make cmdline sigs optional for index

[bluegenes]

Makes the signatures positional arg optional for sourmash index. This frees the user to only pass in signatures from a file or load a file as signatures.

This change means that the positional arguments need to be placed properly: first the index name, then zero or more signature files. To account for this, I changed the order of args in failing tests using index.

I also added an index test (test_index_metagenome_fromfile_no_cmdline_sig)that does not provide any command line sigs.

• 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.

fixes #1066

[bluegenes]

how should this change be documented? @ctb @luizirber

[codecov]

Codecov Report

Merging #1186 into latest will increase coverage by 9.05%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           latest    #1186      +/-   ##
==========================================
+ Coverage   84.12%   93.17%   +9.05%     
==========================================
  Files          99       75      -24     
  Lines        9220     5844    -3376     
==========================================
- Hits         7756     5445    -2311     
+ Misses       1464      399    -1065     

Flag	Coverage Δ
#rusttests	?

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

Impacted Files	Coverage Δ
sourmash/cli/index.py	100.00% <ø> (ø)
sourmash/signature.py	92.53% <0.00%> (-0.29%)	⬇️
sourmash/sbtmh.py	89.52% <0.00%> (-0.20%)	⬇️
sourmash/command_compute.py	97.52% <0.00%> (-0.19%)	⬇️
sourmash/nodegraph.py	93.45% <0.00%> (-0.18%)	⬇️
sourmash/minhash.py	97.11% <0.00%> (-0.16%)	⬇️
sourmash/sbt_storage.py	91.95% <0.00%> (-0.14%)	⬇️
sourmash/index.py	97.56% <0.00%> (-0.09%)	⬇️
sourmash/sbt.py	88.84% <0.00%> (-0.06%)	⬇️
sourmash/lca/lca_db.py	97.16% <0.00%> (-0.05%)	⬇️
... and 25 more

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[ctb]

this looks great - ok to merge when the tests pass! If you put the magic words "fixes #1066" up there it will also auto-close that issue (not to mention linking to the relevant issue in the first place 😜).

please document it in the migration issue over in #1069 - just explain what you did to fix the tests, in suitably general language ;).

[ctb]

note, tests appear to have failed on py 3.7 on linux. although it looks like it may not be your fault - it's in test_sbt.py, test_sbt_ipfsstorage.

[bluegenes]

yeah I saw that but didn't know how to handle - suggestions?

[luizirber]

It seems to be a known error fixed in 3.7.2 (https://bugs.python.org/issue34921). BUT! Travis uses 3.7.1. Sigh.