pip installation

[gph82]

I just created a new environment to test ipywidgets 6:

conda create --name python3.6_for_ipywidgets6 python=3.6

Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6:

The following NEW packages will be INSTALLED:

    openssl:    1.0.2k-1     
    pip:        9.0.1-py36_1 
    python:     3.6.0-0      
    readline:   6.2-2        
    setuptools: 27.2.0-py36_0
    sqlite:     3.13.0-0     
    tk:         8.5.18-0     
    wheel:      0.29.0-py36_0
    xz:         5.2.2-1      
    zlib:       1.2.8-3      

Proceed ([y]/n)? y

#
# To activate this environment, use:
# > source activate python3.6_for_ipywidgets6
#
# To deactivate this environment, use:
# > source deactivate python3.6_for_ipywidgets6
#

gph82@southsea:  ~$ source activate python3.6_for_ipywidgets6

and tried to install molpx first. Two things happen (please scroll till the bottom)

1. pip install molpx fails on installing mdtraj, even mdtraj fails on installing alone

pip install mdtraj 
Collecting mdtraj
  Downloading mdtraj-1.8.0.zip (20.2MB)
    100% |################################| 20.2MB 47kB/s 
    Complete output from command python setup.py egg_info:
    --------------------------------------------------------------------------------
    Error: building mdtraj requires numpy and cython>=0.19
    
    Try running the command ``pip install numpy cython`` or
    ``conda install numpy cython``.
    
    or see http://docs.scipy.org/doc/numpy/user/install.html and
    http://cython.org/ for more information.
    
    If you're feeling lost, we recommend downloading the (free) Anaconda python
    distribution https://www.continuum.io/downloads, because it comes with
    these components included.
    --------------------------------------------------------------------------------
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-tmlqsnoy/mdtraj/

2. after installing it myself via conda install mdtraj -c omnia, then in pip install molpx no problem until but:

Python 3.6.0 |Continuum Analytics, Inc.| (default, Dec 23 2016, 12:22:00) 
Type "copyright", "credits" or "license" for more information.

IPython 5.3.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import molpx
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-84cce9d22026> in <module>()
----> 1 import molpx

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/molpx/__init__.py in <module>()
     10 
     11 from . import generate
---> 12 from . import visualize
     13 from .nbtools import example_notebook, _molpxdir
     14 

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/molpx/visualize.py in <module>()
     12 
     13 from matplotlib import pylab as _plt
---> 14 import nglview as _nglview
     15 import mdtraj as _md
     16 from os.path import basename as _basename

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/nglview/__init__.py in <module>()
     35 # interface
     36 from .config import BACKENDS
---> 37 from .widget import NGLWidget
     38 from .base_adaptor import *
     39 from .adaptor import *

/home/mi/gph82/miniconda3/envs/python3.6_for_ipywidgets6/lib/python3.6/site-packages/nglview/widget.py in <module>()
      7 import numpy as np
      8 from IPython.display import display
----> 9 from ipywidgets import DOMWidget, widget_image
     10 from traitlets import (Unicode, Bool, Dict, List, Int, Integer, observe,
     11                        CaselessStrEnum)

ModuleNotFoundError: No module named 'ipywidgets'

I'm assuming 1) is this related to this: mdtraj/mdtraj#1119, shouldn't 2) be required by nglview itself?

[gph82]

Ok, can we afford the troubles in our requirements so that at least pip install molpx won't fail?

[marscher]

On 14.03.2017 18:50, Guillermo Pérez-Hernández wrote: Ok, can we afford the troubles in our requirements so that at least pip install molpx won't fail?

nope, mdtrajs policy ruins it all :)

[marscher]

On 14.03.2017 18:50, Guillermo Pérez-Hernández wrote: Ok, can we afford the troubles in our requirements so that at least pip install molpx won't fail?

well, you could "fake" depend on cython and numpy. But this doesn't seem to be a clean solution.

[gph82]

Yeah that's what I actually meant. It's not clean, but having a pip install that only works if some other condition is satisfied seems less clean

[gph82]

what about 2), though?

[marscher]

2. is really strange, because nglview itself depends on ipywidgets.

[gph82]

pinging @hainm

[hainm]

I have no ideas how you guys install nglview. There are many conda channels (bioconda, omnia, conda-forge) and pip. If pip, we do not specify dependences for nglview (got trouble before and don't want to deal with it). To avoid the burden of maintenance, I would suggest to stick to bioconda.

PS: I don't see why adding -c bioconda to conda install nglview is an issue for you guys. Really.

[gph82]

we're trying to create a module for which installation is easy and dependable, otherwise the conversation is something like:

• Want to use our software? Then do this, then that, then add that channel, no, not that one, the other one, yeah. Oh, forgot about that other thing. right. Okay, now, go, enjoy.