Download Latest Version
cbmpy-0.7.25.tar.gz (3.3 MB)
Get an email when there's a new version of CBMPy
| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.rst.txt | 2012-12-03 | 4.2 kB | |
| pysces_cbm_mariner.superpack.20120028.zip | 2012-12-03 | 3.7 MB | |
| cbmpy.superpack.20120028.zip | 2012-12-03 | 4.1 MB | |
| Totals: 3 Items | 7.8 MB | 0 | |
CBMPy & PySCeS-CBM/Mariner installation instructions (Windows 32/64)
- Author: Brett G. Olivier (b.g.olivier@vu.nl)
- Date: 20121128
- Version: 1.0
Python and base dependencies
Install Open Source scientific Python distribution available from http://www.pythonxy.com:
- Run Python(x,y)-2.7.3.0.exe
- Agree to licence
- Select the type of install: Full
- Use default directories and start menu options
Test installation:
- Open a terminal
- Execute "ipython"
- In ipython shell, execute "import numpy, h5py, xlrd, xlwt"
No errors/warnings indicate successful installation exit with CTRL-D
Install IBM cplex optimization studio (Academic)
- Run cplex_studio125.win-x86-32.exe
- Select English language and accept licence
- Set "Program" install directory to C:ILOGCPLEX_Studio124
- Set "Samples" install directory to C:ILOGCPLEX_Studio124_samples
- Allow default associations to be set and PATH update
Once installation is complete we need to install the Python bindings
- Open a terminal
- Execute "cd c:ILOGCPLEX_Studio124cplexpythonx86_win32"
- Execute "python setup.py install"
Test installation, in the terminal:
- Execute "cd "
- Execute "ipython"
- Execute "import cplex"
- Execute "lp = cplex.Cplex()"
- Execute "lp.solve()"
A succesful test should return:
In : lp.solve() Tried aggregator 1 time. No LP presolve or aggregator reductions. Presolve time = 0.00 sec.
Exit ipython with CTRL-D
Install libSBML (sbml.org)
- Run libSBML-5.6.0-win-py2.7-packages-x86.exe
Test installation
- Open a terminal
- Execute "ipython"
- Execute "import libsbml"
- Execute "libsbml.LIBSBML_VERSION_STRING"
A successful test should return:
In : libsbml.LIBSBML_VERSION_STRING Out: '50600'
Exit ipython with CTRL-D
Install CBMPy (pysces.sf.net/cbm)
- Run pyscescbm-0.6.2.win32.exe
Test installation:
- Open a terminal
- Execute "ipython"
- Execute "import pyscescbm as cbm"
This should return:
In [1]: import pyscescbm as cbm ********** Welcome to the PySCeS Constraint Based Modelling Toolkit (0.6.2 [r1147]) ********** GLPK not available ***** Using CPLEX ***** No module named CBGUI GUI module not available *** Multiple Environment Module (0.6.2 [r1147]) ***
Exit ipython with CTRL-D
CherryPy, libXML and SOAPlib (www.cherrypy.org, lxml.de)
- Run lxml-2.3.win32-py2.7.exe
- Run CherryPy-3.2.2.win32.exe
- Run soaplib-0.8.1.win32.exe
Test installation:
- Open a terminal
- Execute "ipython"
- Execute "import cherrypy, lxml, soaplib" no errors or warnings should be generated
- Exit ipython with CTRL-D
- change directory to supplied soaplib tests e.g. "cd e:gsktestssoaplib"
- Execute "python binary_test.py"
- Execute "python primitive_test.py"
All tests should pass.
PySCeS-CBM/Mariner (pysces.sf.net/cbm)
- Run pyscesmariner-0.7.3.win32.exe
To test installation:
- Open two terminals and in both
- Change directory to supplied pyscesmariner tests e.g. "cd e:gsktestspyscesmariner"
- In terminal one run "run_server.bat" which should nowdisplay
E:gsktestspyscesmariner>python cbm_server_demo.py Mariner using E:gsktestspyscesmariner as a working directory Mariner server name: 10.0.2.15 Mariner using port: 31313
<snipped>
* Multiple Environment Module (0.6.2 [r1147]) *
PySCeSCBM/Mariner initialising ... this console is now blocked
In terminal two:
- Execute "python cbm_client_demo.py"
This should end without errors and display done. Congratulations you have successfully installed CBMPy and PySCeS-CBM Mariner!