Changelogs » Scvi

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Scvi

0.6.8

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  * scvi is now deprecated, please uninstall and install scvi-tools (available shortly)

0.6.7

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  * downgrade anndata>=0.7 and scanpy>=1.4.6 `galen`_
  * make loompy optional, raise sckmisc import error `adam`_
  * fix PBMCDataset download bug `galen`_
  * fix AnnDatasetFromAnnData _X in adata.obs bug `galen`_

0.6.6

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  * add tqdm to within cluster DE genes `adam`_
  * restore tqdm to use simple bar instead of ipywidget `adam`_
  * move to numpydoc for doctstrings `adam`_
  * update issues templates `adam`_
  * Poisson variable gene selection `valentine-svensson`_
  * BrainSmallDataset set defualt save_path_10X `gokcen-eraslan`_
  * train_size must be float between 0.0 and 1.0 `galen`_
  * bump dependency versions `galen`_
  * remove reproducibility notebook `galen`_
  * fix scanVI dataloading `pierre`_

0.6.5

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  * updates to totalVI posterior functions and notebooks `adam`_
  * update seurat v3 HVG selection now using skmisc loess  `adam`_

0.6.4

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  * add back Python 3.6 support `adam`_
  * get_sample_scale() allows gene selection `valentine-svensson`_
  * bug fix to the dataset to anndata method with how cell measurements are stored `adam`_
  * fix requirements `adam`_

0.6.3

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  * bug in version for Louvian in setup.py `adam`_

0.6.2

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  * update highly variable gene selection to handle sparse matrices `adam`_
  * update DE docstrings `pierre`_
  * improve posterior save load to also handle subclasses `pierre`_
  * Create NB and ZINB distributions with torch and refactor code accordingly `pierre`_
  * typos in autozivae `achille`_
  * bug in csc sparse matrices in anndata data loader `adam`_

0.6.1

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  * handles gene and cell attributes with the same name `han-yuan`_
  * fixes anndata overwriting when loading `adam`_, `pierre`_
  * formatting in basic tutorial `adam`_

0.6.0

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  * updates on TotalVI and LDVAE `adam`_
  * fix documentation, compatibility and diverse bugs `adam`_, `pierre`_ `romain`_
  * fix for external module on scanpy `galen`_

0.5.0

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  * do not automatically upper case genes `adam`_
  * AutoZI `oscar`_
  * Made the intro tutorial more user friendly `adam`_
  * Tests for LDVAE notebook `adam`_
  * black codebase `achille`_ `gabriel`_ `adam`_
  * fix compatibility issues with sklearn and numba `romain`_
  * fix Anndata `francesco-brundu`_
  * docstring, totalVI, totalVI notebook and CITE-seq data `adam`_
  * fix type `eduardo-beltrame`_
  * fixing installation guide `jeff`_
  * improved error message for dispersion `stephen-flemming`_

0.4.1

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  * docstring `achille`_
  * differential expression `oscar`_ `pierre`_

0.4.0

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  * gimVI `achille`_
  * synthetic correlated datasets, fixed bug in marginal log likelihood `oscar`_
  * autotune, dataset enhancements `gabriel`_
  * documentation `jeff`_
  * more consistent posterior API, docstring, validation set `adam`_
  * fix anndataset `michael-raevsky`_
  * linearly decoded VAE `valentine-svensson`_
  * support for scanpy, fixed bugs, dataset enhancements `achille`_
  * fix filtering bug, synthetic correlated datasets, docstring, differential expression `pierre`_
  * better docstring `jamie-morton`_
  * classifier based on library size for doublet detection `david-kelley`_

0.3.0

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  * corrected notebook `jules`_
  * added UMAP and updated harmonization code `chenling`_ `romain`_
  * support for batch indices in csvdataset `primoz-godec`_
  * speeding up likelihood computations `william-yang`_
  * better anndata interop `casey-greene`_
  * early stopping based on classifier accuracy `david-kelley`_

0.2.4

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  * updated to torch v1 `jules`_
  * added stress tests for harmonization `chenling`_
  * fixed autograd breaking `romain`_
  * make removal of empty cells more efficient `john-reid`_
  * switch to os.path.join `casey-greene`_

0.2.2

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  * added baselines and datasets for sMFISH imputation `jules`_
  * added harmonization content `chenling`_
  * fixing bugs on DE `romain`_

0.2.0

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  * annotation notebook `eddie`_
  * Memory footprint management `jeff`_
  * updated early stopping `max`_
  * docstring `james-webber`_

0.1.6

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  * MMD and adversarial inference wrapper `eddie`_
  * Documentation `jeff`_
  * smFISH data imputation `max`_

0.1.5

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  * Dataset additions `eddie`_
  * Documentation `yining`_
  * updated early stopping `max`_

0.1.3

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  * Notebook enhancement `yining`_
  * Semi-supervision `eddie`_

0.1.2

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  * First release on PyPi
  * Skeleton code & dependencies `jeff`_
  * Unit tests `max`_
  * PyTorch implementation of scVI `eddie`_ `max`_
  * Dataset preprocessing `eddie`_ `max`_ `yining`_

0.1.0

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  * First scVI TensorFlow version `romain`_
  
  .. _`romain`: https://github.com/romain-lopez
  .. _`adam`: https://github.com/adamgayoso
  .. _`eddie`: https://github.com/Edouard360
  .. _`jeff`: https://github.com/jeff-regier
  .. _`pierre`: https://github.com/PierreBoyeau
  .. _`max`: https://github.com/maxime1310
  .. _`yining`: https://github.com/imyiningliu
  .. _`gabriel`: https://github.com/gabmis
  .. _`achille`: https://github.com/ANazaret
  .. _`chenling`: https://github.com/chenlingantelope
  .. _`jules`: https://github.com/jules-samaran
  .. _`david-kelley`: https://github.com/davek44
  .. _`william-yang`: https://github.com/triyangle
  .. _`oscar`: https://github.com/oscarclivio
  .. _`casey-greene`: https://github.com/cgreene
  .. _`jamie-morton`: https://github.com/mortonjt
  .. _`valentine-svensson`: https://github.com/vals
  .. _`stephen-flemming`: https://github.com/sjfleming
  .. _`michael-raevsky`: https://github.com/raevskymichail
  .. _`james-webber`: https://github.com/jamestwebber
  .. _`galen`: https://github.com/galenxing
  .. _`francesco-brundu`: https://github.com/fbrundu
  .. _`primoz-godec`: https://github.com/PrimozGodec
  .. _`eduardo-beltrame`: https://github.com/Munfred
  .. _`john-reid`: https://github.com/JohnReid
  .. _`han-yuan`: https://github.com/hy395
  .. _`gokcen-eraslan`: https://github.com/gokceneraslan