@GrahamcOfBorg build python27Packages.pomegranate python27Packages.pyfaidx python27Packages.cnvkit
@GrahamcOfBorg build python37Packages.pomegranate python37Packages.pyfaidx python37Packages.cnvkit

The build failure for python27Packages.pomegranate on darwin is a bit strange. When trying locally it manages to hang itself in random places. That's not a big problem since this PR improves the situation with pomegranate by removing broken = true.

Thanks for the review, I have incorporated all changes.

cc @rybern

@GrahamcOfBorg build python27Packages.pomegranate python27Packages.pyfaidx python27Packages.cnvkit
@GrahamcOfBorg build python37Packages.pomegranate python37Packages.pyfaidx python37Packages.cnvkit

@GrahamcOfBorg build python27Packages.pomegranate python27Packages.pyfaidx python27Packages.CNVkit
@GrahamcOfBorg build python37Packages.pomegranate python37Packages.pyfaidx python37Packages.CNVkit

@GrahamcOfBorg build python27Packages.pomegranate python27Packages.pyfaidx python27Packages.CNVkit
@GrahamcOfBorg build python37Packages.pomegranate python37Packages.pyfaidx python37Packages.CNVkit

@GrahamcOfBorg build python27Packages.pomegranate python27Packages.pyfaidx python27Packages.cnvkit
@GrahamcOfBorg build python37Packages.pomegranate python37Packages.pyfaidx python37Packages.cnvkit

There is a missing numpy dependency:

$ cnvkit.py 
Traceback (most recent call last):
  File "/nix/store/yg84ycby64dwgw3pznqvyrinvdfbyx5j-python2.7-CNVkit-0.9.6/bin/.cnvkit.py-wrapped", line 9, in <module>
    from cnvlib import commands
  File "/nix/store/yg84ycby64dwgw3pznqvyrinvdfbyx5j-python2.7-CNVkit-0.9.6/lib/python2.7/site-packages/cnvlib/__init__.py", line 1, in <module>
    from skgenome.tabio import write
  File "/nix/store/yg84ycby64dwgw3pznqvyrinvdfbyx5j-python2.7-CNVkit-0.9.6/lib/python2.7/site-packages/skgenome/__init__.py", line 1, in <module>
    from . import tabio
  File "/nix/store/yg84ycby64dwgw3pznqvyrinvdfbyx5j-python2.7-CNVkit-0.9.6/lib/python2.7/site-packages/skgenome/tabio/__init__.py", line 13, in <module>
    import pandas as pd
  File "/nix/store/qh3j9z3hb7jvxclbgl1rzs95wg289v5a-python2.7-pandas-0.24.2/lib/python2.7/site-packages/pandas/__init__.py", line 19, in <module>
    "Missing required dependencies {0}".format(missing_dependencies))
ImportError: Missing required dependencies ['numpy']

Also commit messages in our convention should contain the full attribute name: pythonPackages.pomegranate, pythonPackages.pyfaidx, pythonPackages.cnvkit instead of just pomegranate, pyfaidx, CNVkit

That's odd, numpy is a listed dependency, and in any case that's pandas throwing the error and numpy should be a dependency of pandas. This error isn't present in my branch but is when building with nix-review; I'll see if I can track down the commit that broke pandas.

I'm really confused, the branch builds a working executable, rebasing onto the current HEAD also results in a working executable, and rebasing onto the commit nix-review uses results in a working executable. nix-review is somehow producing a failure, but I'm lost how to debug it. Any suggestions?

I think the issue with nix-review is that it asks for python 2 and python 3 packages at the same time and this breaks the environment. When we run nix-shell manually we don't do that, so it doesn't break.

I noticed that python37Packages.cnvkit doesn't build because python37Packages.pandas is already at version 0.25.0 (python27Packages.pandas is at 0.24.2):

Collecting pandas<0.25.0,>=0.20.1 (from CNVkit==0.9.6)
  ERROR: Could not find a version that satisfies the requirement pandas<0.25.0,>=0.20.1 (from CNVkit==0.9.6) (from versions: none)

Looking at the release notes of the latest version 0.9.6 [1] it seems like it doesn't support pandas 0.25 yet.

[1] https://github.com/etal/cnvkit/releases