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[MRG] add some search/gather/prefetch columns to enable ANI estimation #1952

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merged 6 commits into from
Apr 16, 2022

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bluegenes
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@bluegenes bluegenes commented Apr 15, 2022

  • Adds columns to SearchResult, PrefetchResult, GatherResult. Need these cols for ANI estimation (+ some are helpful for general bookkeeping)
  • Use namedtuple._fields to get fieldnames instead of respecifying

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codecov bot commented Apr 15, 2022

Codecov Report

Merging #1952 (644a4dd) into latest (4080b5d) will increase coverage by 7.97%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #1952      +/-   ##
==========================================
+ Coverage   83.25%   91.22%   +7.97%     
==========================================
  Files         126       95      -31     
  Lines       13989     9710    -4279     
  Branches     1913     1913              
==========================================
- Hits        11646     8858    -2788     
+ Misses       2071      580    -1491     
  Partials      272      272              
Flag Coverage Δ
python 91.22% <100.00%> (+<0.01%) ⬆️
rust ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/sourmash/commands.py 88.55% <100.00%> (ø)
src/sourmash/search.py 97.01% <100.00%> (+0.01%) ⬆️
src/core/src/index/linear.rs
src/core/src/encodings.rs
src/core/src/ffi/utils.rs
src/core/src/ffi/index/revindex.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/sketch/nodegraph.rs
src/core/src/errors.rs
src/core/src/from.rs
... and 23 more

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@bluegenes bluegenes changed the title [MRG] add some search/gather/prefetch columns to enable ANI estimation [WIP] add some search/gather/prefetch columns to enable ANI estimation Apr 15, 2022
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ctb commented Apr 15, 2022

@bluegenes bluegenes changed the title [WIP] add some search/gather/prefetch columns to enable ANI estimation [MRG] add some search/gather/prefetch columns to enable ANI estimation Apr 15, 2022
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bluegenes commented Apr 15, 2022

if it's ok, can we just merge this and I'll tackle the other issues in a larger PR?

Dataclass is looking like a good drop-in replacement of the namedtuples after these changes + will also offer some nice simplification

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ended up going for the dataclasses changes in #1955

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a few minor things!

src/sourmash/search.py Outdated Show resolved Hide resolved
src/sourmash/search.py Outdated Show resolved Hide resolved
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thanks!

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2 participants