Permanently set Python path for Anaconda within Cygwin

Question

I'm trying to install Anaconda on my Windows 7 machine. I often use cygwin to for my command-line work, and I would like to manage Anaconda from there. I've worked through the graphic installer without any issues, and checked necessary boxes to reset my default path to this install of python. I go ahead to check where python is and initially I get this...

$ which python
/usr/bin/python

From here python works fine...

$ python
Python 2.7.5 (default, Oct  2 2013, 22:34:09)
[GCC 4.8.1] on cygwin
Type "help", "copyright", "credits" or "license" for more information.

But I'm trying to work from anaconda, so I should just need to redefine my path...

$ export PATH=/cygdrive/c/anaconda:$PATH
$ which python
/cygdrive/c/anaconda/python

And now I should be good to go, but when I try and step into python, it just hangs

$ python

Any idea why this might be happening? verbose return, below...

$ python -v
# installing zipimport hook
import zipimport # builtin
# installed zipimport hook
# C:\anaconda\lib\site.pyc matches C:\anaconda\lib\site.py
import site # precompiled from C:\anaconda\lib\site.pyc
# C:\anaconda\lib\os.pyc matches C:\anaconda\lib\os.py
import os # precompiled from C:\anaconda\lib\os.pyc
import errno # builtin
import nt # builtin
# C:\anaconda\lib\ntpath.pyc matches C:\anaconda\lib\ntpath.py
import ntpath # precompiled from C:\anaconda\lib\ntpath.pyc
# C:\anaconda\lib\stat.pyc matches C:\anaconda\lib\stat.py
import stat # precompiled from C:\anaconda\lib\stat.pyc
# C:\anaconda\lib\genericpath.pyc matches C:\anaconda\lib\genericpath.py
import genericpath # precompiled from C:\anaconda\lib\genericpath.pyc
# C:\anaconda\lib\warnings.pyc matches C:\anaconda\lib\warnings.py
import warnings # precompiled from C:\anaconda\lib\warnings.pyc
# C:\anaconda\lib\linecache.pyc matches C:\anaconda\lib\linecache.py
import linecache # precompiled from C:\anaconda\lib\linecache.pyc
# C:\anaconda\lib\types.pyc matches C:\anaconda\lib\types.py
import types # precompiled from C:\anaconda\lib\types.pyc
# C:\anaconda\lib\UserDict.pyc matches C:\anaconda\lib\UserDict.py
import UserDict # precompiled from C:\anaconda\lib\UserDict.pyc
# C:\anaconda\lib\_abcoll.pyc matches C:\anaconda\lib\_abcoll.py
import _abcoll # precompiled from C:\anaconda\lib\_abcoll.pyc
# C:\anaconda\lib\abc.pyc matches C:\anaconda\lib\abc.py
import abc # precompiled from C:\anaconda\lib\abc.pyc
# C:\anaconda\lib\_weakrefset.pyc matches C:\anaconda\lib\_weakrefset.py
import _weakrefset # precompiled from C:\anaconda\lib\_weakrefset.pyc
import _weakref # builtin
# C:\anaconda\lib\copy_reg.pyc matches C:\anaconda\lib\copy_reg.py
import copy_reg # precompiled from C:\anaconda\lib\copy_reg.pyc
# C:\anaconda\lib\traceback.pyc matches C:\anaconda\lib\traceback.py
import traceback # precompiled from C:\anaconda\lib\traceback.pyc
# C:\anaconda\lib\sysconfig.pyc matches C:\anaconda\lib\sysconfig.py
import sysconfig # precompiled from C:\anaconda\lib\sysconfig.pyc
# C:\anaconda\lib\re.pyc matches C:\anaconda\lib\re.py
import re # precompiled from C:\anaconda\lib\re.pyc
# C:\anaconda\lib\sre_compile.pyc matches C:\anaconda\lib\sre_compile.py
import sre_compile # precompiled from C:\anaconda\lib\sre_compile.pyc
import _sre # builtin
# C:\anaconda\lib\sre_parse.pyc matches C:\anaconda\lib\sre_parse.py
import sre_parse # precompiled from C:\anaconda\lib\sre_parse.pyc
# C:\anaconda\lib\sre_constants.pyc matches C:\anaconda\lib\sre_constants.py
import sre_constants # precompiled from C:\anaconda\lib\sre_constants.pyc
# C:\anaconda\lib\locale.pyc matches C:\anaconda\lib\locale.py
import locale # precompiled from C:\anaconda\lib\locale.pyc
import encodings # directory C:\anaconda\lib\encodings
# C:\anaconda\lib\encodings\__init__.pyc matches C:\anaconda\lib\encodings\__init__.py
import encodings # precompiled from C:\anaconda\lib\encodings\__init__.pyc
# C:\anaconda\lib\codecs.pyc matches C:\anaconda\lib\codecs.py
import codecs # precompiled from C:\anaconda\lib\codecs.pyc
import _codecs # builtin
# C:\anaconda\lib\encodings\aliases.pyc matches C:\anaconda\lib\encodings\aliases.py
import encodings.aliases # precompiled from C:\anaconda\lib\encodings\aliases.pyc
import operator # builtin
# C:\anaconda\lib\functools.pyc matches C:\anaconda\lib\functools.py
import functools # precompiled from C:\anaconda\lib\functools.pyc
import _functools # builtin
import _locale # builtin
# C:\anaconda\lib\encodings\cp1252.pyc matches C:\anaconda\lib\encodings\cp1252.py
import encodings.cp1252 # precompiled from C:\anaconda\lib\encodings\cp1252.pyc
# zipimport: found 13 names in C:\anaconda\lib\site-packages\runipy-0.1.0-py2.7.egg
# zipimport: found 144 names in C:\anaconda\lib\site-packages\setuptools-3.6-py2.7.egg
Python 2.7.7 |Anaconda 2.0.1 (64-bit)| (default, Jun 11 2014, 10:40:02) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and htt

Another (possibly related) issue I'm having is needing to reset the path every time I close/open cygwin. I've entered the following text into .bashrc and .profile to try and set the path permanently:

# Set path to python from anaconda install
export PATH=/cygdrive/c/anaconda:$PATH

After opening and closing cygwin, I return to:

$ which python
/usr/bin/python

Could this be related to setting certain system environment variables?

Answer 1

To work with the interactive Python shell in Cygwin I use the -i option.

To get it from the Anaconda install, I used the steps suggested above:

$ export PATH=/cygdrive/c/anaconda:$PATH
$ which python
/cygdrive/c/anaconda/python

Then I launch python within Cygwin with the -i option:

$ python -i
Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Jul  2 2014, 15:12:11) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://binstar.org
>>>>

The libraries are also working fine. For instance the pandas library (which has been installed through Anaconda) can be imported now.

>>>> import pandas
>>>> pandas.DataFrame
<class 'pandas.core.frame.DataFrame'>

Now to make this permanent I added the path in my bashrc file:

$ echo 'export PATH=/cygdrive/c/anaconda:$PATH' >> .bashrc
$ source .bashrc
$ which python
/cygdrive/c/anaconda/python

I hope this helps.

Answer 2

Path

Regarding your path issue, see Installing anaconda to use with windows on how to fix that. Alternatively, you can just run /cygdrive/c/Anaconda/python.exe to start the Anaconda/windows python and leave the standard python pointing to the cygwin version.

Note that few of the suggestions given on the internet also include the necessary change to PYTHONPATH : if you use the anaconda/windows python, you also want the anaconda python libraries. Binary modules like numpy will surely crash or misbehave if you mix things up. The easiest way to check this is to install a module in cygwin that you do not need in Conda and test whether you can import that from anaconda python. If you can, your path is wrong.

Anaconda python will automatically add c:\\Anconda to your PYTHONPATH, but if you have it set to serve CYGWIN python libraries, those will be found before the Anaconda libs. Try

import sys
sys.path

Terminal

However, this is also a terminal issue: Anaconda (Windows) python expects a windows shell and a modern cygwin shell is like an xterm , so very different. Diagnose this by running python --help , if that works but plain python hangs, the interactive prompt is the problem. This means you can run python programs, you just cannot interact with them.

A way around this is to use the cygwin bash shell instead of the cygwin terminal (both are under Cygwin group in the Start menu). They look very similar, but the font in the bash shell is less pretty and you cannot make the window wider than 80 chars (like all other CMD windows, never understood that 'feature'). This is cygwin bash running inside a CMD window, and your anaconda python will be interactive. The cygwin terminal gives you a bash shell running in a putty derivative, which mimics an xterm and cannot be used by anaconda python.

Answer 3

I too was having an issue getting anaconda set up with my Cygwin / Windows 7 system. What worked was the following:

1. Edited the ~/.bashrc. Add below to the bottom of file.

   export PATH=/cygdrive/c/Anaconda:$PATH

2. This mapped Cygwin's python to the anaconda distribution as proof by entering which python in Cygwin's console. However, when launching python it would hang up forcing me to ^C out of the command. I found that python -i will launch the interactive python interpreter with no issues.

Answer 4

There is another problem with conda's interpretation of cygwin. When you source the activation script for an environment, it prepends eg

/C/Users/Thomas.Harris/AppData/Local/Continuum/Anaconda3/envs/blah
/C/Users/Thomas.Harris/AppData/Local/Continuum/Anaconda3/envs/blah/Library/mingw-w64/bin /C/Users/Thomas.Harris/AppData/Local/Continuum/Anaconda3/envs/blah/Library/usr/bin
/C/Users/Thomas.Harris/AppData/Local/Continuum/Anaconda3/envs/blah/Library/bin
/C/Users/Thomas.Harris/AppData/Local/Continuum/Anaconda3/envs/blah/Scripts

to your PATH. However, these are not proper directories in cygwin.

I fixed this with

ln -s /cygdrive/c /C

and then if you create conda environments with specific versions of python they should work.

Answer 5

Regarding setting your path permanently, edit the .profile in your home directory (it's a hidden file).

.profile (other names are also valid, see the bash man page) contains bash commands. It is executed when bash is started as login shell.

At the bottom of this file, put your set path command:

export PATH=/cygdrive/c/anaconda:$PATH

As for why python is hanging, please provide more information - for example what's the output of python -v ?

Answer 6

I'm a little late in coming to this, but I was having the same problem as you @thomasshouler. Try adding the export line below to the end of the .bash_profile and .profile files as well as your .bashrc file (as mentioned above). Make sure to "source .bash_profile" etc for each file.

export PATH=/cygdrive/c/anaconda:$PATH

Answer 7

Found that for Anaconda 4, do:

vim /home/[Username]/.bash_profile

Append to the last line:

PATH=$PATH:/cygdrive/c/Users/[Username]/Anaconda3/Scripts/

This solution worked for me as the usual anaconda3/bin could not be found.

Answer 8

Once the Cygwin path is updated as mentioned above, you can also add an alias in the .bashrc file:

alias python='python -i'

This will bring up the Anaconda python interpreter in interactive mode from a Cygwin bash prompt