WIP: support RocksDB databases in sourmash proper through FFI

[ctb]

Still early days, but some basic stuff is working!

Build RocksDB:

sourmash sig cat tests/test-data/{2,47,63}.fa.sig -o 3sigs.sig.zip
sourmash scripts index 3sigs.sig.zip -k 31 -s 1000 -o tests/test-data/3sigs.branch_0913.rocksdb

run describe

% sourmash sig describe tests/test-data/3sigs.branch_0913.rocksdb 

== This is sourmash version 4.8.15.dev0. ==
== Please cite Irber et. al (2024), doi:10.21105/joss.06830. ==

---
signature filename: b'tests/test-data/3sigs.branch_0913.rocksdb'
signature: CP001071.1 Akkermansia muciniphila ATCC BAA-835, complete genome
source file: 2.fa
md5: f3a90d4e5528864a5bcc8434b0d0c3b1
k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0
size: 2701
sum hashes: 2701
signature license: CC0

---
signature filename: b'tests/test-data/3sigs.branch_0913.rocksdb'
signature: NC_009665.1 Shewanella baltica OS185, complete genome
source file: 47.fa
md5: 09a08691ce52952152f0e866a59f6261
k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0
size: 5177
sum hashes: 5177
signature license: CC0

---
signature filename: b'tests/test-data/3sigs.branch_0913.rocksdb'
signature: NC_011663.1 Shewanella baltica OS223, complete genome
source file: 63.fa
md5: 38729c6374925585db28916b82a6f513
k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0
size: 5238
sum hashes: 5238
signature license: CC0

loaded 3 signatures total, from 1 files

run gather

% sourmash gather SRR606249.abundtrim.sig tests/test-data/3sigs.branch_0913.rocksdb --no-prefetch

...
overlap     p_query p_match
---------   ------- -------
5.2 Mbp        1.4%   99.0%    NC_011663.1 Shewanella baltica OS223, complete...
2.7 Mbp        0.7%  100.0%    CP001071.1 Akkermansia muciniphila ATCC BAA-83...
5.2 Mbp        0.7%   51.0%    NC_009665.1 Shewanella baltica OS185, complete...
found less than 50.0 kbp in common. => exiting

[codecov]

Codecov Report

Attention: Patch coverage is 14.10256% with 134 lines in your changes missing coverage. Please review.

Project coverage is 48.77%. Comparing base (94a51c8) to head (4b3165d).
Report is 6 commits behind head on latest.

Files with missing lines	Patch %	Lines
src/sourmash/index/revindex.py	20.21%	75 Missing ⚠️
src/core/src/ffi/index/disk_revindex.rs	0.00%	57 Missing ⚠️
src/sourmash/save_load.py	60.00%	1 Missing and 1 partial ⚠️

❗ There is a different number of reports uploaded between BASE (94a51c8) and HEAD (4b3165d). Click for more details.

HEAD has 99 uploads less than BASE

Flag	BASE (94a51c8)	HEAD (4b3165d)
rust	14	1
hypothesis-py	7	1
python	80	0

Additional details and impacted files

@@             Coverage Diff             @@
##           latest    #3545       +/-   ##
===========================================
- Coverage   87.99%   48.77%   -39.22%     
===========================================
  Files         136      137        +1     
  Lines       22230    22385      +155     
  Branches     2225     2240       +15     
===========================================
- Hits        19561    10918     -8643     
- Misses       2356    11267     +8911     
+ Partials      313      200      -113     

Flag	Coverage Δ
hypothesis-py	25.40% <22.22%> (-0.04%)	⬇️
python	?
rust	81.42% <0.00%> (-0.54%)	⬇️

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