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Overhaul SE #52

Merged
merged 48 commits into from
Dec 28, 2023
Merged

Overhaul SE #52

merged 48 commits into from
Dec 28, 2023

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jkanche
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@jkanche jkanche commented Dec 1, 2023

This branch is almost a rewrite of the entire package.

  • Implements functional paradigm to access and set attributes.
  • Can initialize SE/RSE without assays, also initialize an empty SE/RSE
  • row_data and column_data are expected to be BiocFrame objects and will be converted if a pandas DataFrame is provided. This will allows us to reduce complexity and provide consistent downstream operations. If these are not provided, an empty BiocFrame is set as default.
  • On RSE, if row_ranges is not provided, an empty GenomicRangesList is set as default.
  • SE/RSE now contain row_names and column_names that are separate from row_data's and column_data's row names, also helps in simplifying subset operations.
  • Printing SE/RSE objects now looks almost similar to R/Bioc's printing of these objects.
  • Support combine operations, both strict and a flexible combine option when rows or columns do not exactly match.
  • Streamlines subset operation for both SE & RSE.
  • Reduce dependency on a number of external packages.
  • Update docstrings, tests and docs.

@jkanche jkanche marked this pull request as draft December 1, 2023 04:07
pre-commit-ci bot and others added 23 commits December 1, 2023 04:07
@jkanche jkanche marked this pull request as ready for review December 27, 2023 19:31
@jkanche jkanche requested a review from LTLA December 27, 2023 19:33
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jkanche commented Dec 27, 2023

@LTLA do the combine functions make sense?

@jkanche jkanche merged commit df1fa2a into master Dec 28, 2023
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@jkanche jkanche deleted the overhaul-se branch December 28, 2023 03:29
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jkanche commented Dec 28, 2023

FYI: @keviny2 this is finally done. checkout combine_* and relaxed_combine_* operations. you may want to check these out for your package.

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