ImportError: No module named lex

[Anonymous]

In a new install of pysces, with libSBML also newly installed, running

pysces.test()

successfully completes the first 8 "Level 1" tests, but fails in the "Level 2" tests, repeatedly reporting a

ImportError: No module named lex

error.

Similarly, when I try to follow the userguide and load a module (page 9 of the version 0.7 userguide) by running

mod = pysces.model('pysces_test_linear1')

, I receive the same

ImportError: No module named lex

error:

Detailed error messages follow. 

Any help would be much appreciated!

Cheers,
Matthew

In [5]: pysces.test()
Copying pysces_test models if necessary ...
src : /usr/local/lib/python2.7/dist-packages/pysces/pscmodels
dest: /home/mde/Pysces/psc
done.
Level 1 tests
........
----------------------------------------------------------------------
Ran 8 tests in 0.017s
OK
Level 2 tests
EEEEEEEEEEEE
======================================================================
ERROR: test_cc_branch1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 384, in test_cc_branch1
    bra = pysces.model('pysces_test_branch1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_cc_linear1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 361, in test_cc_linear1
    lin = pysces.model('pysces_test_linear1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_cc_moiety1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 416, in test_cc_moiety1
    moi = pysces.model('pysces_test_moiety1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_elas_branch1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 317, in test_elas_branch1
    bra = pysces.model('pysces_test_branch1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_elas_linear1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 301, in test_elas_linear1
    lin = pysces.model('pysces_test_linear1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_elas_moiety1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 336, in test_elas_moiety1
    moi = pysces.model('pysces_test_moiety1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_stateflux_branch1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 285, in test_stateflux_branch1
    bra = pysces.model('pysces_test_branch1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_stateflux_linear1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 277, in test_stateflux_linear1
    lin = pysces.model('pysces_test_linear1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_stateflux_moiety1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 293, in test_stateflux_moiety1
    moi = pysces.model('pysces_test_moiety1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_statemetab_branch1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 261, in test_statemetab_branch1
    bra = pysces.model('pysces_test_branch1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_statemetab_linear1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 253, in test_statemetab_linear1
    lin = pysces.model('pysces_test_linear1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
======================================================================
ERROR: test_statemetab_moiety1 (PyscesTest.PyscesExtendedTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/pysces/PyscesTest.py", line 269, in test_statemetab_moiety1
    moi = pysces.model('pysces_test_moiety1.psc', self.model_dir)
  File "pysces/PyscesModel.py", line 1896, in __init__
    self.ModelLoad()
  File "pysces/PyscesModel.py", line 1909, in ModelLoad
    self.InitialiseInputFile()
  File "pysces/PyscesModel.py", line 2155, in InitialiseInputFile
    pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
  File "pysces/PyscesParse.py", line 1232, in ParsePSC
    reload(pysces.lib.lex)
ImportError: No module named lex
----------------------------------------------------------------------
Ran 12 tests in 0.007s
FAILED (errors=12)
Out[5]: <PyscesTest.PyscesTest instance at 0x3f6d488>
In [6]:

mod = pysces.model('pysces_test_linear1')
Assuming extension is .psc
Using model directory: /home/mde/Pysces/psc
/home/mde/Pysces/psc/pysces_test_linear1.psc loading ..... 
Parsing file: /home/mde/Pysces/psc/pysces_test_linear1.psc
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/home/mde/Pysces/<ipython-input-3-691bd3418afa> in <module>()
----> 1 mod = pysces.model('pysces_test_linear1')
/home/mde/Pysces/pysces/PyscesModel.pyc in __init__(self, File, dir, loader, fString, autoload)
   1894         self.__HAS_PIECEWISE__ = False
   1895         if autoload:
-> 1896             self.ModelLoad()
   1897             self.__PSC_auto_load = True
   1898         else:
/home/mde/Pysces/pysces/PyscesModel.pyc in ModelLoad(self, stoich_load)
   1907 
   1908         """
-> 1909         self.InitialiseInputFile()
   1910         assert self.__parseOK, '\nError in input file, parsing could not complete'
   1911         self.Stoichiometry_Analyse(override=0,load=stoich_load)
/home/mde/Pysces/pysces/PyscesModel.pyc in InitialiseInputFile(self)
   2153         print '\nParsing file: %s' % os.path.join(self.ModelDir, self.ModelFile)
   2154 
-> 2155         pscParser.ParsePSC(self.ModelFile,self.ModelDir,self.ModelOutput)
   2156         print ' '
   2157 
/home/mde/Pysces/pysces/PyscesParse.pyc in ParsePSC(self, modelfile, modeldir, modeloutput)
   1230 
   1231         # 4 hrs of debugging and these two lines solve the problem .... I'm out of here!
-> 1232         reload(pysces.lib.lex)
   1233         reload(pysces.lib.yacc)
   1234         # fixes the obscure reload <--> garbage collection reference overload bug ... who said scripted lang's were
ImportError: No module named lex

[Anonymous]

Some version numbers in case that is helpful..

In [1]: import pysces
Matplotlib interface loaded (pysces.plt.m)
No module named pitcon
Attempting alternate pitcon import ...
No module named nleq2
Attempting alternate nleq2 import ...
continuation routines available
nleq2 routines available
continuation routines available
nleq2 routines available
You are using NumPy (1.6.1) with SciPy (0.11.0)
PySCeS environment
******************
pysces.model_dir = /home/mde/Pysces/psc
pysces.output_dir = /home/mde/Pysces
***********************************************************************
* Welcome to PySCeS (0.8.0rc3) - Python Simulator for Cellular Systems   *
*                http://pysces.sourceforge.net                        *
* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2011  *
* Triple-J Group for Molecular Cell Physiology                        *
* Stellenbosch University, South Africa                               *
* PySCeS is distributed under the PySCeS (BSD style) licence, see     *
* LICENCE.txt (supplied with this release) for details                *
***********************************************************************

[Brett Olivier]

Hi Matthew

Thanks for your post, this is an intriguing problem that I must admit I have never encountered before, to start with could you try some more diagnostics:

1) could you run the tests again, making sure that you are *not* currently in the PySCeS source or installation directory as this has been known to cause import problems.

2) in the PySCeS installation directory (../site-packages/pysces/libs), do the files lex.py yacc.py exist?

3) If possible could you post here (or email bgoli@users.sourceforge.net) your _pyscfg.ini file which should also be located in your pysces installation directory (../site-packages/pysces)

Best regards
Brett