sourmash-bio/sourmash

Split SBT into a submodule

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#177 opened on Apr 17, 2017

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5.0help wantedsbt

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Description

SBT is growing, and is now spread in three different places:

  • sourmash_lib.sbt: the standard SBT implementation, using bloom filters for internal nodes and leaves.
  • sourmash_lib.sbtmh: the MinHash extensions, with a leaf node for MinHashes and a search function.
  • sourmash_lib.sbt_storage: Different storage backends for SBTs

The proposal is to create a new sbt submodule in sourmash, and move the separate files into a new structure:

  • sourmash_lib.sbt, also containing possible subcommand options for SBTs
  • sourmash_lib.sbt.mh
  • sourmash_lib.sbt.storage

Contributor guide

Research direction
Create a new submodule 'sbt' under 'sourmash lib' and move the existing files (sourmash lib/sbt.py, sourmash lib/sbtmh.py, sourmash lib/sbt storage.py) into it. Update imports and init .py files accordingly. Ensure tests still pass.
Tech stack
python
Domain
data
Issue type
Refactor
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Python
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60