Issues installing

[thh32]

I have tried installing the python version by running python setup.py install within the pypi_installer folder.

When I attempt to import the module in python the following happens;

>>> import SBtab Traceback (most recent call last): File "<stdin>", line 1, in <module> File "SBtab.py", line 185 SyntaxError: Non-ASCII character '\xe2' in file SBtab.py on line 185, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details Is there a solution for this?

[tlubitz]

Hi Thomas,

the pypi installer folder is just our system folder for building the pypi installer. It is not intended to be installed the way you describe it. The Python version that you want to install you can get by typing

sudo pip3 install sbtab

on your commandline. You do not require the contents of the pypi folder. Let me know if this clarifies the problem.

[thh32]

Thanks this seems to install SBtab fine now, however when trying to run the sbml2sbtab.py code the following error occurs;

$ python3 

sbml2sbtab.py Acutalibacter_muris.xml Acutalibacter_muris
Traceback (most recent call last):
  File "/home/thomashitch/Downloads/sbtab-0.9.19/sbtab/sbml2sbtab.py", line 667, in <module>
    (sbtabs,warnings) = Sbml_class.makeSBtabs()
AttributeError: 'SBMLDocument' object has no attribute 'makeSBtabs'

The input was created by CarveMe but appears to be a normal SBML file (attached) and the same issue occurs with ModelSEED created SBMLs. Acutalibacter_muris.zip

[tlubitz]

Hi Tom,

sorry for the confusion. You are currently using two different versions of the software:

When you install the SBtab package via the pip installer (sudo pip3 install sbtab) then you can import sbtab in your Python scripts (via import sbtab). This does not necessarily enable you to use SBtab on command line.

When you want to use SBtab on command line (which is for experienced users who install the required packages on their own), you will have to gather the required scripts from the SBtab/python directory and follow the instructions on github.

As a matter of fact, there are very current alterations on the user interface, which is most probably also causing your error. The problem is mainly that the documentation on how to use either the pip version or the command line version is outdated. Give me some time to work this over, then everything will become much clearer again.

Again, sorry for the confusion, Best, Timo

[tlubitz]

Hi Thomas,

if this issue is resolved by now I'll close this report. Let me know if it persists or if there is any other trouble.

Best, Timo