Merge pull request #35 from SystemsBioinformatics/dev

Merge in 0.8.1 development for release

Author: bgoli

CONTRIBUTORS.md

@@ -0,0 +1,10 @@
+Contributors to CBMPy
+=====================
+
+Release 0.8.1
+-------------
+
+Many thanks go to @jonrkarr and @willigot for their suggestions and code contributions.
+
+
+(c) Brett G. Olivier, Amsterdam, 2021

MANIFEST.in

@@ -1,6 +1,8 @@
 include LICENCE_GPLv3.txt
-include README.txt
+include README.md
+include RELEASES.md
+include CONTRIBUTORS.md
+include environment.yml
+include requirements.txt
 include cbmpy/*
-include cbmpy/models/*
-include cbmpy/nosetests/*
 include cbmpy/fluxmodules/*

README.md

@@ -17,7 +17,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>
 
 Author: Brett G. Olivier (@bgoli)
 
-# About
+## About
 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.
@@ -40,36 +40,39 @@ For more information on the development and use of CBMPy (https://github.com/Sys
 CBMPy has been tested on Windows 7 and 8.1, 10, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04, 20.04.
 CBMPy is currently developed on Python 3.7 and Python 3.6 or newer is highly recommended
 
-# Install
-The best way to get the basic CBMPy running is to install with Pip or create an Anaconda environment. CBMPy is developed on GitHub (https://github.com/SystemsBioinformatics/cbmpy)
+## Install
+The best way to get the basic CBMPy running is to install from **PyPI** or create an Anaconda environment. CBMPy is developed on GitHub (https://github.com/SystemsBioinformatics/cbmpy)
 
-## Install with pip using requirements.txt
+### Install with pip using requirements.txt
 From a terrminal or command prompt try:
 
 `pip install -r requirements.txt`
 
-## Install by creating an Anaconda environment using environment.yml
-From a terrminal or command prompt try:
+### New experimental PyPI install method.
+`pip install cbmpy[sbml]`
+
+### Install by creating an Anaconda environment using environment.yml
+From a terminal or command prompt try:
 
 `conda env create -f=environment.yml`
 
-This creates an environment **cbmpy** that can be accessed from the command line using `conda activate cbmpy3`
+This creates an environment **cbmpy3** that can be accessed from the command line using `conda activate cbmpy3`
 
-## Check the basic installation
+### Check the basic installation
 To check you installation follow the installation try the following in a Python shell:
 
 ```
 import cbmpy
 cmod = cbmpy.readSBML3FBC('cbmpy_test_core')
 cbmpy.doFBA(cmod)
 ```
-# Updating CBMPy
+## Updating CBMPy
 Once you have installed CBMPy it can be easily upgraded.
 
-## Pip update
+### Pip update
 `pip install --upgrade cbmpy`
 
-## Anaconda update
+### Anaconda update
 `conda update cbmpy`
 
 (c) Brett G. Olivier, Amsterdam, 2014-2021

RELEASES.md

@@ -0,0 +1,13 @@
+Release history
+===============
+
+Release 0.8.1 (2021-07-23)
+--------------------------
+
+Primarily a bugfix release to fix the SymPy compatability issues as well as improved requirements handling.
+
+
+
+
+
+(c) Brett G. Olivier, Amsterdam, 2021

cbmpy/CBCPLEX.py

@@ -2,7 +2,7 @@
 CBMPy: CBCPLEX module
 =====================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2022 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
@@ -39,6 +39,7 @@
 import time
 import gc
 from collections import OrderedDict
+from packaging import version as pkgver
 
 # this is a hack that needs to be streamlined a bit
 try:
@@ -50,15 +51,16 @@
 try:
     import sympy
 
-    if (
-        int(sympy.__version__.split('.')[1]) >= 7
-        and int(sympy.__version__.split('.')[2]) >= 4
-    ):
+    if pkgver.parse(sympy.__version__) >= pkgver.Version('0.7.4'):
         HAVE_SYMPY = True
     else:
         del sympy
+        print(
+            '\nWARNING: SymPy version 0.7.5 or newer is required for symbolic matrix support.'
+        )
 except ImportError:
     HAVE_SYMPY = False
+
 HAVE_SCIPY = False
 try:
     from scipy.sparse import csr

cbmpy/CBCommon.py

@@ -2,7 +2,7 @@
 CBMPy: CBCommon module
 ======================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2022 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

cbmpy/CBConfig.py

@@ -2,7 +2,7 @@
 CBMPy: CBConfig module
 ======================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2022 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

cbmpy/CBDataStruct.py

@@ -2,7 +2,7 @@
 CBMPy: CBDataStruct module
 ==========================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2022 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

cbmpy/CBDefaultModels.py

@@ -2,7 +2,7 @@
 CBMPy: default model module
 ===========================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2022 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 660 2018-09-24 14:57:04Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBCommon.py 660 2022-09-24 14:57:04Z bgoli $)
 
 """
 
@@ -73901,4 +73901,4 @@
   </model>
 </sbml>
 
-"""
+"""

cbmpy/CBGLPK.py

@@ -2,7 +2,7 @@
 CBMPy: CBGLPK module
 ====================
 PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
-Copyright (C) 2009-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
+Copyright (C) 2009-2022 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
@@ -29,20 +29,24 @@
 
 # from __future__ import unicode_literals
 
+from packaging import version as pkgver
+
 HAVE_SYMPY = False
 try:
     import sympy
 
-    if (
-        int(sympy.__version__.split('.')[1]) >= 7
-        and int(sympy.__version__.split('.')[2]) >= 4
-    ):
+    if pkgver.parse(sympy.__version__) >= pkgver.Version('0.7.5'):
         HAVE_SYMPY = True
+
     else:
         del sympy
+        print(
+            '\nWARNING: SymPy version 0.7.5 or newer is required for symbolic matrix support.'
+        )
 except ImportError:
     HAVE_SYMPY = False
 
+
 import os
 import time
 import numpy
@@ -119,6 +123,9 @@ def glpk_constructLPfromFBA(fba, fname=None):
     - *fname* optional filename if defined writes out the constructed lp
 
     """
+
+    print('\nCBGLPK based on swiglpk: not all methods implimented yet!')
+
     _Stime = time.time()
 
     # define model and add variables