v0.0.9

What's Changed

• Fix: validation caching by @selmanozleyen in #292

Full Changelog: v0.0.8...v0.0.9

v0.0.8

What's Changed

• feat: removed batched as parallelism is ensured by default by not eagerly casting jax to numpy. also added pytest-split to ci by @selmanozleyen in #290

Full Changelog: v0.0.7...v0.0.8

v0.0.7

What's Changed

• deprecation python 3.10 by @MUCDK in #244
• add combosciplex by @MUCDK in #233
• Add solver to callback call by @LeonStadelmann in #215
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #238
• pass rng from cellflow.predict by @MUCDK in #245
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #246
• Feature: Out of Core Dataloading Option by @selmanozleyen in #239
• Feature and Speedup: predict_batch by @selmanozleyen in #235
• Optimization with Huge Speedup: Dask Dataframes Instead of Manual Dataframe Iterations by @selmanozleyen in #240
• Add predict kwargs in validation step by @LeonStadelmann in #228
• Fix control splitting by @joschif in #262
• changes to wandb logging by @joschif in #266
• fix: adata_pca in conftest by @joschif in #268
• add new time embedder by @MUCDK in #264
• perf: jit ema update by @joschif in #270
• don't import external by @MUCDK in #271
• fix predict kwargs by @MUCDK in #272
• Ottjax>0.5 support, optional dependency handling fixes and dataset download fixes by @selmanozleyen in #288

Full Changelog: v0.0.6...v0.0.7

More developments

What's Changed

• Explain conditioning by @LeonStadelmann in #229
• Remove encode conditions from codebase and notebook by @LeonStadelmann in #227
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #225
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #230
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #234
• fix TokenAttention by @MUCDK in #241

Full Changelog: v0.0.5...v0.0.6

v0.0.5

What's Changed

• Reverting the gene embedding test skips by @LeonStadelmann in #207
• fix preprocessing module by @MUCDK in #209
• add paper link and fix preprocessing by @MUCDK in #217
• remove example notebook by @MUCDK in #218
• fix preprocessing by @MUCDK in #219
• different conditioning architectures by @MUCDK in #208
• fix predict docs by @LeonStadelmann in #214
• Improve metrics documentation by @LeonStadelmann in #204
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #210
• iNeuron tutorial by @joschif in #222
• rename flow to probability_path by @MUCDK in #224

Full Changelog: v0.0.4...v0.0.5

v0.0.4

What's Changed

• Add metrics test by @LeonStadelmann in #181
• Fix test failure by @LeonStadelmann in #205
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #203
• misc fixes and additions by @joschif in #198
• add pbmc tutorial by @MUCDK in #192
• finish notebooks for zebrafish by @MUCDK in #206

Full Changelog: v0.0.3...v0.0.4

include stochastic condition encoder

In order for running the tutorials on a released version.

What's Changed

• Feat/datasets by @MUCDK in #176
• fix project name by @MUCDK in #175
• Dev/update packages by @MUCDK in #177
• Stochastic encoder by @MUCDK in #188
• Bug/fix this works by @MUCDK in #187
• adapt order in prepare-model and default values by @MUCDK in #189
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #179
• Fix/one hot c by @MUCDK in #191
• add pbmc dataset by @MUCDK in #193
• Docs/logoandstuff by @joschif in #194

New Contributors

• @pre-commit-ci made their first contribution in #179

Full Changelog: v0.0.2...v0.0.3

v0.0.2

Update

Initial release

To reproduce the paper results, it's still possible to import cfp along cellflow.

Also, not all imports are fixed yet to ensure reproducibility.

Fixes and updates to new ott-jax version will be done in the next release.

What's Changed

CellFlow was born

New Contributors

• @MUCDK made their first contribution in #11
• @joschif made their first contribution in #12
• @dbobrovskiy made their first contribution in #23
• @zimea made their first contribution in #52
• @selmanozleyen made their first contribution in #106
• @guillaumehu made their first contribution in #134
• @LeonStadelmann made their first contribution in #143
• @MLubetzki made their first contribution in #156

Full Changelog: https://github.com/theislab/CellFlow/commits/v0.0.1