installing requirements issue

[kievol]

Hi,

I was trying to install the requirements after downloading the git file. I first typed "pip install -r requirements.txt" but it spat out this:

File "/usr/bin/pip", line 9, in
from pip import main
ImportError: cannot import name main

Then I tried "python -m pip install -r requirements.txt". It ran for a while and then gave me this error message (complete output below):

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-xo3RcQ/matplotlib/

Any suggestions regarding what might cause the problem?

Many thanks in advance!

---

Collecting GPy==1.2.1 (from -r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/39/d4/d971da288b19e770863e992f8c89fd73ab274b8b140ccbe9ad9586ee0f74/GPy-1.2.1.tar.gz
Collecting Jinja2==2.7.3 (from -r requirements.txt (line 2))
Using cached https://files.pythonhosted.org/packages/b0/73/eab0bca302d6d6a0b5c402f47ad1760dc9cb2dd14bbc1873ad48db258e4d/Jinja2-2.7.3.tar.gz
Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3))
Using cached https://files.pythonhosted.org/packages/c0/41/bae1254e0396c0cc8cf1751cb7d9afc90a602353695af5952530482c963f/MarkupSafe-0.23.tar.gz
Collecting Pygments==2.0.2 (from -r requirements.txt (line 4))
Using cached https://files.pythonhosted.org/packages/d7/b8/57216ab6f20ce3b0e37695c76bda8182030de95e9c679ce36e49483b05a0/Pygments-2.0.2-py2-none-any.whl
Collecting Sphinx==1.3.1 (from -r requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/63/2c/0a30c391708f827039be5569164ed039b1e46906a4bff5a348b0abe2945e/Sphinx-1.3.1-py2.py3-none-any.whl
Collecting alabaster==0.7.3 (from -r requirements.txt (line 6))
Using cached https://files.pythonhosted.org/packages/df/64/8266bf8fcbb0f5ad2b3a23518f7d009ea2d98ad477a49288a5a8dd9dad18/alabaster-0.7.3.tar.gz
Requirement already satisfied: argparse==1.2.1 in /usr/lib/python2.7 (from -r requirements.txt (line 7)) (1.2.1)
Collecting backports.ssl-match-hostname==3.4.0.2 (from -r requirements.txt (line 8))
Using cached https://files.pythonhosted.org/packages/3a/15/f9e48bfd2b971ade10ad0c03babab057791c260b05322cbd3f47e27be108/backports.ssl_match_hostname-3.4.0.2.tar.gz
Collecting certifi==14.05.14 (from -r requirements.txt (line 9))
Using cached https://files.pythonhosted.org/packages/c1/ed/4a424a55f77679700452972e583393b64160583c80ffa893b4be9391f3ae/certifi-14.05.14.tar.gz
Collecting decorator==4.0.10 (from -r requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/53/24/cc53f9f216dd5ef269e0af7c7651cbda162554a5b088621a205961c07a6f/decorator-4.0.10-py2.py3-none-any.whl
Collecting docutils==0.12 (from -r requirements.txt (line 11))
Using cached https://files.pythonhosted.org/packages/37/38/ceda70135b9144d84884ae2fc5886c6baac4edea39550f28bcd144c1234d/docutils-0.12.tar.gz
Collecting ipython==3.1.0 (from -r requirements.txt (line 12))
Using cached https://files.pythonhosted.org/packages/90/71/360e0e5d332a0c772fa84f61ae12d977c51665e740e6fd4252fc3abaa613/ipython-3.1.0-py2-none-any.whl
Collecting jdcal==1.2 (from -r requirements.txt (line 13))
Using cached https://files.pythonhosted.org/packages/37/36/3199cfb80fcbf4e4df3a43647733d4f429862c6c97aeadd757613b9e6830/jdcal-1.2.tar.gz
Collecting jsonschema==2.4.0 (from -r requirements.txt (line 14))
Using cached https://files.pythonhosted.org/packages/5e/55/9e973774cb3a47d0d025fc9626c8cff96b104e3764493f91b49fa125d8ec/jsonschema-2.4.0-py2.py3-none-any.whl
Collecting matplotlib==1.4.3 (from -r requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/bb/ac/485df0ecb15aa6fec1991945dc0cabfeb724a64f6729e34bab3c6a766813/matplotlib-1.4.3.tar.gz
Complete output from command python setup.py egg_info:
============================================================================
Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
            matplotlib: yes [1.4.3]
                python: yes [2.7.12 (default, Nov 12 2018, 14:36:49)  [GCC
                        5.4.0 20160609]]
              platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [version 1.11.0]
                   six: yes [using six version 1.10.0]
              dateutil: yes [using dateutil version 2.7.5]
                  pytz: yes [using pytz version 2014.10]
               tornado: yes [tornado was not found. It is required for the
                        WebAgg backend. pip/easy_install may attempt to
                        install it after matplotlib.]
             pyparsing: yes [using pyparsing version 2.0.3]
                 pycxx: yes [Couldn't import.  Using local copy.]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: no  [The C/C++ header for freetype2 (ft2build.h)
                        could not be found.  You may need to install the
                        development package.]
                   png: yes [version 1.2.54]
                 qhull: yes [pkg-config information for 'qhull' could not be
                        found. Using local copy.]

OPTIONAL SUBPACKAGES
           sample_data: yes [installing]
              toolkits: yes [installing]
                 tests: yes [nose 0.11.1 or later is required to run the
                        matplotlib test suite.  pip/easy_install may attempt
                        to install it after matplotlib. / mock is required
                        to run the matplotlib test suite.  pip/easy_install
                        may attempt to install it after matplotlib.]
        toolkits_tests: yes [nose 0.11.1 or later is required to run the
                        matplotlib test suite.  pip/easy_install may attempt
                        to install it after matplotlib. / mock is required
                        to run the matplotlib test suite.  pip/easy_install
                        may attempt to install it after matplotlib.]

OPTIONAL BACKEND EXTENSIONS
                macosx: no  [Mac OS-X only]
                qt5agg: no  [PyQt5 not found]
                qt4agg: no  [PyQt4 not found]
                pyside: no  [PySide not found]
               gtk3agg: yes [installing, version 3.9.18]
             gtk3cairo: yes [installing, version 3.9.18]
                gtkagg: no  [The C/C++ header for gtk (gtk/gtk.h) could not
                        be found.  You may need to install the development
                        package.]
                 tkagg: no  [The C/C++ header for Tk (tk.h) could not be
                        found.  You may need to install the development
                        package.]
                 wxagg: no  [requires wxPython]
                   gtk: no  [The C/C++ header for gtk (gtk/gtk.h) could not
                        be found.  You may need to install the development
                        package.]
                   agg: yes [installing]
                 cairo: yes [installing, pycairo version 1.8.8]
             windowing: no  [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
                dvipng: no
           ghostscript: yes [version 9.26]
                 latex: no
               pdftops: yes [version 0.41.0]

============================================================================
                        * The following required packages can not be built:
                        * freetype

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-xo3RcQ/matplotlib/

[SirRujak]

It appears that the error you are getting is due to matplotlib no longer providing wheels for older versions. I have a branch https://github.com/SirRujak/gp_growth_phenotype that is ported to Python 3 with at least somewhat updated dependencies. If you are still interested in giving it a try and find any issues feel free to let me know.