Spring Code Cleaning

[EdgarMao]

It's spring time! An overall code clean up is long overdue. Let's all take some time to organize our pipeline and improve our coding standards. The following is a list of things we need to do for spring cleaning, feel free to comment on this issue to add to the list.

Code Standard Improvement
Improve the pylint scores of all scripts:

• align
• combine
• fitsio
• secid
• _cli
• display
• init
• snr_function
• test_cmd
• collate
• extract
• ref

Other pylint related issues:

• Removing character limits in a line (or increase the character limit to 200)

Documentation Page Improvement
Check and update the comments in our scripts to make sure they are compatible with Sphinx's auto documentation generation feature:

• align
• combine
• fitsio
• secid
• _cli
• display
• init
• snr_function
• test_cmd
• collate
• extract
• ref

The following is an example for how to create comments compatible with sphinx:

def extract(hduls, stddev_thresh=3.0, read_ext="SUB", write_ext="XRT"):
    """
    Uses sep to find sources on a residual image(s)
    :param hduls: a list of HDUL to use as science data
    :param thresh: a threshold value for source extraction in terms of
        # of stddevs above background noise
    :param read_ext: the HDUL index to use as the base image. Default is 0. For
        LCO, 'SCI' would do the trick; for others 'PRIMARY'.
    :param write_ext: the HDUL index to write the catalog to. Default is 'XRT'
        for eXtRacT (close enough). Can also be a tuple (extname, extver)
    :return: a list of HDUL, each with a new `write_ext` HDU appended that is a
        record of extracted sources
    """

For more information on how to work with sphinx, please reference:
Our wiki on sphinx documentation
The Sphinx documentation page

Other documentation page related issues:

• Add automodule for all new functions to index.rst

• Add other necessary comments/messages we need on the documentation page

• Regenerate the documentation page after all the aforementioned steps are done and push to master

[agthomas-ucsb]

Testing with some exemptions can be accessed via:
pylint --rcfile=/etc/pylintrc --ignored-classes=astropy.units secid.py FILENAME