MRG: make sourmash plot labels/indices arguments make sense

[ctb]

This PR rationalizes sig plot arguments for --labels (show names) and --indices (show numbers), and adds --no-labels and --no-indices, as follows. See #2667 for motivating bug.

1. sourmash plot compare-demo - labels on dendrogram, labels on matrix ✅ (FIXED)

2. sourmash plot compare-demo --labels - labels on both dendrogram and matrix ✅

3. sourmash plot compare-demo --indices - indices on both dendrogram and matrix ✅

4. sourmash plot compare-demo --labels --indices - labels on both ✅ (FIXED - labels override indices)

New arguments from this PR:

5. sourmash plot compare-demo --no-labels - indices on both ✅

6. sourmash plot compare-demo --no-labels --no-indices - no labels/indices on either ✅

7. sourmash plot compare-demo --no-indices - labels on both ✅

The PR also simplifies some of the plot command code as well as code in fig.py.

TODO:

• write some tests for new args
• update documentation
• check to see if notebook code should be updated

Fixes #2667
Closes #2672

[codecov]

Codecov Report

Merging #2790 (b90f761) into latest (24bf474) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           latest    #2790   +/-   ##
=======================================
  Coverage   86.26%   86.27%           
=======================================
  Files         130      130           
  Lines       14742    14750    +8     
  Branches     2621     2623    +2     
=======================================
+ Hits        12717    12725    +8     
  Misses       1724     1724           
  Partials      301      301           

Flag	Coverage Δ
hypothesis-py	25.81% <0.00%> (-0.02%)	⬇️
python	92.85% <100.00%> (+<0.01%)	⬆️
rust	50.92% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
src/sourmash/cli/plot.py	100.00% <100.00%> (ø)
src/sourmash/commands.py	91.48% <100.00%> (+0.08%)	⬆️
src/sourmash/fig.py	88.37% <100.00%> (-0.76%)	⬇️

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[ctb]

Ready for review @sourmash-bio/devs !

Note that the code coverage annotations in the diff are not correct. Not sure what's going on there - I'm going to try rerunning the tests.

[ctb]

well, the code cov report is correct, even if the github diff display is not. 🤷

[AnneliektH]

Arguments all work correctly for my data:

• --no-indices shows no indices, but shows labels
• --no-labels gives no labels, but shows indices
• --no-labels --no-indices gives neither
• --labels --indices chooses labels over indices.

The way indices work make sense, but got me confused for a second, as it starts with 0, and i worked with a dataset named Sample_1 - Sample_10. Sample_1 is 0 in the indices, Sample_10 is 1 in the indices. Which makes sense from a computer perspective, but maybe less from a human perspective.

[ctb]

thanks @AnneliektH ! b90f761 changes the indices to be 1-based. I'll merge when tests pass here!