updated for release 0.7.21

Author: bgoli

README.md

@@ -2,7 +2,7 @@ CBMPy
 =====
 
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2010-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2010-2018 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
@@ -204,4 +204,4 @@ sudo apt-get install python-sip python-sip-dev build-essential
 
 More information in the docs/ directory.
 
-(c) Brett G. Olivier, Amsterdam, 2014-2017
+(c) Brett G. Olivier, Amsterdam, 2014-2018

README.txt

@@ -2,7 +2,7 @@ CBMPy
 =====
 
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2010-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2010-2018 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
@@ -26,9 +26,9 @@ Installation
 
 PySCeS CBMPy (http://cbmpy.sourceforge.net) is a new platform for constraint
 based modelling and analysis. It has been designed using principles developed
-in the PySCeS simulation software project: usability, flexibility and accessibility. 
-Its architecture is both extensible and flexible using data structures that are intuitive 
-to  the biologist (metabolites, reactions, compartments) while transparently translating 
+in the PySCeS simulation software project: usability, flexibility and accessibility.
+Its architecture is both extensible and flexible using data structures that are intuitive
+to  the biologist (metabolites, reactions, compartments) while transparently translating
 these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).
 
 PySCeS CBMPy implements popular analyses such as FBA, FVA, element/charge
@@ -43,7 +43,7 @@ needs PySCeS CBMPy supports user interaction via:
 
 For more information on the development and use of PySCeS CBMPy feel free to contact me:
 
-PySCeS-CBMPy has been tested on Windows 7 and 8.1, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04. 
+PySCeS-CBMPy has been tested on Windows 7 and 8.1, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04.
 It is compatible with both Python 2.7+ and includes experimental support for Python 3.4+ It is highly recommend to use
 Python 2.7 as not all Python package dependencies (extended functionality) are available for Python 3.
 
@@ -64,7 +64,7 @@ CBMPy is now available as a crosss platform Anaconda package available for Win32
 major release using the conda platform and all feedback is welcomed. If you have Anaconda installed (tested with 4.2.0) simply try the following::
 
  conda install -c bgoli -c SBMLTeam cbmpy
- 
+
 which should install CBMPy, libSBML and all the required (non-solver) dependencies. If you do not use Anaconda or would
 like to try install things in a semi-automated way carry on reading.
 
@@ -76,25 +76,25 @@ please see the online documentation http://cbmpy.sourceforge.net/reference/insta
 Auto-dependency configuration
 -----------------------------
 
-I am in the process of creating automated dependency checking and building tools for CBMPy. 
+I am in the process of creating automated dependency checking and building tools for CBMPy.
 
 Ubuntu support is complete with cross platform conda support now available for testing (https://github.com/bgoli/cbmpy-build.git)::
 
 To start with download the install script that will run the system test::
 
- curl --remote-name https://raw.githubusercontent.com/bgoli/cbmpy-build/master/ubuntu/1_install_cbmpy_dependencies.py 
+ curl --remote-name https://raw.githubusercontent.com/bgoli/cbmpy-build/master/ubuntu/1_install_cbmpy_dependencies.py
 
 This script will analyse your Python distribution for missing dependencies and generate a shell script that will auto-install them.
 
 For an installation using the native Python supplied with Ubuntu run::
 
  python 1_install_cbmpy_dependencies.py UBUNTU
- 
+
 For a local user installation of Anaconda try the following. This is not strictly necessary if only CBMPy is going to be installed (see above)::
 
  python 1_install_cbmpy_dependencies.py CONDA
 
-in both cases a shell script `metatoolkit_install_dependencies.sh` is generated and printed to the screen. Run this script 
+in both cases a shell script `metatoolkit_install_dependencies.sh` is generated and printed to the screen. Run this script
 or install the relevant packages by hand.
 
 Installing or upgrading CBMPy

setup.py

@@ -2,7 +2,7 @@
 CBMPy: setup.py
 ===============
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2010-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2010-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: setup.py 646 2018-05-02 13:55:59Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: setup.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 
@@ -44,7 +44,7 @@
 
 # release
 try:
-    STATUS = 'r'+'$Rev: 646 $'.replace('Rev: ','').replace('$','').strip()
+    STATUS = 'r'+'$Rev: 660 $'.replace('Rev: ','').replace('$','').strip()
 except:
     STATUS = 'beta'
 
@@ -56,8 +56,8 @@
  data_files = mydata_files,
  name = "cbmpy",
  summary = "CBMPy: Constraint Based Modelling in Python",
- version = "0.7.20.{}".format(STATUS),
- #version = "0.7.20",
+ #version = "0.7.22.{}".format(STATUS),
+ version = "0.7.21",
  maintainer = 'Brett G. Olivier',
  author = 'Brett G. Olivier',
  author_email = '[email protected]',

setupegg.py

@@ -1,7 +1,7 @@
 """
 CBMPy: Constraint Based Modelling in Python (http://pysces.sourceforge.net/cbm)
 ============
-Copyright (C) 2010-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2010-2018 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
@@ -18,7 +18,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: setupegg.py 574 2017-04-13 12:18:15Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: setupegg.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 

src/CBCPLEX.py

@@ -2,7 +2,7 @@
 CBMPy: CBCPLEX module
 =====================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBCPLEX.py 629 2017-10-24 22:01:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBCPLEX.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -837,8 +837,11 @@ def cplx_getSolutionStatus(c):
     """
     # solution.get_status() returns an integer code
     if c.solution.get_solution_type() == c.solution.type.none:
-        print("\nNo solution available\n")
+        print("No solution available (status={}) type: {}".format(c.solution.get_status_string(), c.solution.get_solution_type()))
         return 'LPS_NONE'
+    else:
+        print("Solution available (status={}) type: {}".format(c.solution.get_status_string(), c.solution.get_solution_type()))
+
     status = c.solution.get_status()
     if status == c.solution.status.optimal:
         if not CPLX_SILENT_MODE:
@@ -859,13 +862,14 @@ def cplx_getSolutionStatus(c):
     elif status == c.solution.status.MIP_optimal:
         print('MILP optimal')
         return 'MILP_OPT'
-    elif status == c.solution.status.MIP_optimal:
-        print('MILP optimal')
-        return 'MILP_OPT'
+    #elif status == c.solution.status.MIP_optimal:
+        #print('MILP optimal')
+        #return 'MILP_OPT'
     elif status == c.solution.status.optimal_tolerance:
         print('MILP optimal within gap tolerance')
         return 'MILP_OPTTOL'
     else:
+        print('Unknown solution status ({}): \"{}\"'.format(c.solution.get_status(), c.solution.get_status_string()))
         return 'LPS_NONE'
 
 def cplx_setObjective(c, pid, expr=None, sense='maximize', reset=True):
@@ -1100,10 +1104,12 @@ def cplx_func_GetCPXandPresolve(fba, pre_opt, objF2constr, quiet=False, oldlpgen
     Returns: pre_sol, pre_oid, pre_oval, OPTIMAL_PRESOLUTION, REDUCED_COSTS
 
     """
+    # debug write out lp file
+    fname = None
     if oldlpgen:
         cpx = cplx_getModelFromObj(fba)
     else:
-        cpx = cplx_constructLPfromFBA(fba, fname=None)
+        cpx = cplx_constructLPfromFBA(fba, fname=fname)
     if quiet:
         cplx_setOutputStreams(cpx, mode=None)
     OPTIMAL_PRESOLUTION = None
@@ -1353,7 +1359,11 @@ def cplx_MinimizeSumOfAbsFluxes(fba, selected_reactions=None, pre_opt=True, tol=
         cplx_writeLPtoLPTfile(cpx, 'MSAF_base_(%s)' % time.time(), title=None, Dir=debug_dir)
         ##  cplx_writeLPtoLPTfile(cpx, 'MSAF_base_%s' % time.time() , title=None, Dir=debug_dir)
 
+    # debug write out lp file
+    #cpx.write('debug_minabssum_{}.lp'.format(str(time.time()).split('.')[0]), filetype='lp')
+
     cplx_Solve(cpx, method=method)
+
     cplx_setFBAsolutionToModel(fba, cpx, with_reduced_costs=with_reduced_costs)
     cplx_setSolutionStatusToModel(fba, cpx)
 

src/CBCommon.py

@@ -2,7 +2,7 @@
 CBMPy: CBCommon module
 ======================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBCommon.py 644 2018-03-14 21:40:47Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBCommon.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info

src/CBConfig.py

@@ -2,7 +2,7 @@
 CBMPy: CBConfig module
 ======================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBConfig.py 637 2017-12-15 11:34:59Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBConfig.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -37,13 +37,13 @@
 # release
 
 try:
-    STATUS = '$Rev: 637 $'.replace('Rev: ', '').replace('$', '').strip()
+    STATUS = '$Rev: 660 $'.replace('Rev: ', '').replace('$', '').strip()
 except Exception:
     STATUS = ''
 
 __CBCONFIG__ = {'VERSION_MAJOR' : 0,
                 'VERSION_MINOR' : 7,
-                'VERSION_MICRO' : 20,
+                'VERSION_MICRO' : 21,
                 'VERSION_STATUS' : STATUS,
                 'VERSION' : None,
                 'DEBUG' : False,

src/CBDataStruct.py

@@ -2,7 +2,7 @@
 CBMPy: CBDataStruct module
 ==========================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBDataStruct.py 575 2017-04-13 12:18:44Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBDataStruct.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 

src/CBGLPK.py

@@ -2,7 +2,7 @@
 CBMPy: CBGLPK module
 ====================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBGLPK.py 645 2018-04-23 22:38:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBGLPK.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """
 

src/CBGUI.py

@@ -2,7 +2,7 @@
 CBMPy: CBGUI module
 ===================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2017 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2018 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
@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBGUI.py 575 2017-04-13 12:18:44Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBGUI.py 660 2018-09-24 14:57:04Z bgoli $)
 
 """