Pydeseq2

What's Changed
* BLD remove `jupyter` from requirements by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/120
* MAINT Expand anndata compatibility by scottgigante-immunai in https://github.com/owkin/PyDESeq2/pull/115
* DOC update readthedocs index (n-level factors are supported) by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/126
* BUG fix `deseq2_norm` bug when applied to a pandas dataframe by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/127
* DOC add bioconda install option to README by mikecuoco in https://github.com/owkin/PyDESeq2/pull/129
* ENH Implement fitType="mean" for vst by scottgigante-immunai in https://github.com/owkin/PyDESeq2/pull/123
* BUG `beta` not initialized in `irls_solver` when the design is not a full rank matrix by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/133
* BUG wrong `lfc_shrink` sign display by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/131
* REL set version to 0.3.4 by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/134

New Contributors
* scottgigante-immunai made their first contribution in https://github.com/owkin/PyDESeq2/pull/119
* mikecuoco made their first contribution in https://github.com/owkin/PyDESeq2/pull/129

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3.3...v0.3.4

What's Changed
* BUG fix slogdet bug due to pandas 2.0 upgrade by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/110
* ENH allow setting the reference level in `DeseqDataSet` by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/109

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3.2...v0.3.3

What's Changed
* BUG fix dispersion prior variance by mikelove in https://github.com/owkin/PyDESeq2/pull/105
* BUG fix `fit_alpha_mle` optimization parameterization by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/107

New Contributors
* mikelove made their first contribution in https://github.com/owkin/PyDESeq2/pull/105

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3.1...v0.3.2

What's Changed
* ENH allow initializing a DeseqDataSet from an AnnData object by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/96
* ENH variance stabilizing transformation (VST) by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/99
* ENH multi-level design support by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/101
* BUG fix size factor fitting with zeroes in each gene by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/98
* DOCS add shiny pydeseq2 logo by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/103


**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3...v0.3.1

Summary
Version 0.3 introduces a breaking change: using [AnnData](https://anndata.readthedocs.io/en/latest/) as a base class for `DeseqDataSet`, towards the integration of PyDESeq2 to the [scverse ecosystem](https://scverse.org/packages/#ecosystem).

What's Changed
* DOC add contribution guidelines by maikia in https://github.com/owkin/PyDESeq2/pull/49
* DOC transforming minimal notebook to become example by maikia in https://github.com/owkin/PyDESeq2/pull/33
* BENCH remove support for TCGA data by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/54
* DOC add mybinder to examples by maikia in https://github.com/owkin/PyDESeq2/pull/55
* DOC improve the "Getting Started" notebook from the example gallery by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/56
* DOC Convert step-by-step notebook to example by maikia in https://github.com/owkin/PyDESeq2/pull/58
* BUG Fix add missing `joblib_verbosity` argument in `fit_genewise_dispersions` by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/61
* DOC: refactoring by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/59
* DOC Update issue templates: bug by maikia in https://github.com/owkin/PyDESeq2/pull/63
* DOC Update issue templates: feat by maikia in https://github.com/owkin/PyDESeq2/pull/65
* DOC Community by maikia in https://github.com/owkin/PyDESeq2/pull/64
* BUG fix DeseqStats test of `dds`'s `replaced` attribute by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/62
* DEP removing the `notebooks`directory by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/67
* DOC Moving docs' requirements into the actual docs' requirements file by mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/72
* BUG set `dds.replaced` to `False` if cohorts don't have enough samples by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/70
* DOC development roadmap by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/24
* CI Basic code coverage by mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/74
* TST Unit test for nb_nll by mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/75
* CI update workflow by maikia in https://github.com/owkin/PyDESeq2/pull/80
* CI add more versions of python to the github workflow by maikia in https://github.com/owkin/PyDESeq2/pull/81
* MAIN Adding code owners by mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/82
* ENH `Anndata` integration by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/66
* ENH implement a getter for normalized counts by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/79
* ENH Support type hinting using `mypy` by illumination-k in https://github.com/owkin/PyDESeq2/pull/68
* DOC fix broken RTD example gallery by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/83
* DOC Improve parameter type display by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/87

New Contributors
* mandreux-owkin made their first contribution in https://github.com/owkin/PyDESeq2/pull/72
* illumination-k made their first contribution in https://github.com/owkin/PyDESeq2/pull/68

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.2.1...v0.3

What's Changed
* DOC rearrange home page by maikia in https://github.com/owkin/PyDESeq2/pull/31
* ENH Index sorting by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/30
* ENH Paired multi-factor analysis by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/32
* BUG debug DeseqStats constrasts by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/40
* BUG calculate Cooks distances with few samples by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/44
* MAINT remove deprecated `_change_lfc_sign` attribute of the `DeseqStats` class by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/47
* BUG raise error when cooks outliers should have been refitted but were not by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/48

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.1.1...v0.2.1