcheck_prg, net_f, pseed_f, target_f ]
     solver = GringoClasp()
-    models = solver.run(prg,nmodels=1,collapseTerms=True,collapseAtoms=False)
+    models = solver.run(prg,collapseTerms=True,collapseAtoms=False)
     os.unlink(net_f)
     os.unlink(pseed_f)
     os.unlink(target_f)
@@ -50,7 +50,7 @@ def get_card_minimal_precursor_sets(net, pseeds, targets):
     prg = [card_min_precursor_prg, net_f, pseed_f, target_f ]
     coptions = '--project --opt-mode=optN'
     solver = GringoClasp(clasp_options=coptions)
-    models = solver.run(prg,nmodels=0,collapseTerms=True,collapseAtoms=False)
+    models = solver.run(prg,collapseTerms=True,collapseAtoms=False)
     os.unlink(net_f)
     os.unlink(pseed_f)
     os.unlink(target_f)
@@ -88,7 +88,7 @@ def get_automatic_pseeds(net, targets):
     target_f = targets.to_file()
     prg = [automatic_pseeds_prg, net_f, target_f ]
     solver = GringoClasp()
-    models = solver.run(prg,nmodels=10,collapseTerms=True,collapseAtoms=False)
+    models = solver.run(prg,collapseTerms=True,collapseAtoms=False)
     os.unlink(net_f)
     os.unlink(target_f)
     return models[0]
@@ -99,8 +99,8 @@ def get_subset_min_precursor_sets(net, pseeds, targets):
     pseed_f = pseeds.to_file('pseed.lp')
     target_f = targets.to_file('targets.lp')
     prg = [precursor_prg, heu_prg, net_f, pseed_f, target_f ]
-    solver = GringoHClasp(clasp_options='--heu=domain --enum-mode=record')
-    solutions = solver.run(prg,nmodels=0,collapseTerms=True,collapseAtoms=False)
+    solver = GringoHClasp(clasp_options='0 --heu=domain --enum-mode=record')
+    solutions = solver.run(prg,collapseTerms=True,collapseAtoms=False)
     os.unlink(net_f)
     os.unlink(pseed_f)
     os.unlink(target_f)