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ENH Anndata integration #66

Merged
merged 44 commits into from
Feb 16, 2023
Merged

ENH Anndata integration #66

merged 44 commits into from
Feb 16, 2023

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BorisMuzellec
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@BorisMuzellec BorisMuzellec commented Jan 26, 2023 •
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This PR aims to support the AnnData data structure towards the integration of pydeseq2 to scverse (#15).

More precisely:

  • The DeseqDataSet class now extends the AnnData class. As such, it inherits from all methods and attributes of AnnData, and parameters (such as size_factors and LFCs) are now stored in the relevant AnnData fields (e.g. obsm and varm),
  • DeseqStats was updated accordingly,
  • Pytests were updated,
  • The sphinx documentation was adapted to handle the AnnData class inheritance,
  • The "Getting Started" notebooks from the sphinx-gallery were updated.

@BorisMuzellec
refactor: switching to AnnData up to genewise dispersion estimation (…
d06120f 
…WIP)
@BorisMuzellec
refactor: switch to AnnData up to fit_dispersion_trend (WIP)
40a81c4
@BorisMuzellec
refactor: switch to AnnData up to calculate_cooks (WIP)
b5a65b6
@BorisMuzellec
refactor: switch to AnnData up to refit_cooks (WIP)
154ba2f
@BorisMuzellec
refactor: porting DeseqStats to anndata (wip)
be8b305
@BorisMuzellec
refactor: port DeseqStats to anndata (wip)
3501712
@BorisMuzellec
refactor: adapting _cooks_filtering to anndata (wip)
c66ba27
@BorisMuzellec
refactor(DeseqStats): port _cooks_filtering to AnnData, now running o…
03b3b86 
…n synthetic outlier-less dataset (wip)
@BorisMuzellec
refactor: step-by-step pipeline running bug-free with anndata
8abb567
@BorisMuzellec
fix(anndata transition): debug behavior when one or more genes have z…
0371a9a 
…eros everywhere
@BorisMuzellec
fix(anndata transition): debug behavior when there are Cooks outliers
c159e64
@BorisMuzellec
refactor: update tests for anndata compatibility
ddf7474
@BorisMuzellec
refactor: DeseqDataSet now extends AnnData
6bfbd82
@BorisMuzellec
refactor: remove counts / clinical index checks, which are performed …
9e36469 
…by AnnData
@BorisMuzellec
refactor: update pytests now that DeseqDataSet extends Anndata
a721932
@BorisMuzellec
ci: remove docstring tests for methods that are inherited from AnnData
faa49be
@BorisMuzellec
docs: remove obselete docstring fields
213b56e
@BorisMuzellec
docs: update docstrings
f5a9985
@BorisMuzellec
refactor(DeseqDataSet): improve handling of all-zero genes
43785cd
@BorisMuzellec
refactor(DeseqStats): clean up comments
0ccda9b
@BorisMuzellec
fix merge conflicts
dfc271e
@BorisMuzellec
refactor: require anndata at installation
11c72b3
@BorisMuzellec
fix: typo
b03423b
@BorisMuzellec
ci: update pytest exceptions to reflect file name change (DeseqDataSe…
ee1a989 
…t.py -> dds.py
@BorisMuzellec
ci: update pytest exceptions to reflect file name change (DeseqDataSe…
6973e1d 
…t.py -> dds.py
@BorisMuzellec
docs: disable auto-generation
a3f9092
@BorisMuzellec
docs: update sphinx examples to reflect anndata integration
8f59204
@BorisMuzellec
docs: update docstrings
832157f
@BorisMuzellec
docs: remove __init__ method from API docs
b1fb51f
@BorisMuzellec
docs: update docstrings
d77a407
@BorisMuzellec BorisMuzellec marked this pull request as ready for review January 30, 2023 16:15
@BorisMuzellec BorisMuzellec marked this pull request as draft January 31, 2023 15:59
@BorisMuzellec BorisMuzellec marked this pull request as ready for review February 1, 2023 16:13
@ghost ghost mentioned this pull request Feb 9, 2023
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ghost
ghost reviewed Feb 9, 2023
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Congrats for the big refactoring work @BorisMuzellec ! The code seems correct to me. I have many cosmetic remarks that we can discuss in the comments. I think we'll be able to merge at the second pass.

docs/source/api/docstrings/pydeseq2.dds.DeseqDataSet.rst Show resolved Hide resolved
docs/source/api/docstrings/pydeseq2.ds.DeseqStats.rst Show resolved Hide resolved
docs/source/api/docstrings/pydeseq2.grid_search.rst Show resolved Hide resolved
docs/source/api/docstrings/pydeseq2.utils.rst Show resolved Hide resolved
docs/source/api/docstrings/pydeseq2.preprocessing.rst Show resolved Hide resolved
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@ghost ghost added the enhancement New feature or request label Feb 10, 2023
@BorisMuzellec BorisMuzellec changed the title Anndata integration ENH Anndata integration Feb 13, 2023
@BorisMuzellec BorisMuzellec requested a review from a user February 13, 2023 16:24
ghost
ghost approved these changes Feb 16, 2023
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🎉 Let's merge! Thanks for all the changes @BorisMuzellec

@BorisMuzellec BorisMuzellec merged commit f9653d2 into main Feb 16, 2023
@BorisMuzellec BorisMuzellec deleted the anndata branch February 16, 2023 09:12
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