Add generic get_referenced_files()

[victorlin]

Description of proposed changes

This PR contains 3 prep commits and 1 main commit. Message from main commit:

Now that other commands accept config files with filepaths marked in schema, the generic get_referenced_files() function is necessary for adoption in Snakemake workflows where referenced files are to be listed as inputs for file change detection.

Some changes were necessary as the previous subsample-specific function hardcoded the schema within the function. The generic function solves this by requiring the $schema key in the config.

Keeping the subsample-specific function around because it's used by some workflows. Will remove once those workflows are updated to use the generic function.

Related issue(s)

Follow-up to #2041 (comment)

Checklist

• Automated checks pass
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs

[codecov]

Codecov Report

❌ Patch coverage is 91.20000% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 74.64%. Comparing base (130695c) to head (b1e78b7).

Files with missing lines	Patch %	Lines
augur/config.py	94.38%	2 Missing and 3 partials ⚠️
augur/subsample.py	66.66%	4 Missing ⚠️
augur/validate.py	90.90%	2 Missing ⚠️

Additional details and impacted files

@@                      Coverage Diff                       @@
##           victorlin/ancestral-config    #2049      +/-   ##
==============================================================
+ Coverage                       74.56%   74.64%   +0.08%     
==============================================================
  Files                              86       86              
  Lines                           10882    10898      +16     
  Branches                         2123     2122       -1     
==============================================================
+ Hits                             8114     8135      +21     
+ Misses                           2373     2370       -3     
+ Partials                          395      393       -2     

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[victorlin]

The newest commit f57365e is necessary for proper nextstrain run support. It's a big change and I'm inclined to move it + all type=InputFile additions to (yes, another) PR at the beginning of the stack. This way, it could be merged first to see the immediate side effects, and would simplify existing workflows by removing the need to call resolve_config_path in many places.

[victorlin]

Moved f57365e and related changes to #2051.

would simplify existing workflows by removing the need to call resolve_config_path in many places.

I was wrong about this. We'd still need resolve_config_path in the inputs block just like how we need get_referenced_files in the input block when using --config.

[victorlin]

After some more thought, I think #2051 is the wrong direction. We can resolve file paths for just values in YAML without affecting CLI. I'll plan to update this PR with that approach and close #2051.

[victorlin]

Moving these changes to #2040 since they're required for that PR to work.