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Feature/v1.7.0 -- adds parquet support #114

Merged
merged 3 commits into from
Jul 8, 2022
Merged

Feature/v1.7.0 -- adds parquet support #114

merged 3 commits into from
Jul 8, 2022

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marcmaxson
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marcmaxson and others added 3 commits July 5, 2022 11:02
* Feature/v1.6.3 (#108)

* GEO download much improved and should handle more datastets; passes tests

* version fix

* changed test dataset to 450k, b/c 27k not fully supported

* correct both addressA and addressB for OOB probes when channel swapping (#111)

* correct both addressA and addressB for OOB probes

* cleaner solution to getting address A and B from lookup

* tests passing; changed ref values slightly

* Addition of negative control based pvalue calculation (#109)

* Update pOOBAH pval calculation

* added feature to output negative control based pvalue - pNegECDF_pval

Co-authored-by: Chavez, Mauro <[email protected]>

Co-authored-by: Mauro Chavez <[email protected]>
Co-authored-by: Chavez, Mauro <[email protected]>
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github-actions bot commented Jul 7, 2022

File Coverage
All files 74%
methylprep/download/array_express.py 14%
methylprep/download/geo.py 63%
methylprep/download/miniml.py 48%
methylprep/download/process_data.py 74%
methylprep/download/samplesheet_sync_idat.py 62%
methylprep/files/idat.py 95%
methylprep/files/manifests.py 92%
methylprep/files/sample_sheets.py 78%
methylprep/models/arrays.py 90%
methylprep/models/controls.py 87%
methylprep/models/probes.py 86%
methylprep/models/samples.py 80%
methylprep/models/sigset.py 83%
methylprep/models/sketchy_probes.py 62%
methylprep/processing/dye_bias.py 91%
methylprep/processing/multi_array_idat_batches.py 85%
methylprep/processing/p_value_probe_detection.py 68%
methylprep/processing/pipeline.py 85%
methylprep/processing/postprocess.py 91%
methylprep/processing/preprocess.py 92%
methylprep/utils/data_frames.py 40%
methylprep/utils/files.py 78%
methylprep/utils/parsing.py 86%
methylprep/utils/progress_bar.py 71%

Minimum allowed coverage is 40%

Generated by 🐒 cobertura-action against ed1a217

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codecov bot commented Jul 7, 2022

Codecov Report

Merging #114 (ed1a217) into master (9828e71) will decrease coverage by 0.17%.
The diff coverage is 68.29%.

@@            Coverage Diff             @@
##           master     #114      +/-   ##
==========================================
- Coverage   75.12%   74.94%   -0.18%     
==========================================
  Files          33       33              
  Lines        3746     3732      -14     
==========================================
- Hits         2814     2797      -17     
- Misses        932      935       +3     
Flag Coverage Δ
unittests 74.94% <68.29%> (-0.18%) ⬇️

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

Impacted Files Coverage Δ
methylprep/download/geo.py 63.67% <26.66%> (-0.13%) ⬇️
methylprep/processing/pipeline.py 85.18% <72.54%> (-0.16%) ⬇️
methylprep/processing/postprocess.py 91.30% <92.30%> (-0.59%) ⬇️
methylprep/models/samples.py 80.00% <100.00%> (ø)
methylprep/version.py 100.00% <100.00%> (ø)

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@marcmaxson marcmaxson merged commit 8a540ce into master Jul 8, 2022
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