0.7.19

Author: bgoli

setup.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: setup.py 628 2017-10-20 12:33:26Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: setup.py 632 2017-11-03 16:11:03Z bgoli $)
 
 """
 
@@ -55,7 +55,7 @@
 
 # release
 try:
-    STATUS = 'r'+'$Rev: 628 $'.replace('Rev: ','').replace('$','').strip()
+    STATUS = 'r'+'$Rev: 632 $'.replace('Rev: ','').replace('$','').strip()
 except:
     STATUS = 'beta'
 
@@ -67,8 +67,8 @@
  data_files = mydata_files,
  name = "cbmpy",
  summary = "CBMPy: Constraint Based Modelling in Python",
- #version = "0.7.19.{}".format(STATUS),
- version = "0.7.18",
+ #version = "0.7.20.{}".format(STATUS),
+ version = "0.7.19",
  maintainer = 'Brett G. Olivier',
  author = 'Brett G. Olivier',
  maintainer_email = 'bgoli@users.sourceforge.net',

src/CBCommon.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBCommon.py 629 2017-10-24 22:01:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBCommon.py 630 2017-11-03 16:06:50Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -301,7 +301,7 @@ def func_getAssociationStrFromGprDict(gprd, out, parent=''):
         out = out[1:-1]
     return out
 
-
+# '( llmg_1896  and  llmg_1897  and  llmg_1898  and  llmg_1899  and  llmg_1900  and  llmg_1901 )'
 def getGPRasDictFromString(node, out):
     """
     Converts a GPR string '((g1 and g2) or g3)' to a gprDict which is returned
@@ -322,12 +322,14 @@ def getGPRasDictFromString(node, out):
         left = node.left.id
         right = node.right.id
         gref = '{}-{}'.format(left, right)
-        print('BinOp: {}'.format(gref))
+        #print('BinOp: {}'.format(gref))
     else:
         if isinstance(node, ast.Expr):
             children = [node.value]
+        elif isinstance(node, ast.BoolOp):
+            children = node.values
         else:
-            #children = node.values
+            print('Childless node: ', type(node))
             children = []
         cntr2 = 0
         for v in children:

src/CBConfig.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBConfig.py 629 2017-10-24 22:01:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBConfig.py 631 2017-11-03 16:09:23Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -29,7 +29,6 @@
 ## use with caution: gets rid of module xxx has no member errors (run once enabled)
 # pylint: disable=E1101
 
-
 # preparing for Python 3 port
 from __future__ import division, print_function
 from __future__ import absolute_import
@@ -38,7 +37,7 @@
 # release
 
 try:
-    STATUS = '$Rev: 629 $'.replace('Rev: ', '').replace('$', '').strip()
+    STATUS = '$Rev: 631 $'.replace('Rev: ', '').replace('$', '').strip()
 except Exception:
     STATUS = ''
 

src/CBModel.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBModel.py 629 2017-10-24 22:01:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBModel.py 630 2017-11-03 16:06:50Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -4670,7 +4670,7 @@ def createAssociationAndGeneRefsFromString(self, assoc, altlabels=None):
             try:
                 ast.parse(assoc)
             except SyntaxError:
-                #err = 'Error in Gene Association String: {}'.format(assoc)
+                print('Error in Gene Association String: {}'.format(assoc))
                 old_gids, assoc2 = extractGeneIdsFromString(assoc, return_clean_gpr=True)
 
                 old_gids.sort()
@@ -4695,6 +4695,7 @@ def createAssociationAndGeneRefsFromString(self, assoc, altlabels=None):
                 del assoc2, old_gids, tempids, rep_map
             try:
                 newtree = getGPRasDictFromString(ast.parse(assoc).body[0], {})
+                #print(newtree)
             except SyntaxError:
                 err = '\nError in Gene Association String: {}\n'.format(assoc)
                 #print(err)

src/__init__.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: __init__.py 575 2017-04-13 12:18:44Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: __init__.py 631 2017-11-03 16:09:23Z bgoli $)
 
 """
 #
@@ -124,7 +124,7 @@ def test():
     #print 'pysces.output_dir = ' + output_dir
 
     print('\n\n***********************************************************************')
-    print('* Welcome to CBMPy ({}) - PySCeS Constraint Based Modelling        *'.format(__version__.replace('.{}'.format(rev),'')))
+    print('* Welcome to CBMPy ({}) - PySCeS Constraint Based Modelling       *'.format(__version__.replace('.{}'.format(rev),'')))
     print('*                http://cbmpy.sourceforge.net                         *')
     print('* Copyright(C) Brett G. Olivier 2014 - 2017                           *')
     print('* Dept. of Systems Bioinformatics                                     *')