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[WIP] Refactor subject database and signature loading for search, gather, and multigather. #934

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[WIP] Refactor subject database and signature loading for search, gather, and multigather. #934

wants to merge 25 commits into from

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ctb
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@ctb ctb commented Apr 4, 2020 •
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(This PR is probably getting abandoned, in favor of an approach based on selectors #1072)

Fixes #809

Lots of work still to be done.

  • 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?

@ctb ctb mentioned this pull request Apr 5, 2020
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ctb added 22 commits April 5, 2020 08:21
@ctb
added utility functions for loading signatures and databases, + params
a096a90
@ctb
added tests for failed selector check
18c5884
@ctb
implement add_database functionality
709b3e0
@ctb
add query signature selection test
39e8365
@ctb
made basic gather code work again
51f49f4
@ctb
fix some minor typos/bugs
aaf460c
@ctb
get tests working, mostly
d385f55
@ctb
fix missing import
268e1fe
@ctb
add selector framework to Index and moltype property to SourmashSigna…
c7a1331 
…ture
@ctb
add selector framework to Index and moltype property to SourmashSigna…
ff7bc9a 
…ture
@ctb
move moltype property to MinHash object
4ca476a
@ctb
add tests for MinHash.moltype property
97926f7
@ctb
remove whitespace
5a98b90
@ctb
test LinearIndex selector function
0f0867b
@ctb
add another selector test, this time for moltype
f5fbcbb
@ctb
Merge branch 'refactor/add_index_selectors' into refactor/load_dbs
b8ed293
@ctb
comments added to the gather command
2cb891c
@ctb
remove moltype from SourmashSignature
38c4d33
@ctb
better error handling, add new structure into 'search'
1c77365
@ctb
comment out debug print
75dfd6c
@ctb
found and fixed a test for improved functionality
8e598cc
@ctb
most tests working, now need to work on scaled vs num
81a1368
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sonarqubecloud bot commented Apr 7, 2020

SonarCloud Quality Gate failed.

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities (and Security Hotspot 0 Security Hotspots to review)
Code Smell A 23 Code Smells

No Coverage information No Coverage information
5.4% 5.4% Duplication

This was referenced May 3, 2020
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@ctb ctb mentioned this pull request Jul 2, 2020
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@bluegenes bluegenes mentioned this pull request Jul 11, 2020
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@ctb ctb mentioned this pull request May 15, 2021
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ctb commented Mar 30, 2022

addressed in #1406

@ctb ctb closed this Mar 30, 2022
@ctb ctb deleted the refactor/load_dbs branch March 30, 2022 03:28
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Successfully merging this pull request may close these issues.

sourmash gather doesn't automatically figure out ksize from database
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