Lukas Heumos

https://jupyterbook.org/en/stable/content/components.html#dropdown-admonitions https://jupyterbook.org/en/stable/interactive/hiding.html#hide-cell-outputs Use this in many places as appropriate

Should hopefully prevent errors such as the following: ``` lamindb/core/loaders.py:56: in load_fcs return readfcs.read(*args, **kwargs) /opt/hostedtoolcache/Python/3.13.1/x64/lib/python3.13/site-packages/readfcs/_core.py:250: in read fcsfile = ReadFCS(filepath) /opt/hostedtoolcache/Python/3.13.1/x64/lib/python3.13/site-packages/readfcs/_core.py:98: in __init__ self._flow_data = flowio.read_multiple_data_sets(filepath)[data_set] /opt/hostedtoolcache/Python/3.13.1/x64/lib/python3.13/site-packages/flowio/utils.py:47: in read_multiple_data_sets...

Add pronto CI

1

Dear everyone, this PR: 1. Cleans up the Github Actions workflow file. All of the comments are noise because the code speaks for itself in this case. (not always the...

### Description of feature This is very important because it's very common that categorical + numerical values are mixed. Also noticed that in Lennart's project. We should at least provide...

Ensure that PR previews also deploy on forked repositories

2

See e.g .https://github.com/theislab/single-cell-best-practices/actions/runs/14578921423/job/40891103457?pr=358 gives a permission denied error. Secrets are not available to forks. Need to figure out why this doesn't work for forks here.

- [x] Consider renaming `analysis frameworks and tools` to `data structures and frameworks` - [ ] Ensure that the existing content still runs with the latest versions (https://www.sc-best-practices.org/introduction/analysis_tools.html) - [...

Hi, I was wondering whether you'd be able to upload a release to pypi? It would make the package easier to install and more accessible. Thanks!

Fix IO warning

2

Fixes ``` /home/lukas/miniforge3/envs/lamindb/lib/python3.12/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead. warnings.warn(msg, FutureWarning) ``` also modernizes the setup a tiny but and removes ancient flake8 and other stuff

pre-release CI fails

1

### Please make sure these conditions are met - [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on...

### Report ``` tests/metadata/test_cell_line.py::test_gdsc_annotation /home/zeth/miniconda3/envs/pertpy/lib/python3.13/site-packages/anndata/_core/anndata.py:740: UserWarning: AnnData expects .obs.index to contain strings, but got values like: [14, 47, 1124, 952, 14] Inferred to be: integer value_idx = self._prep_dim_index(value.index, attr) tests/metadata/test_cell_line.py::test_prism_annotation...