filter: Reduce file size with filter_support/

[victorlin]

Description of proposed changes

Currently, filter.py at 1897 lines is large and can be difficult to work with. This PR introduces a filter_support/ directory similar to util_support/, to help reduce the size of the subcommand files.

Starting with these, up for discussion:

• FilterException -> filter_support.exceptions.FilterException
• filter_kwargs_to_str -> filter_support.output.filter_kwargs_to_str

Thinking about the future, this also allows easier sharing of functions/variables between internal engines (see #920 (comment)).

Related issue(s)

N/A

Testing

Doctests updated accordingly.

[codecov]

Codecov Report

Merging #937 (0613b21) into master (5916362) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #937      +/-   ##
==========================================
+ Coverage   59.34%   59.35%   +0.01%     
==========================================
  Files          42       44       +2     
  Lines        6011     6013       +2     
  Branches     1539     1539              
==========================================
+ Hits         3567     3569       +2     
  Misses       2185     2185              
  Partials      259      259              

Impacted Files	Coverage Δ
augur/filter.py	96.13% <100.00%> (-0.11%)	⬇️
augur/filter_support/exceptions.py	100.00% <100.00%> (ø)
augur/filter_support/output.py	100.00% <100.00%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 5916362...0613b21. Read the comment docs.

[victorlin]

Looking back at this, using filter_support/ seems to go backwards on #949 which replaced io.py+io_support/ with modular files under io/. I like that direction, but ran into some troubles replacing filter.py + filter_support/ with filter/. This is because io.py does not represent a subcommand while filter.py does, and subcommands currently require a top-level module (file) to be exposed:

augur/augur/__init__.py

Lines 134 to 145 in 0d06558

	def command_name(command):
	"""
	Returns a short name for a command module.
	"""
	def remove_prefix(prefix, string):
	return re.sub('^' + re.escape(prefix), '', string)
	package = command.__package__
	module_name = command.__name__
	return remove_prefix(package, module_name).lstrip(".").replace("_", "-")

[victorlin]

#997 is an alternative to this PR.

[victorlin]

Closing in favor of #997.