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Big refactor on the rust codebase #692

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merged 1 commit into from Jul 7, 2019

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commented Jul 6, 2019

(this doesn't touch anything in the current sourmash/C++ layers)

  • 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?
Big refactor on the rust codebase
save semi-working
initial bigsi
basic oracle test working
Rename Leaf to Dataset
remove storage from readdata trait
const fn
basic search working
start best_only
UKHS save and load, expose draff command
move ffi to mod dir
split ffi functions
ukhs bump
initial draff command
keeping track of unique kmers with a Nodegraph
Fix overcounting, add HLL storage
fix errors
make tests deterministic
clippy fixes
move Signature from root to submodule
move KmerMinHash into submodule
fix finch
make index consistent with other submodules
starting support for multiple signature types
move add_sequence and check_compatible to SigsTrait
use unimplemented if something is missing
initial docs and warnings cleanup
fixing tests and imports
unimplemented is better than wrong
move sbt into submodule
reorganize sbt module
insertion working for SBT
less wrong storage
fix storage
Replace derive_builder with typed_builder
testing merge func for ukhstree
using fastx parser from rust-bio
search saves output
Rename Signatures enum to Sketch
Move nodegraph into sketch
prepare skeleton
Storage args are a proper enum now
explicit sig and dataset conversion
Use syntax inspired by czbiohub/extract_kmers for codon table
  original commit: https://github.com/czbiohub/extract_kmers/blob/d036145000bff96454ec383b193f8913fc5e2b16/src/codon_table.rs
demo command for counting unique hashes in an SBT
implement sbt v4 parsing, and clean up clippy warnings
Start replacing the Factory struct with an enum
move smrs bin to src/bin
split draff commands from smrs
fix v4 loading

@luizirber luizirber force-pushed the ukhs_sig branch from 9774d7a to 274f260 Jul 6, 2019

@codecov

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commented Jul 7, 2019

Codecov Report

Merging #692 into master will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #692   +/-   ##
=======================================
  Coverage   89.11%   89.11%           
=======================================
  Files          27       27           
  Lines        4237     4237           
  Branches       39       39           
=======================================
  Hits         3776     3776           
  Misses        461      461

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@luizirber luizirber merged commit 0d69b79 into master Jul 7, 2019

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Travis CI - Pull Request Build Errored
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codecov/patch Coverage not affected when comparing 534d269...274f260
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codecov/project 89.11% remains the same compared to 534d269
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@luizirber luizirber deleted the ukhs_sig branch Jul 7, 2019

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