Pydeseq2

What's Changed
* MAINT Factor out inference routines by adamgayoso in https://github.com/owkin/PyDESeq2/pull/191
* ENH Split vst functions into fit & transform by hippolyteheuberger in https://github.com/owkin/PyDESeq2/pull/185
* REL set version 0.4.3 by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/209

New Contributors
* hippolyteheuberger and SimonGrouard made their first contribution in https://github.com/owkin/PyDESeq2/pull/185

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.4.2...v0.4.3

What's Changed
* BUG division by zero when ``num_samples == num_vars`` by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/175
* MAINT Drop iPython dependency and simple print instead by adamgayoso in https://github.com/owkin/PyDESeq2/pull/188
* CI Add ruff pre-commit hook by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/192
* CI Remove precommit from workflow by adamgayoso in https://github.com/owkin/PyDESeq2/pull/195
* CI remove test_docstrings (duplicate with ruff, which runs pydocstyle) by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/196
* DOC update frontpage with latest features and Bioinformatics paper ref by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/200
* BUG set normed_counts in sub_dds before recomputing genewise dispersions when refitting by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/207

New Contributors
* adamgayoso made their first contribution in https://github.com/owkin/PyDESeq2/pull/188
* pre-commit-ci made their first contribution in https://github.com/owkin/PyDESeq2/pull/193

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.4.1...v0.4.2

What's Changed
* ENH Added lfc null and alt hypothesis in Wald tests by vcabeli in https://github.com/owkin/PyDESeq2/pull/172
* MAINT reduce the number of arguments in ``_fit_rough_dispersions`` by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/166
* MAINT test against pre-release versions of dependencies by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/171
* REL set release version to 0.4.1 by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/173

New Contributors
* vcabeli made their first contribution in https://github.com/owkin/PyDESeq2/pull/172

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.4.0...v0.4.1

What's Changed

PyDESeq2 now supports continuous covariates!

* ENH continuous covariates by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/163
* BUG fix empty `old_ref` bug caused by split `_` by hermanzhaozzzz in https://github.com/owkin/PyDESeq2/pull/141

New Contributors
* hermanzhaozzzz made their first contribution in https://github.com/owkin/PyDESeq2/pull/141

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3.6...v0.4.0

What's Changed
* ENH Introduce quiet attribute to `DeseqDataSet` that is checked before printing status updates by noamteyssier in https://github.com/owkin/PyDESeq2/pull/146
* DOC Add I/O with pandas and pickle tutorial by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/152
* DOC Degrees of freedom corner case by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/153
* ENH Add ``plotMA()`` functionality by emmcauley in https://github.com/owkin/PyDESeq2/pull/145
* MAINT change ``clinical`` variable name to ``metadata`` by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/161
* REL set to v0.3.6 by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/162

New Contributors
* noamteyssier made their first contribution in https://github.com/owkin/PyDESeq2/pull/146

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3.5...v0.3.6

What's Changed
* CI runs every week day at 3:30 UTC by mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/135
* ENH Add plot_dispersions() by emmcauley in https://github.com/owkin/PyDESeq2/pull/137
* DOC add dds.DeseqDataSet.plot_dispersions and utils.make_scatter to… by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/138
* BUG check that `save_path` is not `None` before saving in `plot_dispersions` by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/140
* MAINT turn rank deficiency exception to warning by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/139
* BUG add ref_level argument to sub_dds when refitting cooks outliers by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/143
* REL set to version 0.3.5 by BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/144

New Contributors
* emmcauley made their first contribution in https://github.com/owkin/PyDESeq2/pull/137

**Full Changelog**: https://github.com/owkin/PyDESeq2/compare/v0.3.4...v0.3.5