refactor align helper functions out of align.py

[joanise]

PR Goal?

align.py is a monster file doing too much stuff. This PR takes the alignment I/O out to align_utils.py.

The work was inspired by #170, which is non essential, but I decided to do it because it makes the code somewhat cleaner, and the Heroku image leaner.

Not done: I'm not sure how to declare, when updating requirements.txt from pyproject.toml, to exclude soundswallower... (added documentation to do it on update).

Fixes?

Fixes #170

Priority?

low

Tests added?

This was almost all already covered by existing tests. I just had to do minor tweaks on the heroku workflow to streamline it.

Confidence?

high

Version change?

no

[semanticdiff-com]

Review changes with  

Changed Files

File	Status
readalongs/web_api.py	97% smaller
readalongs/cli.py	58% smaller
readalongs/align.py	2% smaller
.github/workflows/tests.yml	Unsupported file format
bin/post_compile	Unsupported file format
readalongs/align_utils.py	0% smaller
readalongs/api.py	0% smaller
readme-heroku.md	Unsupported file format
requirements.txt	Unsupported file format
test/test_force_align.py	0% smaller
test/test_make_xml_cli.py	0% smaller

[codecov]

Codecov Report

Attention: Patch coverage is 98.36066% with 3 lines in your changes missing coverage. Please review.

Project coverage is 88.08%. Comparing base (17073b6) to head (cb053cd).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
readalongs/align_utils.py	98.29%	1 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #259      +/-   ##
==========================================
+ Coverage   88.04%   88.08%   +0.03%     
==========================================
  Files          21       22       +1     
  Lines        1824     1830       +6     
  Branches      330      330              
==========================================
+ Hits         1606     1612       +6     
  Misses        180      180              
  Partials       38       38              

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[roedoejet]

straightforward refactor - thanks @joanise !