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[MRG] add initial progress reporting wrapper for load_file_as_signatures #1083

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merged 12 commits into from
Jul 13, 2020

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ctb
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@ctb ctb commented Jul 5, 2020

Partial fix for #1082

% sourmash sig describe podar-ref.sbt.zip  podar-ref.sbt.zip podar-ref.lca.json.gz  ../charcoal/db/gtdb-release89-k31.sbt.zip  > /dev/null

produces

loaded 64 sigs from 'podar-ref.sbt.zip'
loaded 64 sigs from 'podar-ref.sbt.zip'
loaded 64 sigs from 'podar-ref.lca.json.gz'
...loading from '../charcoal/db/gtdb-release89-k31.sbt.zip' / 510 sigs total

This is all UX tweaking, no new tests.

  • 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 Jul 5, 2020

Codecov Report

Merging #1083 into master will increase coverage by 9.13%.
The diff coverage is 91.95%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1083      +/-   ##
==========================================
+ Coverage   83.77%   92.90%   +9.13%     
==========================================
  Files          99       74      -25     
  Lines        9005     5754    -3251     
==========================================
- Hits         7544     5346    -2198     
+ Misses       1461      408    -1053     
Flag Coverage Δ
#rusttests ?
Impacted Files Coverage Δ
sourmash/sig/__main__.py 93.03% <88.88%> (-0.35%) ⬇️
sourmash/sourmash_args.py 95.27% <94.73%> (-0.10%) ⬇️
sourmash/commands.py 86.64% <100.00%> (ø)
sourmash/sbt.py 88.85% <100.00%> (ø)
src/core/src/from.rs
src/core/tests/test.rs
src/core/tests/minhash.rs
src/core/src/ffi/minhash.rs
src/core/src/wasm.rs
src/core/src/ffi/nodegraph.rs
... and 20 more

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@ctb ctb changed the title [WIP] add initial progress reporting wrapper for load_file_as_signatures [MRG] add initial progress reporting wrapper for load_file_as_signatures Jul 6, 2020
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ctb commented Jul 6, 2020

Ready for review & merge!

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ctb commented Jul 8, 2020

hmm, while it's still open -- I might

  • add shortening of line so it fits all on one
  • double check -q behavior

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This lgtm and seems to work :). I guess my main concern is not feeling familiar enough w/ all the code to be able to easily see if there's any spots you missed adding SignatureLoadingProgress?

@ctb ctb merged commit 0804556 into master Jul 13, 2020
@ctb ctb deleted the add_sig_load_progress branch July 13, 2020 19:24
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2 participants