[MRG] refactor ZipFileLinearCollection and SaveSignatures_ZipFile to use ZipStorage

[ctb]

This refactors ZipFileLinearCollection (reading) and SaveSignatures_ZipFile (creation) to use ZipStorage underneath, per #1441.

Fixes #1441.

In detail, this PR:

• in index.py, replaces most direct access to files via ZipFileLinearIndex.zf (a zipfile.ZipFile object) with access via sbt_storage.ZipStorage;
• in sourmash_args.py, changes SaveSignatures_ZipFile to use ZipStorage underneath;
• we also extend SaveSignatures_ZipFile to append in situations where there is an existing zipfile + manifest;
• updates sbt_storage.py:ZipStorage to play more nicely with others - basically, a few new situations are encountered so we upgrade code accordingly;
• fixes a bug in manifest.py where with_abundance was incorrectly specified to be an integer - turns out that int works on a boolean False, but not a string 'False' ;)
• updates and adds tests for new behaviors.

Notes

This is a mostly-clean PR, with one exception - in ZipFileLinearIndex, we have to break Storage encapsulation and go directly to the zipfile to get a list of all files, in cases where there is no manifest. (Listing all files is not an option supported through the current Storage interface.) There are two options for fixing this -

1. provide a way to list all (relevant) files in a Storage. It's not clear to me that this is a good idea, because a Storage may contain many files and many signatures.
2. require manifests when using zipfile collections. This seems fine to me, but would (I think) require a 5.0 release.

Ultimately I think we will probably want to implement both, but not today :)

(In this PR, we do require manifests in order to append signatures to an existing zipfile, but they are not required to read from an existing zipfile.)

TODO:

• test on some wonky, hand-constructed .zip files

[ctb]

@luizirber this is another PR you can look at; it doesn't have a lot of extraneous picklist and manifest stuff in it.

[codecov]

Codecov Report

Merging #1598 (9c530a5) into add/picklist_zf_manifests (39abe57) will increase coverage by 0.54%.
The diff coverage is 93.33%.

@@                      Coverage Diff                      @@
##           add/picklist_zf_manifests    #1598      +/-   ##
=============================================================
+ Coverage                      87.53%   88.08%   +0.54%     
=============================================================
  Files                             77       77              
  Lines                           6933     6942       +9     
  Branches                        1251     1250       -1     
=============================================================
+ Hits                            6069     6115      +46     
+ Misses                           637      600      -37     
  Partials                         227      227              

Flag	Coverage Δ
python	88.08% <93.33%> (+0.54%)	⬆️

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

Impacted Files	Coverage Δ
src/sourmash/sourmash_args.py	92.41% <88.00%> (-1.31%)	⬇️
src/sourmash/index.py	88.92% <100.00%> (+6.88%)	⬆️
src/sourmash/sbt_storage.py	90.86% <100.00%> (+0.96%)	⬆️
src/sourmash/signature.py	92.38% <0.00%> (+0.95%)	⬆️

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[codecov-commenter]

Codecov Report

Merging #1598 (4bfe8a9) into latest (5accf22) will increase coverage by 6.68%.
The diff coverage is 91.93%.

@@            Coverage Diff             @@
##           latest    #1598      +/-   ##
==========================================
+ Coverage   83.42%   90.11%   +6.68%     
==========================================
  Files         113       87      -26     
  Lines       12107     8413    -3694     
  Branches     1555     1557       +2     
==========================================
- Hits        10100     7581    -2519     
+ Misses       1749      574    -1175     
  Partials      258      258              

Flag	Coverage Δ
python	90.11% <91.93%> (+<0.01%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/sbt_storage.py	90.95% <66.66%> (+0.58%)	⬆️
src/sourmash/sourmash_args.py	92.70% <90.00%> (-1.12%)	⬇️
src/sourmash/index.py	95.95% <100.00%> (+0.41%)	⬆️
src/sourmash/manifest.py	90.26% <100.00%> (ø)
src/core/src/cmd.rs
src/core/src/lib.rs
src/core/src/signature.rs
src/core/tests/minhash.rs
src/core/src/index/mod.rs
... and 24 more

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[ctb]

note to self: I might use this, or a related PR, to write some simple tests demonstrating FSStorage and ZipStorage as encouragement and partial documentation in support of #1752.

[ctb]

Ready for review @mr-eyes @luizirber!

[mr-eyes]

Ready for review @mr-eyes @luizirber!

TFTM, I'm on it.

[mr-eyes]

LGTM!