Bruno's edits

[BrunoGrandePhD]

The code is already pretty polished. All I ended doing are minor edits. Here's a summary of the changes that I've made:

• I updated the docstrings to be more consistent. When listing function arguments, some docstrings used is instead of colons (:). To be consistent with the Google Python Style Guide, I've tried to switch all lists to using colons. I've also ensured that the same docstring headings were used throughout the codebase (e.g. Args:, Returns:).
• I deleted any unnecessary variables assignments, i.e. variables that are never used. There are detected automatically by my text editor. I've done the same with unnecessary module imports.
• I replaced any print statements with calls to logging.
• I added a few comments when I wasn't sure how to update the code but still had a concern. You can find these by searching the codebase for # TODO (bgrande).

Feel free to address my inline comments (tagged with # TODO (bgrande)) by pushing to this branch before merging into master. I can help with the merge once you review my pull request.

[BrunoGrandePhD]

By the way, to remove the print statements in xyalign/xyalign.py, I had to move the logging.getLogger() call to the top of the file. I'm not sure if this is correct or if it will work. Please fix as necessary.

[thw17]

Hi Bruno - Thanks!

• As I mentioned in our email, unfortunately you had just opened this pull request as I had finished switching all of the docstrings in the package over to Numpy format to be human-readable, yet easily handled by Sphinx. I would prefer to keep them in Numpy format, but open to changing if you feel strongly.

• I like the logging switch in xyalign.py. I haven't tried using it yet, but if it works, I think it's great.

• Removing unused variable and imports sounds great.

• As you were working on this, I independently changed all functions ending in "pass" to return 0 instead. I liked the idea of them returning something. Do you have strong preferences one way or the other?

• I have cleaned up the try/except block in variants.hist_read_balance. Does the version in master look good to you?

• In xyalign.py, I like the utils.validate_dir function. I also like the new "setup param dictionary" section; did you run any tests to compare its behavior to the previous code?