[MRG] Accept file list in sourmash sig cat

[luizirber]

Current behavior of sourmash sig cat doesn't support passing a file list as input. I would like to run sourmash sig cat filelist.txt and be able to load signatures from filelist.txt (one signature path per line).

I think load_file_as_signatures (called here) is missing the call to load_file_list_of_signatures?

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 #1236 into latest will increase coverage by 9.43%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #1236      +/-   ##
==========================================
+ Coverage   83.29%   92.72%   +9.43%     
==========================================
  Files         103       76      -27     
  Lines        9588     5977    -3611     
==========================================
- Hits         7986     5542    -2444     
+ Misses       1602      435    -1167     

Flag	Coverage Δ
rusttests	?

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Impacted Files	Coverage Δ
sourmash/sourmash_args.py	95.57% <100.00%> (+0.15%)	⬆️
sourmash/sbt_storage.py	86.44% <0.00%> (-5.09%)	⬇️
src/core/src/index/sbt/mhbt.rs
src/core/src/ffi/signature.rs
src/core/tests/minhash.rs
src/core/src/sketch/minhash.rs
src/core/src/ffi/cmd/compute.rs
src/core/src/signature.rs
src/core/src/index/search.rs
src/core/src/index/linear.rs
... and 19 more

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[ctb]

On Thu, Nov 05, 2020 at 01:25:52PM -0800, Luiz Irber wrote: @luizirber commented on this pull request. > @@ -402,6 +402,21 @@ def _load_database(filename, traverse_yield_all, *, cache_size=None): except Exception as exc: pass + if not loaded: # try load signatures from single file (list of signature paths) + try: + db = [] + with open(filename, 'rt') as fp: + for line in fp: + line = line.strip() + if line: + sig = sourmash.load_signatures(line, quiet=True, do_raise=True) I implemented it in `_load_database`, but the file list could potentially contains indices too (not only paths to signatures). Should this be a test case? (it wouldn't be too hard to change, I could change this line to use `load_file_as_signatures` instead...)

sure! I was thinking about doing that Back When but just got lazy :)

[luizirber]

Ready for review and merge

[ctb]

Looks good. I think there are probably some edge cases that we will discover later ;)