Gregor Sturm

Delete docs/Makefile

1

How to build docs is defined via hatch in `pyproject.toml` This Makefile is the default from sphinx, but I don't think we should keep it anymore as the pyproject.toml is...

> Right now, in the contribution guide, we recommend hatch, but also show how `pip` can be used instead. I think it's a good thing to not be overly opinionated...

replace changelog.md with support for github releases

7

* more developer-friendly because no merge conflicts on changelog * more user-friendly because nice integration in github UI * organize with labels, see e.g. https://github.com/scverse/spatialdata/blob/main/.github/release.yml HT @LucaMarconato

Setup a github action that can build and publish a released verision to PyPI automatically whenever a new release is created on github. See [cookiecutter scverse](https://github.com/scverse/cookiecutter-scverse/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/.github/workflows/release.yaml) for an example and...

As discussed in the core dev meeting, please add documentation how to make a release of this package.

Memory leak in bounding_box_query?

1

I am working with a spatialdata object with 49 visium samples: sdata ``` SpatialData object, with associated Zarr store: /cfs//02_nfcore_spatialvi/output/aggregation/data/merged_sdata.zarr ├── Images │ ├── 'study1_sample1_hires_image': DataArray[cyx] (3, 2000, 2000) │...

### Description of feature Some bugs have been fixed in samsehe 0.2.10. Please update the module accordingly.

Consider splitting quarto reports into QC and results

2

### Description of feature I feel the current quarto report addresses two different audiences: 1) the bioinformatician who can assess the more technical information and QC metrics (e.g. was sample...

### Description of feature With a single, fitted model, multiple contrasts can be tested. We should consider allowing to specify multiple contrasts for each model definition. This saves runtime because...

Support for linear mixed effects models via DREAM

3

### Description of feature In #325/#339, an attempt was made to add support for limma mixed models. However, I believe this approach is not ideal for the following reasons *...