[MRG] fix issue with identifiers in the LCA code

[ctb]

This fixes some problems with identifiers due to the changes to SourmashSignature.name in #1179.

This should probably go into 4.0.0...

Brief writeup of my understanding of the issues so far:

• sig.name can be empty if no name is given on the signature, but this then causes problems in both sourmash lca index and LCA_Database.insert(...)
• this also revealed a problem in the reporting on identifiers in sourmash lca index - if the identifiers are identical (in this case '', but in whatever case) then the number of leftover signatures gets mis-reported.

A particularly simple situation where this arises is in the test test_index_empty_sketch_name, where we:

1. sketch some DNA sequences using sourmash sketch dna, without providing a name;
2. try to index them with lca index;
3. sig.name is now empty, which triggers a problem in LCA_Database.insert(...) with duplicate identifiers;
4. the number of unused identifiers tracked in record_no_lineage is now miscounted as 1 instead of 2, because we used a set.

This PR fixes the following issues:

• sourmash sketch and sourmash compute no longer create empty signatures from empty files and stdin;
• sourmash sketch and sourmash compute set sig.filename to empty string when filename is -;
• in sourmash lca index, record_no_lineage is now a list instead of set;
• in sourmash lca index, ident is taken from sig.filename if sig.name is empty.
• in LCA_Database, ident defaults to str(sig)

TODO:

• XX add tests for new sketch filename behavior on stdin (punted to adjust screed to allow replacement of stdin input #1348)
• add direct lca_db.insert(...) tests
• add test for new sourmash sig describe behavior

Checklist

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov]

Codecov Report

Merging #1347 (5e73f0a) into latest (6623151) will increase coverage by 5.36%.
The diff coverage is 97.11%.

@@            Coverage Diff             @@
##           latest    #1347      +/-   ##
==========================================
+ Coverage   88.74%   94.11%   +5.36%     
==========================================
  Files         123       96      -27     
  Lines       18124    14593    -3531     
  Branches     1399     1405       +6     
==========================================
- Hits        16084    13734    -2350     
+ Misses       1801      621    -1180     
+ Partials      239      238       -1     

Flag	Coverage Δ
python	94.11% <97.11%> (+0.04%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/lca/lca_db.py	92.40% <66.66%> (+0.55%)	⬆️
src/sourmash/command_compute.py	94.96% <91.66%> (-0.57%)	⬇️
src/sourmash/lca/command_index.py	91.53% <100.00%> (+1.16%)	⬆️
src/sourmash/sig/__main__.py	90.79% <100.00%> (ø)
tests/test_cmd_signature.py	100.00% <100.00%> (ø)
tests/test_lca.py	99.87% <100.00%> (+<0.01%)	⬆️
tests/test_sourmash_sketch.py	100.00% <100.00%> (ø)
src/core/src/lib.rs
src/core/src/ffi/mod.rs
src/core/src/errors.rs
... and 25 more

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[ctb]

I think this is ready, @luizirber and @bluegenes. And I think it should go into 4.0 release, because it is a problem that is triggered by #1179, which is one of the "breaking backwards compatibility" PRs going into 4.0.

[ctb]

Fixed! thanks @bluegenes!

[ctb]

thanks!