cobrapy

[deepa]

Hello Everyone,

I am attempting to install cobra 0.6.1 using pip in python 3.4(32-bit).
I am not able to find the 32-bit cobra 0.6.1 installation file.

Could someone provide me a link to the installation file ?

I would be grateful for any help you can offer.

Thanks

[sparkz_alot]

To install the latest version (0.8.1) simply type pip install cobra , if you want all optional packages as well, type pip install cobra[all] . You can find additional information and links on their PyPi page cobrapy.

If, for some reason, you absolutely need to have to the old version, you might contact the developers and see if they have an old copy.  You could also take the new version, remove any new features and reintroduce any bugs that were fixed.

[deepa]

Thanks a lot for your help.
pip install cobra[all] shows an error.
Error:
Command "python setup.py egg_info" failed with error code 1 in C:\Users\DEEPA\AppData\Local\Temp\pip-build-4rm1wkub\pymatbridge\

To be more specific on my problem,I am trying to install sbmlutils package which requires cobrapy 0.6.1
using pip install sbmlutils gives an error.

Error:
Collecting cobra>=0.6.1 (from sbmlutils)
Could not find a version that satisfies the requirement cobra>=0.6.1 (from sbmlutils) (from versions: 0.2.0, 0.2.1, 0.3.0b1, 0.3.0b2, 0.3.0b3, 0.3.0b4, 0.3.0, 0.3.1, 0.3.2, 0.4.0a1, 0.4.0a2, 0.4.0a3, 0.4.0a4, 0.4.0b1, 0.4.0b2, 0.4.0b3, 0.4.0b4, 0.4.0b6, 0.4.0b7, 0.4.0, 0.4.1, 0.4.2b1, 0.4.2b2, 0.5.0b2, 0.5.1b1, 0.5.1b1.post14, 0.5.1b2, 0.5.1b3, 0.5.2b3, 0.5.2, 0.5.3, 0.5.3.post3, 0.5.4, 0.5.6b1, 0.5.6b2, 0.5.6, 0.5.7, 0.5.8, 0.5.9b1, 0.5.9, 0.5.10, 0.5.11)
No matching distribution found for cobra>=0.6.1 (from sbmlutils)

[snippsat]

Test in virtual environment with cobra all(which is about 20 packages).
You should use pip version 9.0.1

(cobra) E:\1py_div\cobra
λ pip -V
pip 9.0.1 from e:\1py_div\cobra\lib\site-packages (python 3.6)

Need to first install pip install pyzmq
From Gohlke Scipy wheel.
The run:

Hide/Show

# install pyzmq
(cobra) E:\1py_div\cobra
λ pip install pyzmq
Collecting pyzmq
  Downloading pyzmq-16.0.2-cp36-cp36m-win32.whl (790kB)
    100% |████████████████████████████████| 798kB 973kB/s
Installing collected packages: pyzmq
Successfully installed pyzmq-16.0.2

# Install Scipy wheel
(cobra) E:\1py_div\cobra
λ pip install scipy-0.19.1-cp36-cp36m-win32.whl
Processing e:\1py_div\cobra\scipy-0.19.1-cp36-cp36m-win32.whl
Collecting numpy>=1.8.2 (from scipy==0.19.1)
  Using cached numpy-1.13.1-cp36-none-win32.whl
Installing collected packages: numpy, scipy
Successfully installed numpy-1.13.1 scipy-0.19.1

# Cobra all
(cobra) E:\1py_div\cobra
λ pip install cobra[all]
Requirement already satisfied: cobra[all] in e:\1py_div\cobra\lib\site-packages
Requirement already satisfied: six in e:\1py_div\cobra\lib\site-packages (from cobra[all])
Requirement already satisfied: numpy>=1.6; extra == "all" in e:\1py_div\cobra\lib\site-packages (from cobra[all])
Collecting pytest-benchmark; extra == "all" (from cobra[all])
  Downloading pytest_benchmark-3.1.1-py2.py3-none-any.whl (52kB)
    100% |████████████████████████████████| 61kB 498kB/s
Collecting pymatbridge; extra == "all" (from cobra[all])
  Using cached pymatbridge-0.5.2.tar.gz
Collecting lxml; extra == "all" (from cobra[all])
  Using cached lxml-3.8.0-cp36-cp36m-win32.whl
Collecting palettable; extra == "all" (from cobra[all])
  Using cached palettable-3.0.0-py2.py3-none-any.whl
Collecting pandas>=0.17.0; extra == "all" (from cobra[all])
  Downloading pandas-0.20.3-cp36-cp36m-win32.whl (7.5MB)
    100% |████████████████████████████████| 7.5MB 165kB/s
Collecting matplotlib; extra == "all" (from cobra[all])
  Using cached matplotlib-2.0.2-cp36-cp36m-win32.whl
Requirement already satisfied: scipy>=0.11.0; extra == "all" in e:\1py_div\cobra\lib\site-packages (from cobra[all])
Collecting pytest; extra == "all" (from cobra[all])
  Using cached pytest-3.2.0-py2.py3-none-any.whl
Collecting tabulate; extra == "all" (from cobra[all])
  Using cached tabulate-0.7.7-py2.py3-none-any.whl
Collecting Cython>=0.21; extra == "all" (from cobra[all])
  Using cached Cython-0.26-cp36-none-win32.whl
Collecting python-libsbml; extra == "all" (from cobra[all])
  Downloading python_libsbml-5.15.0-cp36-cp36m-win32.whl (5.2MB)
    100% |████████████████████████████████| 5.2MB 222kB/s
Collecting py-cpuinfo (from pytest-benchmark; extra == "all"->cobra[all])
  Downloading py-cpuinfo-3.3.0.tar.gz (76kB)
    100% |████████████████████████████████| 81kB 2.6MB/s
Collecting python-dateutil>=2 (from pandas>=0.17.0; extra == "all"->cobra[all])
  Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
    100% |████████████████████████████████| 194kB 1.9MB/s
Collecting pytz>=2011k (from pandas>=0.17.0; extra == "all"->cobra[all])
  Downloading pytz-2017.2-py2.py3-none-any.whl (484kB)
    100% |████████████████████████████████| 491kB 1.4MB/s
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib; extra == "all"->cobra[all])
  Using cached pyparsing-2.2.0-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib; extra == "all"->cobra[all])
  Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting py>=1.4.33 (from pytest; extra == "all"->cobra[all])
  Using cached py-1.4.34-py2.py3-none-any.whl
Collecting colorama; sys_platform == "win32" (from pytest; extra == "all"->cobra[all])
  Using cached colorama-0.3.9-py2.py3-none-any.whl
Requirement already satisfied: setuptools in e:\1py_div\cobra\lib\site-packages (from pytest; extra == "all"->cobra[all])
Installing collected packages: py, colorama, pytest, py-cpuinfo, pytest-benchmark, pymatbridge, lxml, palettable, python-dateutil, pytz, pandas, pyparsing, cycler, matplotlib, tabulate, Cython, python-libsbml
  Running setup.py install for py-cpuinfo ... done
  Running setup.py install for pymatbridge ... done
Successfully installed Cython-0.26 colorama-0.3.9 cycler-0.10.0 lxml-3.8.0 matplotlib-2.0.2 palettable-3.0.0 pandas-0.20.3 py-1.4.34 py-cpuinfo-3.3.0 pymatbridge-0.5.2 pyparsing-2.2.0 pytest-3.2.0 pytest-benchmark-3.1.1 python-dateutil-2.6.1 python-libsbml-5.15.0 pytz-2017.2 tabulate-0.7.7