release 0.7.4

src/CBConfig.py

@@ -19,10 +19,10 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBConfig.py 432 2016-04-15 13:38:26Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBConfig.py 445 2016-04-18 21:44:38Z bgoli $)
 
 """
-## gets rid of "invalid variable name" info #
+## gets rid of "invalid variable name" info 
 # pylint: disable=C0103
 ## gets rid of "line to long" info
 # pylint: disable=C0301
@@ -38,7 +38,7 @@
 # release
 
 try:
-    STATUS = '$Rev: 432 $'.replace('Rev: ', '').replace('$', '').strip()
+    STATUS = '$Rev: 445 $'.replace('Rev: ', '').replace('$', '').strip()
 except Exception:
     STATUS = ''
 

src/CBVersion.py

@@ -1,4 +1,3 @@
-<<<<<<< .mine
 """
 CBMPy: CBVersion module
 =======================
@@ -20,10 +19,10 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBVersion.py 432 2016-04-15 13:38:26Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBVersion.py 445 2016-04-18 21:44:38Z bgoli $)
 
 """
-# bump 1
+# bump 2
 # preparing for Python 3 port
 from __future__ import division, print_function
 from __future__ import absolute_import
@@ -33,7 +32,7 @@
 MINOR = 7
 MICRO = 4
 try:
-    STATUS = '$Rev: 432 $'.replace('Rev: ','').replace('$','').strip()
+    STATUS = '$Rev: 445 $'.replace('Rev: ','').replace('$','').strip()
 except:
     STATUS = ''
 
@@ -46,100 +45,3 @@ def current_version_tuple():
 __version__ = current_version()
 __DEBUG__ = True
 __DEBUG__ = False
-||||||| .r428
-"""
-CBMPy: CBVersion module
-=======================
-PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2015 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>
-
-Author: Brett G. Olivier
-Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBVersion.py 432 2016-04-15 13:38:26Z bgoli $)
-
-"""
-# bump
-# preparing for Python 3 port
-from __future__ import division, print_function
-from __future__ import absolute_import
-#from __future__ import unicode_literals
-
-MAJOR = 0
-MINOR = 7
-MICRO = 4
-try:
-    STATUS = '$Rev: 432 $'.replace('Rev: ','').replace('$','').strip()
-except:
-    STATUS = ''
-
-def current_version():
-    return '%s.%s.%s.r%s' % (MAJOR, MINOR, MICRO, STATUS)
-
-def current_version_tuple():
-    return (MAJOR, MINOR, MICRO)
-
-__version__ = current_version()
-__DEBUG__ = True
-__DEBUG__ = False
-=======
-"""
-CBMPy: CBVersion module
-=======================
-PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2015 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>
-
-Author: Brett G. Olivier
-Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBVersion.py 432 2016-04-15 13:38:26Z bgoli $)
-
-"""
-# bump 1
-# preparing for Python 3 port
-from __future__ import division, print_function
-from __future__ import absolute_import
-#from __future__ import unicode_literals
-
-MAJOR = 0
-MINOR = 7
-MICRO = 4
-try:
-    STATUS = '$Rev: 432 $'.replace('Rev: ','').replace('$','').strip()
-except:
-    STATUS = ''
-
-def current_version():
-    return '%s.%s.%s.r%s' % (MAJOR, MINOR, MICRO, STATUS)
-
-def current_version_tuple():
-    return (MAJOR, MINOR, MICRO)
-
-__version__ = current_version()
-__DEBUG__ = True
-__DEBUG__ = False
->>>>>>> .r442

src/CBXML.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBXML.py 435 2016-04-15 14:37:38Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBXML.py 443 2016-04-18 21:28:42Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -2404,6 +2404,7 @@ def sbml_readCOBRASBML(fname, work_dir=None, return_sbml_model=False, delete_int
     """
     try:
         new_file = sbml_convertCOBRASBMLtoFBC(fname, outname=None, work_dir=work_dir, output_dir=output_dir)
+        print(new_file)
     except Exception as why:
         print('\nCOBRA file conversion failed:\n\"{}\"'.format(why))
         return None

src/__init__.py

@@ -19,10 +19,10 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: __init__.py 432 2016-04-15 13:38:26Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: __init__.py 445 2016-04-18 21:44:38Z bgoli $)
 
 """
-###
+##
 # preparing for Python 3 port
 from __future__ import division, print_function
 from __future__ import absolute_import

src/nosetests/test_loadSBML.py

@@ -3,7 +3,10 @@
 MDIR = os.path.join(os.path.split(cDir)[0], 'models')
 MDIR = cDir
 
-import nose
+try:
+    import nose
+except ImportError:
+    print('WARNING: To run tests please install python-nose')
 from nose.tools import assert_equal
 from nose.tools import assert_almost_equal
 from nose.tools import assert_not_equal
@@ -48,8 +51,7 @@ def test_load_L2FBA_iJR904(self):
         assert_not_equal(cmod, None)
 
     def test_load_L2CBR_iJR904(self):
-        print('\n\nThis test fails under Linux.\n\n')
-        cmod = cbmpy.readCOBRASBML(os.path.join(MDIR, 'L2CBR_iJR904.glc.xml'), work_dir=self.CDIR,\
+        cmod = cbmpy.readCOBRASBML('L2CBR_iJR904.glc.xml', work_dir=MDIR,\
                                                 output_dir=self.CDIR, delete_intermediate=False)
         assert_not_equal(cmod, None)
 
@@ -61,8 +63,8 @@ def setup_class(klass):
         klass.m = {}
         for m in DATA:
             if m.startswith('L2CBR_'):
-                cmod = cbmpy.readCOBRASBML(os.path.join(MDIR, m), work_dir=self.CDIR,\
-                                           output_dir=self.CDIR, delete_intermediate=False)
+                cmod = cbmpy.readCOBRASBML(m, work_dir=MDIR,\
+                                           output_dir=self.CDIR, delete_intermediate=True)
             elif m.startswith('L2FBA_'):
                 cmod = cbmpy.readSBML2FBA(os.path.join(MDIR, m))
             elif m.startswith('L3FBCV1_') or m.startswith('L3FBCV2_'):
@@ -84,9 +86,9 @@ def test_load(self):
 
     def test_run_fba_cobra(self):
         print('\n\nThis test fails under Linux.\n\n')
-        cmod = cbmpy.readCOBRASBML(os.path.join(MDIR, 'L2CBR_iJR904.glc.xml'), work_dir=self.CDIR,\
-                                                        output_dir=self.CDIR, delete_intermediate=False)
-        cmod2 = cbmpy.readSBML3FBC(os.path.join(MDIR, 'L3FBCV1_iJR904.glc.xml'))
+        cmod = cbmpy.readCOBRASBML('L2CBR_iJR904.glc.xml', work_dir=MDIR,\
+                                                        output_dir=self.CDIR, delete_intermediate=True)
+        cmod2 = cbmpy.readSBML3FBC('L3FBCV1_iJR904.glc.xml', work_dir=MDIR)
         fba1 = cbmpy.doFBA(cmod)
         fba2 = cbmpy.doFBA(cmod2)
         del cmod, cmod2