Cleanup for dev env and CLI entry.

[jonn-smith]

• Missed a cython requirement in pysam.
• Tested with a fresh checkout and cython is now required for development.
• Fixed main module entry point. Somehow this was not tested correctly.

[winni2k]

PS: @jonn-smith I assume you plan on using cython for something else down the line and that's why you are adding it now?

[jonn-smith]

@winni2k Not right now, however when I made a clean checkout I ran into a problem involving cython and pysam:

$ pip install -e .
Obtaining file:///juffowup/tesserae2
Requirement already satisfied: numpy in ./venv/lib/python3.6/site-packages (from tesserae==1.2.0)
Collecting pysam (from tesserae==1.2.0)
  Using cached https://files.pythonhosted.org/packages/25/7e/098753acbdac54ace0c6dc1f8a74b54c8028ab73fb027f6a4215487d1fea/pysam-0.15.4.tar.gz
    Complete output from command python setup.py egg_info:
    # pysam: no cython available - using pre-compiled C
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-r2_6rwvn/pysam/setup.py", line 193, in <module>
        .format(fn))
    ValueError: no cython installed, but can not find pysam/libchtslib.c.Make sure that cython is installed when building from the repository

[winni2k]

I see. It looks like there have been some cython related issues with pysam-0.15.4 (https://github.com/pysam-developers/pysam/issues/860#issuecomment-576194976). It also appears that if this is the issue, then it won't be fixed just yet. It looks like an alternative might be to downgrade to pysam-0.15.3, but let's stick with installing cython for now. Perhaps we can remove it when the next pysam version comes out.

[jonn-smith]

Oh, interesting.

Yeah - I can imagine us wanting to use cython eventually, so in the mean time it's not a stretch to leave it in.