Alex Wolf

anndata paper

3

We transitioned from editing the paper in https://github.com/ivirshup/anndata-paper to editing it in this PR, as required for submitting to https://joss.theoj.org/. This branch does not need to be merged into the...

from anndata import AnnData fails with flit

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In one instance of treating anndata as a dependency within flit, I now get: ``` from anndata import AnnData -> ImportError: cannot import name 'AnnData' from 'anndata' ``` When I...

Make numpydoc respect `autodoc_member_order`

2

autodoc comes with the parameter `autodoc_member_order`, which can be set to one of {'alphabetical', 'groubwise', 'bysource'}: http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order numpydoc doesn't respect that parameter, but always orders class attributes and methods alphabetically,...

Moving files via `UPath.rename` to absolute path locations

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Because of this: https://github.com/fsspec/universal_pathlib/blob/380144c18f291f0f0a15fe8a02bc265233dd594b/upath/core.py#L942-L954 the following happens: ``` from upath import UPath path = UPath("s3://lamin-us-west-2/wXDsTYYd/.lamindb/S78k5961PekVzaLrQkGq") path.rename("s3://lamin-us-west-2/wXDsTYYd/.lamindb/S78k5961PekVzaLrQkGq.csv") # > S3Path('s3://lamin-us-west-2/wXDsTYYd/.lamindb/s3://lamin-us-west-2/wXDsTYYd/.lamindb/S78k5961PekVzaLrQkGq.csv') ``` To allow moving files across directories, `.rename()` should behave as...

Dear Christopher, we were having some issues in reproducing the cell proportion plot in Figure 2a. It would be fantastic if you provided the script to generate it. Thank you,...

Make `strings_to_categoricals` upon `.write()` optional

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To illustrate that it'd be a simple change, this PR adds the 3 lines for what @ivirshup suggested [here](https://github.com/scverse/anndata/issues/534#issuecomment-813901847) 3 years ago: > I think I'd be fine with a...

Warn if AnnDataWrapper options are empty as it would result in empty list for `vc['datasets']['files']`

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I didn't find a unit test for this, but I found a notebook in the repo: When I run it and look at the `dict` I get an empty list...

TODO: Backwards-compat breaking changes

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A list for keeping track of things that we might change when breaking backwards compat at some point: - [x] merge sparse pca - [x] merge https://github.com/theislab/scanpy/pull/1111 - [ ]...

Uncaught error during pretty print

2

After writing the object to disk, the pretty print functionality triggered by just displaying the `sdata` blobs object in a notebook runs into this uncaught error. ```python File /opt/hostedtoolcache/Python/3.12.10/x64/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:1073, in...