MRG: support proper manifest creation with --relpath for sig check and sig collect

[ctb]

This PR updates sig collect and sig check so that they can produce standalone manifests that work properly with default sourmash loading behavior. The default behavior produces broken manifests in some situations and is not changed, but will be deprecated in v5.

Details

Currently, sig collect and sig check default to producing standalone manifests with internal path locations relative to the current working directory. This conflicts with the default StandaloneManifest behavior implemented in save_load.py that loads path locations relative to the manifest location. As a result, whenever the manifest was in a subdirectory, the standalone manifests output by sig check and sig collect were broken. The only way to make good manifests in this situation was to use sig collect --abspath, but sig check didn't support --abspath, and using absolute paths is brittle in situations where you want to distribute manifests.

This PR adds --relpath to both sig check and sig collect, and adds --abspath to sig check. It also demonstrates the bad behavior in tests and annotates the tests appropriately.

See #3008 (comment) for more detailed discussion of why I think --relpath is the right behavior for the future.

• adds --abspath and --relpath to sig check, to properly support relative paths;
• adds --relpath to sig collect, to properly support relative paths;
• documents this behavior properly for creating standalone manifests;
• create issue to change default sig check and sig collect behavior for v4, and disable cwd behavior.

Techie TODO:

• explicitly test relpath and abspath behavior in sig check;
• explicitly test relpath behavior in sig collect
• write some tests for sig check and sig collect to explore the relative path loading issue, with all three combinations of relpath: mf in cwd, sigs in subdir; mf in subdir, sigs in cwd; mf in subdir, sigs in subdir.

Related issues:

• Addresses standalone manifests and storage and internal_location - what do we recommend? #3008
• Addresses issues in can we turn picklists + collections into manifests? #3048 by updating sig check to support --relpath;
• Fixes relative path interpretation for manifests is a little fubar #3053 - --relpath again

[codecov]

Codecov Report

Attention: Patch coverage is 97.50000% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 86.79%. Comparing base (d578157) to head (1e3688a).

Files	Patch %	Lines
src/sourmash/sig/__main__.py	96.96%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           latest    #3054      +/-   ##
==========================================
+ Coverage   86.78%   86.79%   +0.01%     
==========================================
  Files         136      136              
  Lines       15524    15559      +35     
  Branches     2626     2635       +9     
==========================================
+ Hits        13472    13505      +33     
- Misses       1751     1752       +1     
- Partials      301      302       +1     

Flag	Coverage Δ
hypothesis-py	25.46% <0.00%> (-0.08%)	⬇️
python	92.86% <97.50%> (+<0.01%)	⬆️
rust	61.21% <ø> (ø)

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[ctb]

Ready for review & merge @sourmash-bio/devs !

[bluegenes]

lgtm! This will definitely help with manifest utility 🎉