Scib

What's Changed
* Make rpy2 and anndata2ri optional by mumichae in https://github.com/theislab/scib/pull/339
* Fix batch silhouette bug by mumichae in https://github.com/theislab/scib/pull/342
* General optimised clustering function by mumichae in https://github.com/theislab/scib/pull/343
* Only pass max_epochs to SCVI.train if set by scottgigante-immunai in https://github.com/theislab/scib/pull/345
* add harmony by adamgayoso in https://github.com/theislab/scib/pull/317
* Fix kBET import issue by mumichae in https://github.com/theislab/scib/pull/350
* Update louvain to 0.8 by scottgigante-immunai in https://github.com/theislab/scib/pull/346

New Contributors
* scottgigante-immunai made their first contribution in https://github.com/theislab/scib/pull/345

**Full Changelog**: https://github.com/theislab/scib/compare/v1.0.4...v1.0.5

What's Changed
* Update to scvi tools again, also scgen which now uses scvi tools by adamgayoso in https://github.com/theislab/scib/pull/316
* Fix scanvi bug by mumichae in https://github.com/theislab/scib/pull/327
* Fix deprecation warning by mumichae in https://github.com/theislab/scib/pull/326
* Bump rp2y dependency by mumichae in https://github.com/theislab/scib/pull/334


**Full Changelog**: https://github.com/theislab/scib/compare/v1.0.3...v1.0.4

What's Changed
* Add pre-commit by MxMstrmn in https://github.com/theislab/scib/pull/307
* Fix duplicate cols scanorama by MxMstrmn in https://github.com/theislab/scib/pull/306
* Fix scanorama batch reordering by mumichae in https://github.com/theislab/scib/pull/309
* Add option to use leiden by scottgigante in https://github.com/theislab/scib/pull/203
* Avoid filtering in normalization by scottgigante in https://github.com/theislab/scib/pull/208

New Contributors
* MxMstrmn made their first contribution in https://github.com/theislab/scib/pull/307

**Full Changelog**: https://github.com/theislab/scib/compare/v1.0.2...v1.0.3

What's Changed
* Add pre-commit by MxMstrmn in https://github.com/theislab/scib/pull/307
* Fix duplicate cols scanorama by MxMstrmn in https://github.com/theislab/scib/pull/306
* Fix scanorama batch reordering by mumichae in https://github.com/theislab/scib/pull/309
* Add option to use leiden by scottgigante in https://github.com/theislab/scib/pull/203
* Avoid filtering in normalization by scottgigante in https://github.com/theislab/scib/pull/208

New Contributors
* MxMstrmn made their first contribution in https://github.com/theislab/scib/pull/307

**Full Changelog**: https://github.com/theislab/scib/compare/v1.0.2...v1.0.3

What's Changed
* Addressing installation issues by mumichae in https://github.com/theislab/scib/pull/297
* Update highly_variable_genes.py by danielStrobl in https://github.com/theislab/scib/pull/269
* Documentation by mumichae in https://github.com/theislab/scib/pull/279
* Improve LISI multiprocessing specification by mumichae in https://github.com/theislab/scib/pull/301
* Fix LISI warning error by mumichae in https://github.com/theislab/scib/pull/302


**Full Changelog**: https://github.com/theislab/scib/compare/v1.0.1...v1.0.2

What's Changed
* Added embed to opt_louvain in metrics function (277) by lauradmartens in https://github.com/theislab/scib/pull/281
* [WIP] fixed clisi scaling bug by LuckyMD in https://github.com/theislab/scib/pull/287
* Remove `,` in `bool` var by johnarevalo in https://github.com/theislab/scib/pull/295
* Update dependency versions by mumichae in https://github.com/theislab/scib/pull/294

New Contributors
* lauradmartens made their first contribution in https://github.com/theislab/scib/pull/281
* johnarevalo made their first contribution in https://github.com/theislab/scib/pull/295

**Full Changelog**: https://github.com/theislab/scib/compare/v1.0.0...v1.0.1

What's Changed
* Add igraph to dependencies by scottgigante in https://github.com/theislab/scib/pull/134
* [WIP] DESC integration by LuckyMD in https://github.com/theislab/scib/pull/131
* Add louvain dependency by scottgigante in https://github.com/theislab/scib/pull/135
* Add fastMNN prototype by lazappi in https://github.com/theislab/scib/pull/126
* added saucie by danielStrobl in https://github.com/theislab/scib/pull/129
* don't overwrite adata.X in combat integration by danielStrobl in https://github.com/theislab/scib/pull/138
* Add scGen to data integration benchmark by LuckyMD in https://github.com/theislab/scib/pull/127
* Error for saucie if input is dense by danielStrobl in https://github.com/theislab/scib/pull/139
* Unintegrated metrics by mumichae in https://github.com/theislab/scib/pull/133
* Removed undefined palette definition by danielStrobl in https://github.com/theislab/scib/pull/142
* Rescale lisi (updated to latest master) by mumichae in https://github.com/theislab/scib/pull/143
* scIB not compatible with scanpy >= 1.5 by scottgigante in https://github.com/theislab/scib/pull/144
* Update metrics.py by danielStrobl in https://github.com/theislab/scib/pull/146
* added log-transform argument to normalize function by LisaSikkema in https://github.com/theislab/scib/pull/149
* add scanvi to scib by danielStrobl in https://github.com/theislab/scib/pull/132
* Improve documentation for isolated label score by mumichae in https://github.com/theislab/scib/pull/152
* Update integration.py by danielStrobl in https://github.com/theislab/scib/pull/151
* Fixing F1 isolated label score by mumichae in https://github.com/theislab/scib/pull/154
* Enable Bioconductor 3.11 compatibility by LuckyMD in https://github.com/theislab/scib/pull/162
* Revert "Enable Bioconductor 3.11 compatibility" by LuckyMD in https://github.com/theislab/scib/pull/163
* Update scran normalization for bioc 3.11, closes 141 by scottgigante in https://github.com/theislab/scib/pull/157
* changed trajectory metric to only consider largest connected component by danielStrobl in https://github.com/theislab/scib/pull/165
* Modify how embeddings are stored in Seurat objects by lazappi in https://github.com/theislab/scib/pull/167
* Catch metrics errors by danielStrobl in https://github.com/theislab/scib/pull/161
* added Seurat RPCA mode by LuckyMD in https://github.com/theislab/scib/pull/172
* [WIP] Free memory after running normalize by LuckyMD in https://github.com/theislab/scib/pull/156
* Coerce to Csparsematrix for C++ conversion efficiency by scottgigante in https://github.com/theislab/scib/pull/164
* added new methods names by martaint in https://github.com/theislab/scib/pull/174
* Update runMethods.R by danielStrobl in https://github.com/theislab/scib/pull/176
* Fix small bug in scanvi function by danielStrobl in https://github.com/theislab/scib/pull/181
* Fix finding optimal resolution for clustering by mumichae in https://github.com/theislab/scib/pull/184
* Merge benchmarks into a single output file by lazappi in https://github.com/theislab/scib/pull/179
* Include LISI files during package installation by mumichae in https://github.com/theislab/scib/pull/186
* Add UMAP plots to metrics by lazappi in https://github.com/theislab/scib/pull/169
* Isolated label fix by mumichae in https://github.com/theislab/scib/pull/187
* Check for empty files when merging benchmarks by lazappi in https://github.com/theislab/scib/pull/190
* Added error checks for scran normalization by LuckyMD in https://github.com/theislab/scib/pull/194
* Handle empty input files when saving embedding plots by lazappi in https://github.com/theislab/scib/pull/193
* Bugfix in PCA regression by mumichae in https://github.com/theislab/scib/pull/197
* Fix LISI error for small values by mbuttner in https://github.com/theislab/scib/pull/188
* change adata to adata_tmp in LISI_graph by mbuttner in https://github.com/theislab/scib/pull/201
* Deactivate anndata2ri after preprocessing by scottgigante in https://github.com/theislab/scib/pull/202
* Analysis notebook updates by LuckyMD in https://github.com/theislab/scib/pull/206
* further analysis notebook update by LuckyMD in https://github.com/theislab/scib/pull/207
* Update scIB-python.yml by danielStrobl in https://github.com/theislab/scib/pull/147
* fix bug in silhouete calculation by Hrovatin in https://github.com/theislab/scib/pull/212
* updated version of plotting function by martaint in https://github.com/theislab/scib/pull/199
* Tidy my plotting functions by lazappi in https://github.com/theislab/scib/pull/214
* Isolated label asw embed by mumichae in https://github.com/theislab/scib/pull/213
* Fix: Anndata concatenate causes shuffled batches by mumichae in https://github.com/theislab/scib/pull/215
* GitHub actions integration by mumichae in https://github.com/theislab/scib/pull/205
* [WIP] Remove scanpy<1.5 requirement by danielStrobl in https://github.com/theislab/scib/pull/218
* Remove method dependencies by danielStrobl in https://github.com/theislab/scib/pull/223
* Remove locked dependencies by danielStrobl in https://github.com/theislab/scib/pull/224
* Update integration.py by danielStrobl in https://github.com/theislab/scib/pull/231
* add mapping orthologous genes by martaint in https://github.com/theislab/scib/pull/234
* Update README.md by danielStrobl in https://github.com/theislab/scib/pull/232
* update scanpy and anndata by LuckyMD in https://github.com/theislab/scib/pull/243
* Remove redundant cc score code by mumichae in https://github.com/theislab/scib/pull/241
* Moving files to scib-pipeline and scib-reproducibility by mumichae in https://github.com/theislab/scib/pull/217
* Allow specific pseudotime column for TI metric by mumichae in https://github.com/theislab/scib/pull/249
* Update docstring for get_root by mumichae in https://github.com/theislab/scib/pull/250
* Fix TI metric by mumichae in https://github.com/theislab/scib/pull/251
* Allow CSR sparse matrix for PCR by mumichae in https://github.com/theislab/scib/pull/252
* Catch RootCellError and return score of 0 by mumichae in https://github.com/theislab/scib/pull/254
* Refactor metrics by mumichae in https://github.com/theislab/scib/pull/256
* fix missing metrics module by mumichae in https://github.com/theislab/scib/pull/258
* fix kbet metric by mbuttner in https://github.com/theislab/scib/pull/257
* Check dependies in functions by mumichae in https://github.com/theislab/scib/pull/262
* Reimplement ARI by mumichae in https://github.com/theislab/scib/pull/263
* Check kbet lisi by mbuttner in https://github.com/theislab/scib/pull/264
* Refactor metrics by mumichae in https://github.com/theislab/scib/pull/265
* Check metrics by mumichae in https://github.com/theislab/scib/pull/268
* add per batch trajectory score by danielStrobl in https://github.com/theislab/scib/pull/273
* Packaging by mumichae in https://github.com/theislab/scib/pull/272

New Contributors
* scottgigante made their first contribution in https://github.com/theislab/scib/pull/134
* LisaSikkema made their first contribution in https://github.com/theislab/scib/pull/149
* Hrovatin made their first contribution in https://github.com/theislab/scib/pull/212

**Full Changelog**: https://github.com/theislab/scib/compare/0.2.0...v1.0.0