Packaging Python Projects

robraddi commented 5 years ago

Reminder that packaging via pip and conda have issues (possibly from closed issue — #54 ) The issue #54 was fixed by placing mdtraj inside a separate requirements.txt, but this may have caused this current issue: BICePs is able to be installed via pip (found in package manager list), but ...

the code is not installing from egg

robraddi commented 4 years ago

Here is an error message that I just received when creating a new environment (python 2.7) and attempting to install biceps via pip.

(py2)
PATH= ~
--> pip install biceps
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting biceps
  Downloading https://files.pythonhosted.org/packages/ee/d4/a6e0db0982811d0437ba3183f8e12ae77f009d9cfb7712a735581193447b/biceps-2.0b0-py2-none-any.whl
Collecting cython>=0.28 (from biceps)
  Downloading https://files.pythonhosted.org/packages/eb/a2/94619e1ff36f10ced5ae5b86053a25de36f52591cef2be11a4434f5e2869/Cython-0.29.12-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (2.8MB)
     |████████████████████████████████| 2.8MB 1.8MB/s
Collecting numpy>=1.7.0 (from biceps)
  Downloading https://files.pythonhosted.org/packages/8f/0b/1a2c21bb69138337dc079841aa4a45e5b2fc7a4260c0907f5254fb08f02e/numpy-1.16.4-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.9MB)
     |████████████████████████████████| 13.9MB 4.6MB/s
Collecting mdtraj==1.9.1 (from biceps)
  Using cached https://files.pythonhosted.org/packages/af/93/8ad08f58668db6e3bf85e402c9c753fa4425c249de276b55f20c08e3fff7/mdtraj-1.9.1.tar.gz
    ERROR: Complete output from command python setup.py egg_info:
    ERROR: --------------------------------------------------------------------------------
    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.
    --------------------------------------------------------------------------------
    ----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/51/0y80t4jx71jcgpyqxn5p39w80000gn/T/pip-install-BwFImS/mdtraj/

robraddi commented 4 years ago

Notes (continued):

What had previously worked on VAV6 no longer works on macOS Mojave version 10.14.6 Anaconda 4.7.5 with environment using python 2.7

I was forced to manually install:

numpy
cython
six  (???)
1) pip install biceps  --------- had trouble with mdtraj again....
2) attempted to install mdtraj via pip ---- failed (error: could not build wheels for mdtraj, which use PEP517)
- receiving error messages with pip
3) used pip install --upgrade pip  (19.1.1 --> 19.2.1)
- made no difference... PEP517 error from mdtraj
4) pip install pymbar (successful)
5) mdtraj fails with PEP517
ERROR: Could not build wheels for mdtraj which use PEP 517 and cannot be installed directly

robraddi commented 4 years ago

conda install -c omnia mdtraj (successful) 

pip install biceps (unsuccessful -- module not found.)

: (

robraddi commented 4 years ago

pip install biceps is now successful. Moving onto condo install.

Future work:

2to3 biceps/* for python 3 compatibility.

vvoelz / biceps