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[MRG] refactor LCA_Database to support programmatic creation. #946

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merged 38 commits into from
Apr 18, 2020

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@ctb ctb commented Apr 15, 2020

#942 made it clear that programmatic creation of LCAs was ...lacking. This PR refactors the LCA_Database class by moving functionality from command_index into the LCA_Database class. It also provides incremental insertion of new signatures and brings the API further into line with the basic Index API.

TODO:

  • write some tests around newly exposed API functionality
  • consider exposing more of lca_utils at sourmash.lca level
  • test load/add/save
  • support lca db creation in sourmash index as alternative to sourmash lca index, or punt to issue (=> moved to support LCA/revindex database creation in sourmash index? #949)
  • test find_signatures/search/gather in a bit more detail, or punt to issue

  • 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?

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codecov bot commented Apr 15, 2020

Codecov Report

Merging #946 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #946   +/-   ##
=======================================
  Coverage   91.89%   91.89%           
=======================================
  Files          71       71           
  Lines        5021     5021           
=======================================
  Hits         4614     4614           
  Misses        407      407           

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@ctb ctb changed the title [WIP] refactor LCA_Database to support programmatic creation. [MRG] refactor LCA_Database to support programmatic creation. Apr 18, 2020
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ctb commented Apr 18, 2020

Ready for review!

@ctb ctb mentioned this pull request Apr 18, 2020
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@luizirber luizirber left a comment

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Good job!

@luizirber luizirber merged commit b90fad7 into master Apr 18, 2020
@luizirber luizirber deleted the refactor/lca_db_create branch April 18, 2020 23:04
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ctb commented Apr 18, 2020

yay!!

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2 participants