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Add BGZIP reader to python read_text #11802

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merged 5 commits into from
Oct 7, 2022

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@upsj upsj commented Sep 28, 2022

Description

Adds the missing integration, plus some tests. I decided to extend the read_text interface rather than add a new one. For details on the bgzip format, see #11652

Checklist

  • I am familiar with the Contributing Guidelines.
  • New or existing tests cover these changes.
  • The documentation is up to date with these changes.

@upsj upsj added the 3 - Ready for Review Ready for review by team label Sep 28, 2022
@upsj upsj added this to the Genomics read_text support milestone Sep 28, 2022
@upsj upsj self-assigned this Sep 28, 2022
@upsj upsj requested a review from a team as a code owner September 28, 2022 14:51
@upsj upsj requested review from vyasr and galipremsagar September 28, 2022 14:51
@github-actions github-actions bot added the Python Affects Python cuDF API. label Sep 28, 2022
@upsj upsj added improvement Improvement / enhancement to an existing function non-breaking Non-breaking change labels Sep 28, 2022
python/cudf/cudf/io/text.py Outdated Show resolved Hide resolved
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upsj commented Sep 28, 2022

rerun tests

@upsj upsj linked an issue Sep 29, 2022 that may be closed by this pull request
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upsj commented Sep 29, 2022

rerun tests

@upsj upsj added the cuIO cuIO issue label Sep 29, 2022
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upsj commented Oct 3, 2022

rerun tests

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codecov bot commented Oct 3, 2022

Codecov Report

Base: 87.40% // Head: 87.50% // Increases project coverage by +0.09% 🎉

Coverage data is based on head (04a4a5a) compared to base (f72c4ce).
Patch coverage: 94.11% of modified lines in pull request are covered.

Additional details and impacted files
@@               Coverage Diff                @@
##           branch-22.12   #11802      +/-   ##
================================================
+ Coverage         87.40%   87.50%   +0.09%     
================================================
  Files               133      133              
  Lines             21833    21828       -5     
================================================
+ Hits              19084    19101      +17     
+ Misses             2749     2727      -22     
Impacted Files Coverage Δ
python/cudf/cudf/core/udf/__init__.py 50.00% <ø> (ø)
python/cudf/cudf/utils/ioutils.py 79.47% <ø> (ø)
...thon/dask_cudf/dask_cudf/tests/test_distributed.py 18.86% <ø> (+4.94%) ⬆️
python/cudf/cudf/io/text.py 91.66% <66.66%> (-8.34%) ⬇️
python/cudf/cudf/__init__.py 90.69% <100.00%> (ø)
python/cudf/cudf/core/scalar.py 90.52% <100.00%> (+1.25%) ⬆️
python/dask_cudf/dask_cudf/sorting.py 93.29% <100.00%> (+2.11%) ⬆️
python/strings_udf/strings_udf/__init__.py 86.27% <100.00%> (-10.61%) ⬇️
python/strings_udf/strings_udf/_typing.py 94.73% <0.00%> (-1.06%) ⬇️
... and 2 more

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@galipremsagar galipremsagar added 5 - Ready to Merge Testing and reviews complete, ready to merge and removed 3 - Ready for Review Ready for review by team labels Oct 7, 2022
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@gpucibot merge

@rapids-bot rapids-bot bot merged commit 4c4acd5 into rapidsai:branch-22.12 Oct 7, 2022
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Successfully merging this pull request may close these issues.

[BUG] read_text doesn't apply a default
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