Sergei Rybakov

Fix diffmap plotting

12

Fixes https://github.com/scverse/scanpy/issues/2254 https://github.com/scverse/scanpy/issues/2227 Before there was a hard coded offset for the diffmap basis (https://github.com/scverse/scanpy/blob/8736fc3b02a6af3b7214481c2cf78a3f8f5e06bd/scanpy/plotting/_tools/scatterplots.py#L1077) and later it disappeared. This restores the offset for diffmap, and also provides an option...

Allow additional arguments for SCVI encoder and decoder

2

related to https://github.com/scverse/scvi-tools/issues/1510 Allows to do this `set_activation = dict(activation_fn=torch.nn.Softplus)` `vae = scvi.model.SCVI(adata, encoder_kwargs=set_activation, decoder_kwargs=set_activation)`

Activation functions other than ReLU

3

Is there a way to pass an activation function class to SCVI? I don't see it in the arguments. I am trying to use differential geometry to analyze the manifold...

Add support for sparse matrices.

1

The models should support sparse `adata.X`.

Fix zarr partial reads for sparse and dense arrays

2

For sparse array `read_partial` wasn't registered. For dense arrays it actually didn't work.

Add continuous covariate to expimap

1

subj

`S3Path.touch` with `exist_ok=True` on existing file raises an error

3

`S3Path.touch` with `exist_ok=True` on existing file raises an error. [Here](https://github.com/fsspec/universal_pathlib/blob/569ceabb73503c20521949b6a5c7e3de8c6d411f/upath/core.py#L756) `exist_ok=True` sets `truncate` to `False` and this raises the error [here ](https://github.com/fsspec/s3fs/blob/3966b39c5d57ba14fc8fb543c1d80f66648a4096/s3fs/core.py#L1095) On 0.1.4 it worked fine.

This small edit makes the package compatible with the newer versions of sklearn.

Fix UPath.rename for absolute paths

1

https://github.com/fsspec/universal_pathlib/issues/206

Calling HTTPFileSystem.get on large files looks problematic

4

The problem is that when `HTTPFileSystem.get is called`, it checks if it is a directory [here](https://github.com/fsspec/filesystem_spec/blob/90c7cd9e6c939fc37341fd793831a399753ebfd9/fsspec/asyn.py#L639), but to check that this is a directory, it downloads the whole body of...