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[MRG] fix manifest load function to properly catch gzip.BadGzipFile #2375

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merged 4 commits into from
Nov 30, 2022

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ctb
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@ctb ctb commented Nov 25, 2022

The code in sourmash_args for manifest loading wasn't properly catching the gzip.BadGzipFile exception.

Fixes #2370

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codecov bot commented Nov 25, 2022

Codecov Report

Merging #2375 (0cf1bf9) into latest (8a13376) will increase coverage by 8.12%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2375      +/-   ##
==========================================
+ Coverage   84.07%   92.19%   +8.12%     
==========================================
  Files         130      101      -29     
  Lines       15061    11516    -3545     
  Branches     2212     2212              
==========================================
- Hits        12662    10617    -2045     
+ Misses       2103      603    -1500     
  Partials      296      296              
Flag Coverage Δ
python 92.19% <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/manifest.py 95.02% <ø> (ø)
src/sourmash/sourmash_args.py 93.09% <100.00%> (+0.03%) ⬆️
src/core/src/ffi/cmd/compute.rs
src/core/src/index/sbt/mhbt.rs
src/core/src/sketch/minhash.rs
src/core/src/errors.rs
src/core/src/signature.rs
src/core/src/index/linear.rs
src/core/src/sketch/hyperloglog/estimators.rs
src/core/src/index/mod.rs
... and 21 more

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ctb commented Nov 25, 2022

Ready for review & merge @sourmash-bio/devs

@ctb ctb enabled auto-merge (squash) November 30, 2022 22:30
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ctb commented Nov 30, 2022

Updated with latest PRs - ready for review ;)

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Looks good to me!

@ctb ctb merged commit dcd035d into latest Nov 30, 2022
@ctb ctb deleted the fix/badgz_manifest_load branch November 30, 2022 23:18
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Successfully merging this pull request may close these issues.

sourmash_args._load_database barfs on non-gzipped files with .gz extension
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