cobrapy

[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:

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# 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