Add core packages #292
Add core packages #292
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Rename authors -> contact and add field for logos
Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>
Instead, collect all errors until the end and print all of them
Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
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What about anndataR? Do we add this to the main install:
pypi: anndata
conda: conda-forge::anndata
bioconductor: anndataRor as a separate (core-datastructures? ecosystem?) package? right now, it's not listed at all. |
I'd say ecosystem for now and when the R devs say it's mature enough and used, we can pick up the conversation again. |
Depends on how you define the categories but ecosystem sounds fine. The preprint is here https://www.biorxiv.org/content/10.1101/2025.08.18.669052v1. While you are updating things would it make sense to add a language tag (that defaults to Python)? I'm not sure how many non-Python things there are but could be useful to mark those some how. |
This is partly implied by the |
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I extracted the “add mandatory field” part to #307, so we don’t have to manually update this PR anymore all the time. |
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anndata and scanpy look good!
| publications: | ||
| - 10.1038/s41587-021-01206-w # Scvi-tools library paper, NBT 2022 | ||
| - 10.1038/s41587-022-01272-8 # DestVI | ||
| - 10.1038/s41592-020-01050-x # totalVI | ||
| - 10.15252/msb.20209620 # scANVI | ||
| - 10.48550/arXiv.1905.02269 # gimVI | ||
| - 10.1101/794289 # scvi-tools DE analysis | ||
| - 10.1093/bioinformatics/btaa169 # Interpretable factor models, Bioinformatics 2020 | ||
| - 10.1101/794875 # AutoZI | ||
| - 10.1038/s41592-018-0229-2 # scVI | ||
| - 10.1038/s41592-023-01909-9 # multiVI | ||
| - 10.1016/j.crmeth.2022.100182 # peakVI | ||
| - 10.1038/s41592-025-02808-x # MrVI | ||
| - 10.1038/s41592-025-02799-9 # scVI hub | ||
| - 10.1101/2025.01.20.634005 # resolVI | ||
| - 10.1038/s41592-023-01994-w # VeloVI | ||
| - 10.1101/2025.09.07.674699 # CytoVI | ||
| - 10.1101/2025.06.01.657182 # ScVIVA |
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@ori-kron-wis @canergen does that look right?
Adding core packages to the ecosystem package registry. A new field
categoryhas been added to distinguish package types.The purpose of this is to use the package registry as the single point of truth for our package listing.
The publications listed here will be used to collect citation stats.
@scverse/core-devs, please review your packages. In particular make sure that authors are correct and all relevant papers are added.
CC @maltekuehl