bgoli
commented
5 years ago Thanks for the detailed report. This is a permissions issue with the built in testsuite, that I am currently looking into improving.
Closed mabawsa closed 5 years ago
bgoli
commented
5 years ago Thanks for the detailed report. This is a permissions issue with the built in testsuite, that I am currently looking into improving.
bgoli
commented
5 years ago Just an update the testsuite code has been moved out of the source into it's own branch and the example models are now stored as Python strings. Implemented in trunk, needs some multios testing.
mabawsa
commented
5 years ago Just tried to install on a new machine and it seems even python 2.7 has regressed:
dougie@celldynamics:~$ sudo -H python2 -m pip install --upgrade cbmpy
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Requirement already up-to-date: cbmpy in /usr/local/lib/python2.7/dist-packages (0.7.21)
dougie@celldynamics:~$ python2
Python 2.7.15+ (default, Nov 27 2018, 23:36:35)
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import cbmpy
WARNING: SBML support not available, please install libSBML, Python bindings with FBC (sbml.org)
INFO: SBML+GROUPS support not available, update to latest version of libSBML if required
GLPK not available
No module named cplex
CPLEX not available
*****
WARNING: No linear solver present, please install IBM CPLEX with Python bindings or PyGLPK, please see http://cbmpy.sourceforge.net for Windows binary or http://tfinley.net/software/pyglpk for source.
*****
No solver present, unable to create shortcuts
WARNING: No SBML support, top-level SBML read/write functions disabled.
Installing default models ...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/cbmpy/__init__.py", line 91, in <module>
from . import CBModel, CBDataStruct, CBModelTools, CBRead, CBReadtxt, CBTools, CBWrite, CBXML, CBNetDB, CBPlot, CBMultiModel
File "/usr/local/lib/python2.7/dist-packages/cbmpy/CBRead.py", line 90, in <module>
zfile.extractall(path=__example_model_path__)
File "/usr/lib/python2.7/zipfile.py", line 1063, in extractall
self.extract(zipinfo, path, pwd)
File "/usr/lib/python2.7/zipfile.py", line 1051, in extract
return self._extract_member(member, path, pwd)
File "/usr/lib/python2.7/zipfile.py", line 1106, in _extract_member
file(targetpath, "wb") as target:
IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/cbmpy/models/core_memesa_model.l3.xml'
>>> and python 3:
dougie@celldynamics:~$ sudo -H python3 -m pip install --upgrade cbmpy
Requirement already up-to-date: cbmpy in /usr/local/lib/python3.6/dist-packages (0.7.21)
dougie@celldynamics:~$ python3
Python 3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cbmpy
INFO: No xlwt module available, Excel spreadsheet creation disabled
GLPK not available
*****
Using CPLEX
*****
Installing default models ...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.6/dist-packages/cbmpy/__init__.py", line 61, in <module>
from .CBRead import loadModel, readSBML3FBC, readSBML2FBA, readCOBRASBML
File "/usr/local/lib/python3.6/dist-packages/cbmpy/CBRead.py", line 90, in <module>
zfile.extractall(path=__example_model_path__)
File "/usr/lib/python3.6/zipfile.py", line 1524, in extractall
self._extract_member(zipinfo, path, pwd)
File "/usr/lib/python3.6/zipfile.py", line 1578, in _extract_member
open(targetpath, "wb") as target:
PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.6/dist-packages/cbmpy/models/core_memesa_model.l3.xml'
>>> Everything works OK if I copy over the contents of \models\ and \nosetests\ from another machine with the old installation.
bgoli
commented
5 years ago Hi, it's taking a while to for me to wrap up a new release (hopefully as soon as next week) but I've fixed this problem so that CBMPy no longer creates temporary files. Right now you need to clone the source repository and run sudo python setup.py install to install the latest code.
The Python 2.7 warning is from pip and can be ignored.
bgoli
commented
5 years ago This has been fixes in the 0.7.25 release now available from PyPI Conda etc
OS: ubuntu 18.04 CBMPy (0.7.21) scenario: installing using pip3 on a python 2.7 default system. I require both to refactor code.
Python 2.7 works just fine, but when I try installing in Python 3, cbmpy comes up with the following error:
seems a file may be missing:
when I link the xml files I then get:
In summary I needed to do the following to resolve this: