[MRG] refactor argparse.FileType out of sourmash argument handling.

[ctb]

argparse.FileType('wt') is annoying because it opens the specified file immediately upon argument parsing, which overwrites it. As shown in #571, this can destroy outputs unnecessarily.

This PR changes most of the FileType arguments in sourmash to string filenames, which are only opened at the time of write. I add a FileOutput context manager that behaves properly wrt default arguments encountered in the wild.

Fixes #571, overwriting files even on error.
May pave the way for --inplace behavior, ref #625.
Also cleans up an accidental duplication of the describe implementation 😆

• 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 #853 into master will increase coverage by 12.1%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #853      +/-   ##
==========================================
+ Coverage   79.03%   91.14%   +12.1%     
==========================================
  Files          82       69      -13     
  Lines        6874     4913    -1961     
  Branches      470        0     -470     
==========================================
- Hits         5433     4478     -955     
+ Misses       1139      435     -704     
+ Partials      302        0     -302

Flag	Coverage Δ
#pytests	?
#rusttests	?

Impacted Files	Coverage Δ
sourmash/sbt_storage.py	85.39% <0%> (-1.28%)	⬇️
sourmash/signature.py	86.59% <0%> (-0.47%)	⬇️
sourmash/sbtmh.py	84.28% <0%> (-0.23%)	⬇️
sourmash/_minhash.py	97.33% <0%> (-0.11%)	⬇️
sourmash/index.py	98.38% <0%> (-0.08%)	⬇️
sourmash/cli/__init__.py	98.83% <0%> (-0.02%)	⬇️
src/core/src/from.rs
src/core/src/sketch/minhash.rs
src/core/src/lib.rs
src/core/src/index/storage.rs
... and 13 more

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[ctb]

@luizirber would be useful to get your opinion on this when you have a chance. So far it's lookin' good to me.

[luizirber]

argparse.FileType('wt') is annoying because it opens the specified file immediately upon argument parsing, which overwrites it. As shown in #571, this can destroy outputs unnecessarily.

This PR changes most of the FileType arguments in sourmash to string filenames, which are only opened at the time of write. I add a FileOutput context manager that behaves properly wrt default arguments encountered in the wild.

Nice! I think this also fixes the output argument problem in compute in the Python CLI, mentioned at the end of #245 (comment)