Releases: owkin/PyDESeq2
Releases · owkin/PyDESeq2
v0.4.10
What's Changed
- BUG initialize
beta_init
when the design matrix is not full rank by @BorisMuzellec in #281 - MAINT Replace np.NaN with np.nan -> numpy 2.0 compat by @Zethson in #282
- BUG enable vst be used "blindly" and to fit its own dispersion by @laudmt in #268
- CHORE update code owners by @mandreux-owkin in #289
- MAINT summary function uses quiet to print by @yihming in #286
- ENH Poscount implementation & diag(XXT) optimization by @asistradition in #284
- BUG Inference n_cpus overwritten issue by @yihming in #293
- DOC specify what happens if n_cpus and inference are set by @umarteauowkin in #294
- DOC fix text format in DeseqStats docstring by @BorisMuzellec in #297
- ENH Remove count DataFrame from calculate_cooks by @asistradition in #292
- MAINT cast counts to int when initialising a DeseqDataSet from anndata by @BorisMuzellec in #299
New Contributors
- @Zethson made their first contribution in #282
- @laudmt made their first contribution in #268
- @yihming made their first contribution in #286
- @asistradition made their first contribution in #284
- @umarteauowkin made their first contribution in #294
Full Changelog: v0.4.9...v0.4.10
v0.4.9
What's Changed
- DOCS Fix latex display in sphinx doc by @tanguy-marchand in #266
- ENH Add adapt = False (prior_scale=1) option to lfc_shrink() by @awalsh17 in #267
- BUG update genewise dispersions and fitted dispersions of refitted genes by @BorisMuzellec in #274
New Contributors
- @tanguy-marchand made their first contribution in #266
- @awalsh17 made their first contribution in #267
Full Changelog: v0.4.8...v0.4.9
v0.4.8
What's Changed
- MAINT upgrade python version by @jeandut in #256
- BUG return output with same dimensions as input with mean disp fuction by @BorisMuzellec in #253
- BUG add
continuous_factors
argument tosub_dds
by @BorisMuzellec in #260
New Contributors
Full Changelog: v0.4.7...v0.4.8
v0.4.7
v0.4.6
What's Changed
- BUG fix independent filtering by @BorisMuzellec in #243
Full Changelog: v0.4.5...v0.4.6
v0.4.5
What's Changed
- MAINT Add back
n_cpus
argument inDeseqDataSet
by @vcabeli in #226 - MAINT Remove statsmodels by @BorisMuzellec in #236
- BUG Fix new all zero replace by @BorisMuzellec in #239
- TST ignore the DeprecationWarning from pandas
is_categorical_dtype
by @BorisMuzellec in #223 - DOC update sphinx requirements by @BorisMuzellec in #228
- CI ignore the deprecation warning about the future Pyarrow dependency by @BorisMuzellec in #229
- REL bump version number by @BorisMuzellec in #240
Full Changelog: v0.4.4...v0.4.5
v0.4.4
What's Changed
- BUG Fix min replicates by @BorisMuzellec in #218
- BUG use
self._backend
instead of'loky'
directly by @adamgayoso in #215
Full Changelog: v0.4.3...v0.4.4
v0.4.3
What's Changed
- MAINT Factor out inference routines by @adamgayoso in #191
- ENH Split vst functions into fit & transform by @hippolyteheuberger in #185
- REL set version 0.4.3 by @BorisMuzellec in #209
New Contributors
- @hippolyteheuberger and @SimonGrouard made their first contribution in #185
Full Changelog: v0.4.2...v0.4.3
v0.4.2
What's Changed
- BUG division by zero when
num_samples == num_vars
by @BorisMuzellec in #175 - MAINT Drop iPython dependency and simple print instead by @adamgayoso in #188
- CI Add ruff pre-commit hook by @BorisMuzellec in #192
- CI Remove precommit from workflow by @adamgayoso in #195
- CI remove test_docstrings (duplicate with ruff, which runs pydocstyle) by @BorisMuzellec in #196
- DOC update frontpage with latest features and Bioinformatics paper ref by @BorisMuzellec in #200
- BUG set normed_counts in sub_dds before recomputing genewise dispersions when refitting by @BorisMuzellec in #207
New Contributors
- @adamgayoso made their first contribution in #188
- @pre-commit-ci made their first contribution in #193
Full Changelog: v0.4.1...v0.4.2
v0.4.1
What's Changed
- ENH Added lfc null and alt hypothesis in Wald tests by @vcabeli in #172
- MAINT reduce the number of arguments in
_fit_rough_dispersions
by @BorisMuzellec in #166 - MAINT test against pre-release versions of dependencies by @BorisMuzellec in #171
- REL set release version to 0.4.1 by @BorisMuzellec in #173
New Contributors
Full Changelog: v0.4.0...v0.4.1