use pyasp-1.3.3

update version to 1.2.2

CHANGES.txt

@@ -1,3 +1,7 @@
+1.2.2
+----------
+use pyasp-1.3.3
+
 1.2.1
 ----------
 use pyasp-1.3.1

README

@@ -17,16 +17,16 @@ For more options you can ask for help as follows::
 
 	$ precursor.py --help
 	usage: precursor.py [-h] [--autoseeds] net inputs
-
+  
 	positional arguments:
 	  net          metabolic network in SBML format
 	  inputs       targets in XML format
-
+  
 	optional arguments:
 	  -h, --help   show this help message and exit
 	  --autoseeds  compute possible seed metabolites
 
-	  
+
 Samples
 =======
 

setup.py

@@ -33,7 +33,7 @@ def run(self):
 
 setup(cmdclass={'install': install},
       name='precursor',
-      version='1.2.1',
+      version='1.2.2',
       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 @@ def run(self):
       package_data = {'__precursor__' : ['encodings/*.lp']},
       scripts = ['precursor.py'],
       install_requires=[
-        "pyasp == 1.3.1"
+        "pyasp == 1.3.3"
       ]
 )

src/query.py

@@ -99,7 +99,7 @@ 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='0 --heu=domain --enum-mode=record')
+    solver = GringoClasp(clasp_options='0 --dom-mod=6 --heu=Domain --enum-mode=record')
     solutions = solver.run(prg,collapseTerms=True,collapseAtoms=False)
     os.unlink(net_f)
     os.unlink(pseed_f)

src/utils.py

@@ -27,7 +27,9 @@ def clean_up() :
 
 
 def print_seeds(precursor) :
-  for p in precursor: print str(p.arg(0)),
+  for p in precursor:
+    if p.pred()=="new_seed" :
+       print str(p.arg(0)),
   print " "