Py3 fixes and update to r666

Author: bgoli

src/CBModel.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBModel.py 661 2018-09-24 15:20:05Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBModel.py 665 2018-11-07 14:27:31Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -1150,13 +1150,13 @@ def addReaction(self, reaction, create_default_bounds=False, silent=False):
                 if not silent:
                     print('\nReaction \"{}\" bounds set to: 0 <= {} <= INF'.format(rid, rid))
 
-    def addUserConstraint(self, pid, fluxes=None, operator='=', rhs=0.0):
+    def addUserConstraint(self, pid, fluxes=None, operator='>=', rhs=0.0):
         """
         Add a user defined constraint to FBA model, this is additional to the automatically determined Stoichiometric constraints.
 
          - *pid* user constraint name/id, use `None` for auto-assign
          - *fluxes* a list of (coefficient, reaction id) pairs where coefficient is a float
-         - *operator* is one of = > < >= <=
+         - *operator* is one of '=', '>=' or '<=' (< and > will be interpreted as >= or <=)
          - *rhs* a float
 
         """

src/CBMultiCore.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBMultiCore.py 660 2018-09-24 14:57:04Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBMultiCore.py 666 2018-11-21 22:02:35Z bgoli $)
 
 """
 
@@ -52,9 +52,16 @@
 
 from .CBConfig import __CBCONFIG__ as __CBCONFIG__
 
-def grouper(n, iterable, padvalue=None):
-    "grouper(3, 'abcdefg', 'x') --> ('a','b','c'), ('d','e','f'), ('g','x','x')"
-    return itertools.izip_longest(*[iter(iterable)]*n, fillvalue=padvalue)
+# this is to deal with itertools 2/3 differences
+try:
+    itertools.__getattribute__('izip_longest')
+    def grouper(n, iterable, padvalue=None):
+        "grouper(3, 'abcdefg', 'x') --> ('a','b','c'), ('d','e','f'), ('g','x','x')"
+        return itertools.izip_longest(*[iter(iterable)]*n, fillvalue=padvalue)
+except AttributeError:
+    def grouper(n, iterable, padvalue=None):
+        "grouper(3, 'abcdefg', 'x') --> ('a','b','c'), ('d','e','f'), ('g','x','x')"
+        return itertools.zip_longest(*[iter(iterable)]*n, fillvalue=padvalue)
 
 def runMultiCoreFVA(fba, selected_reactions=None, pre_opt=True, tol=None, objF2constr=True, rhs_sense='lower',\
                     optPercentage=100.0, work_dir=None, quiet=True, debug=False, oldlpgen=False, markupmodel=True, procs=2):
@@ -73,7 +80,7 @@ def runMultiCoreFVA(fba, selected_reactions=None, pre_opt=True, tol=None, objF2c
     fba.serializeToDisk(fN, protocol=-1)
     fN = os.path.abspath(fN)
     subprocess.call(['python', MULTIFVAFILE, str(procs), fN])
-    F = file(fN, 'rb')
+    F = open(fN, 'rb')
     res = pickle.load(F)
     F.close()
     os.remove(fN)
@@ -115,11 +122,11 @@ def runMultiCoreFVA(fba, selected_reactions=None, pre_opt=True, tol=None, objF2c
         #MEargs = [fN+'.lp', selected_reactions, tol, rhs_sense, optPercentage, work_dir, debug]
         #print(MEargs)
         #print(fN)
-        #F = file(fN, 'wb')
+        #F = open(fN, 'wb')
         #pickle.dump(MEargs, F, protocol=-1)
         #F.close()
         #subprocess.call(['python', MULTIENVFVAFILE, str(procs), fN])
-        #F = file(fN, 'rb')
+        #F = open(fN, 'rb')
         #res = pickle.load(F)
         #F.close()
         #os.remove(fN)

src/_multicorefva.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: _multicorefva.py 660 2018-09-24 14:57:04Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: _multicorefva.py 666 2018-11-21 22:02:35Z bgoli $)
 
 """
 
@@ -86,14 +86,14 @@ def multiCoreFVA(fvamod, procs=2, timeout=None):
     print(os.sys.argv)
 
     cores = int(os.sys.argv[1])
-    F = file(os.sys.argv[2],'rb')
+    F = open(os.sys.argv[2],'rb')
     cmod = pickle.load(F)
     F.close()
 
     cbmpy.CBSolver.analyzeModel(cmod, oldlpgen=False)
     res = multiCoreFVA(cmod, procs=cores)
 
-    F = file(os.sys.argv[2], 'wb')
+    F = open(os.sys.argv[2], 'wb')
     pickle.dump(res, F, protocol=-1)
     F.flush()
     F.close()