From d710c66810e77014abaf59e92f8481f54e1a0397 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 27 Jan 2026 10:03:08 +0100
Subject: [PATCH 1/2] =?UTF-8?q?fix:=20use=20default=20page=20version=20so?=
 =?UTF-8?q?=20links=20don=E2=80=99t=20break?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 README.md                               | 2 +-
 packages/CellAnnotator/meta.yaml        | 2 +-
 packages/CellMapper/meta.yaml           | 2 +-
 packages/CellRank/meta.yaml             | 4 ++--
 packages/Cell_BLAST/meta.yaml           | 2 +-
 packages/CellphoneDB/meta.yaml          | 2 +-
 packages/Cirrocumulus/meta.yaml         | 4 ++--
 packages/DRVI/meta.yaml                 | 4 ++--
 packages/DoubletDetection/meta.yaml     | 4 ++--
 packages/LazySlide/meta.yaml            | 2 +-
 packages/Multivelo/meta.yaml            | 4 ++--
 packages/PILOT/meta.yaml                | 4 ++--
 packages/ParTIpy/meta.yaml              | 4 ++--
 packages/PathML/meta.yaml               | 4 ++--
 packages/PyDESeq2/meta.yaml             | 2 +-
 packages/SCALEX/meta.yaml               | 2 +-
 packages/STMiner/meta.yaml              | 2 +-
 packages/TreeData/meta.yaml             | 4 ++--
 packages/anndata/meta.yaml              | 4 ++--
 packages/annsel/meta.yaml               | 4 ++--
 packages/bento-tools/meta.yaml          | 4 ++--
 packages/cell2location/meta.yaml        | 4 ++--
 packages/cookiecutter-scverse/meta.yaml | 2 +-
 packages/dandelion/meta.yaml            | 4 ++--
 packages/decoupler/meta.yaml            | 4 ++--
 packages/delnx/meta.yaml                | 4 ++--
 packages/dynamo-release/meta.yaml       | 4 ++--
 packages/epiScanpy/meta.yaml            | 4 ++--
 packages/eschr/meta.yaml                | 4 ++--
 packages/flowsom/meta.yaml              | 4 ++--
 packages/gssnng/meta.yaml               | 2 +-
 packages/hotspot/meta.yaml              | 4 ++--
 packages/infercnvpy/meta.yaml           | 4 ++--
 packages/kompot/meta.yaml               | 2 +-
 packages/liana/meta.yaml                | 4 ++--
 packages/maxspin/meta.yaml              | 2 +-
 packages/moscot/meta.yaml               | 2 +-
 packages/mudata/meta.yaml               | 4 ++--
 packages/muon/meta.yaml                 | 4 ++--
 packages/panpipes/meta.yaml             | 4 ++--
 packages/pegasus/meta.yaml              | 4 ++--
 packages/pertpy/meta.yaml               | 4 ++--
 packages/popV/meta.yaml                 | 2 +-
 packages/pySCENIC/meta.yaml             | 4 ++--
 packages/pyUCell/meta.yaml              | 4 ++--
 packages/pycea/meta.yaml                | 4 ++--
 packages/pychromVAR/meta.yaml           | 4 ++--
 packages/pytximport/meta.yaml           | 4 ++--
 packages/rapids-singlecell/meta.yaml    | 4 ++--
 packages/scFates/meta.yaml              | 4 ++--
 packages/scGen/meta.yaml                | 4 ++--
 packages/scXpand/meta.yaml              | 4 ++--
 packages/scanpro/meta.yaml              | 2 +-
 packages/scanpy/meta.yaml               | 4 ++--
 packages/schist/meta.yaml               | 2 +-
 packages/scirpy/meta.yaml               | 2 +-
 packages/sctriangulate/meta.yaml        | 4 ++--
 packages/scverse-tutorials/meta.yaml    | 4 ++--
 packages/scvi-tools/meta.yaml           | 4 ++--
 packages/sincei/meta.yaml               | 2 +-
 packages/spatial-eggplant/meta.yaml     | 4 ++--
 packages/spatialdata/meta.yaml          | 4 ++--
 packages/squidpy/meta.yaml              | 2 +-
 packages/tangram/meta.yaml              | 4 ++--
 packages/wsidata/meta.yaml              | 2 +-
 65 files changed, 109 insertions(+), 109 deletions(-)

diff --git a/README.md b/README.md
index e12766ba..8c3ca50d 100644
--- a/README.md
+++ b/README.md
@@ -65,4 +65,4 @@ How does the package use scverse data structures (please describe in a few sente
 
 [^2]: Continuous integration means that software tests are automatically executed on every push to the git repository. This guarantees they are always run and that they are run in a clean environment. Scverse ecosystem packages most commonly use [GitHub Actions](https://github.com/features/actions) for CI. For an example, check out our [cookiecutter template](https://github.com/scverse/cookiecutter-scverse).
 
-[^3]: By API documentation, we mean an overview of _all_ public functions provided a package, with documentation of their parameters. For an example, see the [Scanpy documentation](https://scanpy.readthedocs.io/en/stable/api/preprocessing.html). In simple cases, this can be done manually in a README file. For anything more complex, we recommend the [Sphinx Autodoc plugin](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html)
+[^3]: By API documentation, we mean an overview of _all_ public functions provided a package, with documentation of their parameters. For an example, see the [Scanpy documentation](https://scanpy.readthedocs.io/page/api/preprocessing.html). In simple cases, this can be done manually in a README file. For anything more complex, we recommend the [Sphinx Autodoc plugin](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html)
diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml
index bc84d0f2..2a627f18 100644
--- a/packages/CellAnnotator/meta.yaml
+++ b/packages/CellAnnotator/meta.yaml
@@ -2,7 +2,7 @@ name: CellAnnotator
 description: |
   CellAnnotator is a lightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study.
 project_home: https://github.com/quadbio/cell-annotator
-documentation_home: https://cell-annotator.readthedocs.io/en/latest/
+documentation_home: https://cell-annotator.readthedocs.io/
 install:
   pypi: cell-annotator
 tags:
diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml
index 32f903cb..2a67bfdc 100644
--- a/packages/CellMapper/meta.yaml
+++ b/packages/CellMapper/meta.yaml
@@ -2,7 +2,7 @@ name: CellMapper
 description: |
   CellMapper is a leightweight tool to transfer labels, expression values and embeddings from reference to query datasets using k-NN mapping. It's fast and versatile, applicable to mapping scenarios in space, across modalities, or from an atlas to a new query dataset.
 project_home: https://github.com/quadbio/cellmapper
-documentation_home: https://cellmapper.readthedocs.io/en/latest/
+documentation_home: https://cellmapper.readthedocs.io/
 install:
   pypi: cellmapper
 tags:
diff --git a/packages/CellRank/meta.yaml b/packages/CellRank/meta.yaml
index fa85b61a..0b2f2661 100644
--- a/packages/CellRank/meta.yaml
+++ b/packages/CellRank/meta.yaml
@@ -4,8 +4,8 @@ description: |
   It contains two main modules - kernels compute cell-cell transition probabilities and estimators generate
   hypothesis based on these.
 project_home: https://github.com/theislab/cellrank
-documentation_home: https://cellrank.readthedocs.io/en/stable/
-tutorials_home: https://cellrank.readthedocs.io/en/stable/
+documentation_home: https://cellrank.readthedocs.io/
+tutorials_home: https://cellrank.readthedocs.io/
 publications:
   - 10.1038/s41592-021-01346-6
 install:
diff --git a/packages/Cell_BLAST/meta.yaml b/packages/Cell_BLAST/meta.yaml
index f0acb615..d1b72f69 100644
--- a/packages/Cell_BLAST/meta.yaml
+++ b/packages/Cell_BLAST/meta.yaml
@@ -2,7 +2,7 @@ name: Cell_BLAST
 description: |
   Cell BLAST is a cell querying tool for single-cell transcriptomics data.
 project_home: https://github.com/gao-lab/Cell_BLAST
-documentation_home: https://cblast.readthedocs.io/en/latest/
+documentation_home: https://cblast.readthedocs.io/
 publications:
   - 10.1038/s41467-020-17281-7
 install:
diff --git a/packages/CellphoneDB/meta.yaml b/packages/CellphoneDB/meta.yaml
index dc3f69ec..f41781b4 100644
--- a/packages/CellphoneDB/meta.yaml
+++ b/packages/CellphoneDB/meta.yaml
@@ -2,7 +2,7 @@ name: CellphoneDB
 description: |
   CellphoneDB is a publicly available repository of HUMAN curated receptors, ligands and their interactions paired with a tool to interrogate your own single-cell transcriptomics data (or even bulk transcriptomics data if your samples represent pure populations!). A distinctive feature of CellphoneDB is that the subunit architecture of either ligands and receptors is taken into account, representing heteromeric complexes accurately. This is crucial, as cell communication relies on multi-subunit protein complexes that go beyond the binary representation used in most databases and studies. CellphoneDB also incorporates biosynthetic pathways in which we use the last representative enzyme as a proxy of ligand abundance, by doing so, we include interactions involving non-peptidic molecules. CellphoneDB includes only manually curated and reviewed molecular interactions with evidenced role in cellular communication.
 project_home: https://github.com/ventolab/CellphoneDB
-documentation_home: https://cellphonedb.readthedocs.io/en/latest/
+documentation_home: https://cellphonedb.readthedocs.io/
 tutorials_home: https://github.com/ventolab/CellphoneDB/tree/master/notebooks
 publications:
   - 10.1038/s41586-018-0698-6
diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml
index 8a0ba053..c2102e13 100644
--- a/packages/Cirrocumulus/meta.yaml
+++ b/packages/Cirrocumulus/meta.yaml
@@ -2,8 +2,8 @@ name: Cirrocumulus
 description: |
   Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data.
 project_home: https://github.com/lilab-bcb/cirrocumulus
-documentation_home: https://cirrocumulus.readthedocs.io/en/latest/
-tutorials_home: https://cirrocumulus.readthedocs.io/en/latest/
+documentation_home: https://cirrocumulus.readthedocs.io/
+tutorials_home: https://cirrocumulus.readthedocs.io/
 publications:
   - 10.1038/s41592-020-0905-x
 install:
diff --git a/packages/DRVI/meta.yaml b/packages/DRVI/meta.yaml
index d86cad5f..c4011935 100644
--- a/packages/DRVI/meta.yaml
+++ b/packages/DRVI/meta.yaml
@@ -6,8 +6,8 @@ description: |
   and highlight developmental stages. DRVI is implemented using scvi-tools and includes a
   set of utility functions for interacting with latent dimensions.
 project_home: https://github.com/theislab/DRVI
-documentation_home: https://drvi.readthedocs.io/latest/
-tutorials_home: https://drvi.readthedocs.io/latest/tutorials/index.html
+documentation_home: https://drvi.readthedocs.io/
+tutorials_home: https://drvi.readthedocs.io/page/tutorials/index.html
 publications:
   - 10.1101/2024.11.06.622266
 install:
diff --git a/packages/DoubletDetection/meta.yaml b/packages/DoubletDetection/meta.yaml
index 38fbf16f..6cc2fd0d 100644
--- a/packages/DoubletDetection/meta.yaml
+++ b/packages/DoubletDetection/meta.yaml
@@ -3,8 +3,8 @@ description: |
   DoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell
   RNA-seq count matrices.
 project_home: https://github.com/JonathanShor/DoubletDetection
-documentation_home: https://doubletdetection.readthedocs.io/en/stable/
-tutorials_home: https://doubletdetection.readthedocs.io/en/stable/
+documentation_home: https://doubletdetection.readthedocs.io/
+tutorials_home: https://doubletdetection.readthedocs.io/
 publications:
   - 10.1016/j.cels.2019.03.003
 install:
diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml
index 52f4a4fc..98dc00d6 100644
--- a/packages/LazySlide/meta.yaml
+++ b/packages/LazySlide/meta.yaml
@@ -2,7 +2,7 @@ name: LazySlide
 description: |
   LazySlide is a Python library for processing whole slide images (WSI) analysis. It provides a simple interface to perform robust preprocessing and advanced analysis for WSI.
 project_home: https://github.com/rendeirolab/lazyslide
-documentation_home: https://lazyslide.readthedocs.io/en/latest/
+documentation_home: https://lazyslide.readthedocs.io/
 install:
   pypi: lazyslide
 tags:
diff --git a/packages/Multivelo/meta.yaml b/packages/Multivelo/meta.yaml
index 29abbdde..9b696232 100644
--- a/packages/Multivelo/meta.yaml
+++ b/packages/Multivelo/meta.yaml
@@ -3,8 +3,8 @@ description: |
   A mechanistic model of gene expression that extends the popular RNA velocity
   framework by incorporating epigenomic data.
 project_home: https://github.com/welch-lab/MultiVelo
-documentation_home: https://multivelo.readthedocs.io/en/latest/api.html
-tutorials_home: https://multivelo.readthedocs.io/en/latest/MultiVelo_Demo.html
+documentation_home: https://multivelo.readthedocs.io/page/api.html
+tutorials_home: https://multivelo.readthedocs.io/page/MultiVelo_Demo.html
 publications:
   - 10.1038/s41587-022-01476-y
 install:
diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml
index 55a7a222..eb6715f4 100644
--- a/packages/PILOT/meta.yaml
+++ b/packages/PILOT/meta.yaml
@@ -2,8 +2,8 @@ name: PILOT
 description: |
   PILOT is a Python library for Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport.
 project_home: https://github.com/CostaLab/PILOT
-documentation_home: https://pilot.readthedocs.io/en/latest/api.html
-tutorials_home: https://pilot.readthedocs.io/en/latest/
+documentation_home: https://pilot.readthedocs.io/page/api.html
+tutorials_home: https://pilot.readthedocs.io/
 publications:
   - 10.1038/s44320-023-00003-8
 install:
diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml
index 19bbc425..2c34ab2a 100644
--- a/packages/ParTIpy/meta.yaml
+++ b/packages/ParTIpy/meta.yaml
@@ -2,8 +2,8 @@ name: ParTIpy
 description: |
   Implements Pareto task inference and archetypal analysis for analyzing functional trade-offs in single-cell and spatial omics data.
 project_home: https://github.com/saezlab/ParTIpy
-documentation_home: https://partipy.readthedocs.io/en/latest/
-tutorials_home: https://partipy.readthedocs.io/en/latest/
+documentation_home: https://partipy.readthedocs.io/
+tutorials_home: https://partipy.readthedocs.io/
 install:
   pypi: partipy
 license: MIT
diff --git a/packages/PathML/meta.yaml b/packages/PathML/meta.yaml
index 49553080..dcd97c21 100644
--- a/packages/PathML/meta.yaml
+++ b/packages/PathML/meta.yaml
@@ -2,8 +2,8 @@ name: PathML
 description: |
   An open-source toolkit for computational pathology and machine learning.
 project_home: https://pathml.org/
-documentation_home: https://pathml.readthedocs.io/en/latest/
-tutorials_home: https://pathml.readthedocs.io/en/latest/
+documentation_home: https://pathml.readthedocs.io/
+tutorials_home: https://pathml.readthedocs.io/
 publications:
   - 10.1158/1541-7786.MCR-21-0665
 install:
diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml
index 0f1d9156..a84b4aee 100644
--- a/packages/PyDESeq2/meta.yaml
+++ b/packages/PyDESeq2/meta.yaml
@@ -4,7 +4,7 @@ description: |
   from scratch of the main features of the R package DESeq2 (Love et al. 2014).
 project_home: https://github.com/owkin/PyDESeq2
 documentation_home: https://pydeseq2.readthedocs.io
-tutorials_home: https://pydeseq2.readthedocs.io/en/latest/auto_examples/index.html
+tutorials_home: https://pydeseq2.readthedocs.io/page/auto_examples/index.html
 install:
   pypi: pydeseq2
 license: MIT
diff --git a/packages/SCALEX/meta.yaml b/packages/SCALEX/meta.yaml
index 25e442b6..d86c8662 100644
--- a/packages/SCALEX/meta.yaml
+++ b/packages/SCALEX/meta.yaml
@@ -2,7 +2,7 @@ name: SCALEX
 description: |
   SCALEX is an integration and projection tool for atlas-level single-cell RNA-seq and ATAC-seq data.
 project_home: https://github.com/jsxlei/SCALEX
-documentation_home: https://scalex.readthedocs.io/en/latest/?badge=stable
+documentation_home: https://scalex.readthedocs.io/
 publications:
   - 10.1038/s41467-022-33758-z
 install:
diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml
index f2a0e45f..531fdad1 100644
--- a/packages/STMiner/meta.yaml
+++ b/packages/STMiner/meta.yaml
@@ -2,7 +2,7 @@ name: STMiner
 description: |
   Gene-centric spatial transcriptomics for deciphering complex spatial omics data
 project_home: https://github.com/xjtu-omics/STMiner
-documentation_home: https://stminerdoc.readthedocs.io/en/latest
+documentation_home: https://stminerdoc.readthedocs.io/
 install:
   pypi: stminer
 tags:
diff --git a/packages/TreeData/meta.yaml b/packages/TreeData/meta.yaml
index 16fa697d..f0f26392 100644
--- a/packages/TreeData/meta.yaml
+++ b/packages/TreeData/meta.yaml
@@ -3,8 +3,8 @@ description: |
   TreeData is a lightweight wrapper around AnnData which adds two additional attributes, obst and vart,
   to store nx.DiGraph trees for observations and variables.
 project_home: https://github.com/YosefLab/treedata
-documentation_home: https://treedata.readthedocs.io/en/latest/
-tutorials_home: https://treedata.readthedocs.io/en/latest/
+documentation_home: https://treedata.readthedocs.io/
+tutorials_home: https://treedata.readthedocs.io/
 install:
   pypi: treedata
 tags:
diff --git a/packages/anndata/meta.yaml b/packages/anndata/meta.yaml
index d3e5e31a..fddef4c9 100644
--- a/packages/anndata/meta.yaml
+++ b/packages/anndata/meta.yaml
@@ -4,8 +4,8 @@ description: |
   positioned between pandas and xarray. anndata offers a broad range of computationally
   efficient features including, among others, sparse data support, lazy operations, and GPU support.
 project_home: https://github.com/scverse/anndata
-documentation_home: https://anndata.readthedocs.io/en/latest/
-tutorials_home: https://anndata.readthedocs.io/en/latest/tutorials/index.html
+documentation_home: https://anndata.readthedocs.io/
+tutorials_home: https://anndata.readthedocs.io/page/tutorials/index.html
 publications:
   - 10.1101/2021.12.16.473007
 install:
diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml
index 016dbf5c..6201ceea 100644
--- a/packages/annsel/meta.yaml
+++ b/packages/annsel/meta.yaml
@@ -3,8 +3,8 @@ description: |
   Annsel is a user-friendly library that brings familiar dataframe-style operations to AnnData objects such as
   selection, filtering and group by's.
 project_home: https://github.com/srivarra/annsel
-documentation_home: https://annsel.readthedocs.io/en/latest/
-tutorials_home: https://annsel.readthedocs.io/en/latest/notebooks/all_of_annsel.html
+documentation_home: https://annsel.readthedocs.io/
+tutorials_home: https://annsel.readthedocs.io/page/notebooks/all_of_annsel.html
 install:
   pypi: annsel
 license: MIT
diff --git a/packages/bento-tools/meta.yaml b/packages/bento-tools/meta.yaml
index f2799175..86840863 100644
--- a/packages/bento-tools/meta.yaml
+++ b/packages/bento-tools/meta.yaml
@@ -2,8 +2,8 @@ name: bento-tools
 description: |
   A Python toolkit for subcellular analysis of spatial transcriptomics data
 project_home: https://github.com/ckmah/bento-tools
-documentation_home: https://bento-tools.readthedocs.io/en/latest/
-tutorials_home: https://bento-tools.readthedocs.io/en/latest/tutorials.html
+documentation_home: https://bento-tools.readthedocs.io/
+tutorials_home: https://bento-tools.readthedocs.io/page/tutorials.html
 publications:
   - 10.1101/2022.06.10.495510
 install:
diff --git a/packages/cell2location/meta.yaml b/packages/cell2location/meta.yaml
index 297cc961..83c1c0b2 100644
--- a/packages/cell2location/meta.yaml
+++ b/packages/cell2location/meta.yaml
@@ -5,8 +5,8 @@ description: |
   of variation and borrows statistical strength across locations, thereby enabling the integration of single-cell
   and spatial transcriptomics with higher sensitivity and resolution than existing tools.
 project_home: https://github.com/BayraktarLab/cell2location
-documentation_home: https://cell2location.readthedocs.io/en/latest/
-tutorials_home: https://cell2location.readthedocs.io/en/latest/
+documentation_home: https://cell2location.readthedocs.io/
+tutorials_home: https://cell2location.readthedocs.io/
 publications:
   - 10.1038/s41587-021-01139-4
 install:
diff --git a/packages/cookiecutter-scverse/meta.yaml b/packages/cookiecutter-scverse/meta.yaml
index 7bb48a6a..1324b53a 100644
--- a/packages/cookiecutter-scverse/meta.yaml
+++ b/packages/cookiecutter-scverse/meta.yaml
@@ -2,7 +2,7 @@ name: cookiecutter-scverse
 description: |
   Cookiecutter template for scverse packages offering automated template sync
 project_home: https://github.com/scverse/cookiecutter-scverse
-documentation_home: https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html
+documentation_home: https://cookiecutter-scverse-instance.readthedocs.io/page/template_usage.html
 tags:
   - template
   - cookiecutter
diff --git a/packages/dandelion/meta.yaml b/packages/dandelion/meta.yaml
index bfa99e76..81b41860 100644
--- a/packages/dandelion/meta.yaml
+++ b/packages/dandelion/meta.yaml
@@ -5,8 +5,8 @@ description: |
   integrates with scanpy/anndata for single-cell BCR/TCR analysis. It also includes a
   couple of functions for visualization.
 project_home: https://github.com/zktuong/dandelion
-documentation_home: https://sc-dandelion.readthedocs.io/en/latest/
-tutorials_home: https://sc-dandelion.readthedocs.io/en/latest/
+documentation_home: https://sc-dandelion.readthedocs.io/
+tutorials_home: https://sc-dandelion.readthedocs.io/
 publications:
   - 10.1038/s41591-021-01329-2
   - 10.1101/2022.11.18.517068
diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml
index 039c6e6b..468e5720 100644
--- a/packages/decoupler/meta.yaml
+++ b/packages/decoupler/meta.yaml
@@ -3,8 +3,8 @@ description: |
   decoupler is a framework containing different enrichment statistical methods to extract
   biologically driven scores from omics data within a unified framework.
 project_home: https://github.com/scverse/decoupler
-documentation_home: https://decoupler.readthedocs.io/en/latest/
-tutorials_home: https://decoupler.readthedocs.io/en/latest/notebooks/index.html
+documentation_home: https://decoupler.readthedocs.io/
+tutorials_home: https://decoupler.readthedocs.io/page/notebooks/index.html
 publications:
   - 10.1093/bioadv/vbac016
 install:
diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml
index ec060be2..0dd91937 100644
--- a/packages/delnx/meta.yaml
+++ b/packages/delnx/meta.yaml
@@ -2,8 +2,8 @@ name: delnx
 description: |
   delnx is a python package for differential expression analysis of (single-cell) genomics data. It enables scalable analyses of atlas-level datasets through GPU-accelerated regression models and statistical tests implemented in JAX and provides a consistent interface to perform DE analysis with other methods, such as statsmodels and PyDESeq2.
 project_home: https://github.com/joschif/delnx
-documentation_home: https://delnx.readthedocs.io/en/latest/
-tutorials_home: https://delnx.readthedocs.io/en/latest/
+documentation_home: https://delnx.readthedocs.io/
+tutorials_home: https://delnx.readthedocs.io/
 install:
   pypi: delnx
 tags:
diff --git a/packages/dynamo-release/meta.yaml b/packages/dynamo-release/meta.yaml
index 5c761c99..47a9111c 100644
--- a/packages/dynamo-release/meta.yaml
+++ b/packages/dynamo-release/meta.yaml
@@ -4,8 +4,8 @@ description: |
   vector field reconstruction, potential landscape mapping, differential geometry analyses,
   and most probably paths / in silico perturbation predictions.
 project_home: https://github.com/aristoteleo/dynamo-release
-documentation_home: https://dynamo-release.readthedocs.io/en/latest/
-tutorials_home: https://dynamo-release.readthedocs.io/en/latest/
+documentation_home: https://dynamo-release.readthedocs.io/
+tutorials_home: https://dynamo-release.readthedocs.io/
 publications:
   - 10.1016/j.cell.2021.12.045
 install:
diff --git a/packages/epiScanpy/meta.yaml b/packages/epiScanpy/meta.yaml
index 2c60044d..64dbc5f2 100644
--- a/packages/epiScanpy/meta.yaml
+++ b/packages/epiScanpy/meta.yaml
@@ -3,8 +3,8 @@ description: |
   EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell
   DNA methylation (for example scBS-seq) data.
 project_home: https://github.com/colomemaria/epiScanpy
-documentation_home: https://episcanpy.readthedocs.io/en/latest/
-tutorials_home: https://episcanpy.readthedocs.io/en/latest/
+documentation_home: https://episcanpy.readthedocs.io/
+tutorials_home: https://episcanpy.readthedocs.io/
 publications:
   - 10.1038/s41467-021-25131-3
 install:
diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml
index 40ac20b5..6ba0bb5a 100644
--- a/packages/eschr/meta.yaml
+++ b/packages/eschr/meta.yaml
@@ -3,8 +3,8 @@ description: |
   ESCHR is an ensemble clustering method that provides hard clustering along with
   uncertainty scores and soft clustering outputs for enhanced interpretability.
 project_home: https://github.com/zunderlab/eschr
-documentation_home: https://eschr.readthedocs.io/en/latest/
-tutorials_home: https://eschr.readthedocs.io/en/latest/notebooks/paul15_mouse_hematopoiesis.html
+documentation_home: https://eschr.readthedocs.io/
+tutorials_home: https://eschr.readthedocs.io/page/notebooks/paul15_mouse_hematopoiesis.html
 publications:
   - 10.1186/s13059-024-03386-5
 install:
diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml
index c8a9c457..f69f2d09 100644
--- a/packages/flowsom/meta.yaml
+++ b/packages/flowsom/meta.yaml
@@ -6,8 +6,8 @@ description: |
   FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and
   can help to gain deeper insights in fields such as immunology and oncology.
 project_home: https://github.com/saeyslab/FlowSOM_Python
-documentation_home: https://flowsom.readthedocs.io/en/latest/
-tutorials_home: https://flowsom.readthedocs.io/en/latest/notebooks/example.html
+documentation_home: https://flowsom.readthedocs.io/
+tutorials_home: https://flowsom.readthedocs.io/page/notebooks/example.html
 publications:
   - 10.1093/bioinformatics/btae179
   - 10.1002/cyto.a.22625
diff --git a/packages/gssnng/meta.yaml b/packages/gssnng/meta.yaml
index 6548cd02..6d41f6f7 100644
--- a/packages/gssnng/meta.yaml
+++ b/packages/gssnng/meta.yaml
@@ -2,7 +2,7 @@ name: gssnng
 description: |
   Single-cell gene set scoring with nearest neighbor graph smoothed data.
 project_home: https://github.com/IlyaLab/gssnng
-documentation_home: https://gssnng.readthedocs.io/en/latest/
+documentation_home: https://gssnng.readthedocs.io/
 tutorials_home: https://github.com/IlyaLab/gssnng/tree/main/notebooks
 publications:
   - 10.1093/bioadv/vbad150
diff --git a/packages/hotspot/meta.yaml b/packages/hotspot/meta.yaml
index d86d5a3e..0ec6c1a9 100644
--- a/packages/hotspot/meta.yaml
+++ b/packages/hotspot/meta.yaml
@@ -2,8 +2,8 @@ name: hotspot
 description: |
   Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset.
 project_home: https://github.com/yoseflab/hotspot
-documentation_home: https://hotspot.readthedocs.io/en/latest/
-tutorials_home: https://hotspot.readthedocs.io/en/latest/
+documentation_home: https://hotspot.readthedocs.io/
+tutorials_home: https://hotspot.readthedocs.io/
 publications:
   - 10.1016/j.cels.2021.04.005
 install:
diff --git a/packages/infercnvpy/meta.yaml b/packages/infercnvpy/meta.yaml
index 383d925c..b97d1f5e 100644
--- a/packages/infercnvpy/meta.yaml
+++ b/packages/infercnvpy/meta.yaml
@@ -2,8 +2,8 @@ name: infercnvpy
 description: |
   Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
 project_home: https://github.com/icbi-lab/infercnvpy
-documentation_home: https://infercnvpy.readthedocs.io/en/latest/
-tutorials_home: https://infercnvpy.readthedocs.io/en/latest/tutorials.html
+documentation_home: https://infercnvpy.readthedocs.io/
+tutorials_home: https://infercnvpy.readthedocs.io/page/tutorials.html
 install:
   pypi: infercnvpy
 tags:
diff --git a/packages/kompot/meta.yaml b/packages/kompot/meta.yaml
index 4fd65c99..e52c0beb 100644
--- a/packages/kompot/meta.yaml
+++ b/packages/kompot/meta.yaml
@@ -8,7 +8,7 @@ description: |
   inference with calibrated uncertainty estimates and capturing both global and cell-state-specific effects of perturbation.
 project_home: https://github.com/settylab/kompot
 documentation_home: https://kompot.readthedocs.io/
-tutorials_home: https://kompot.readthedocs.io/en/latest/notebooks/01_getting_started.html
+tutorials_home: https://kompot.readthedocs.io/page/notebooks/01_getting_started.html
 publications:
   - 10.1101/2025.06.03.657769
 install:
diff --git a/packages/liana/meta.yaml b/packages/liana/meta.yaml
index 2e781340..11504563 100644
--- a/packages/liana/meta.yaml
+++ b/packages/liana/meta.yaml
@@ -2,8 +2,8 @@ name: liana
 description: |
   Python package to infer cell-cell communication events from omics data using a collection of methods.
 project_home: https://github.com/saezlab/liana-py
-documentation_home: https://liana-py.readthedocs.io/en/latest/
-tutorials_home: https://liana-py.readthedocs.io/en/latest/
+documentation_home: https://liana-py.readthedocs.io/
+tutorials_home: https://liana-py.readthedocs.io/
 install:
   pypi: liana
 tags:
diff --git a/packages/maxspin/meta.yaml b/packages/maxspin/meta.yaml
index 68bd66fe..0e9944c9 100644
--- a/packages/maxspin/meta.yaml
+++ b/packages/maxspin/meta.yaml
@@ -4,7 +4,7 @@ description: |
 publications:
   - 10.1016/j.crmeth.2023.100507
 project_home: https://github.com/dcjones/maxspin
-documentation_home: https://maxspin.readthedocs.io/en/latest/
+documentation_home: https://maxspin.readthedocs.io/
 tutorials_home: https://github.com/dcjones/maxspin/blob/main/tutorial.ipynb
 install:
   pypi: maxspin
diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml
index 46decb5b..fb1f9ebe 100644
--- a/packages/moscot/meta.yaml
+++ b/packages/moscot/meta.yaml
@@ -2,7 +2,7 @@ name: moscot
 description: |
   moscot is a scalable toolbox for multiomics single-cell optimal transport applications.
 project_home: https://github.com/theislab/moscot
-documentation_home: https://moscot.readthedocs.io/en/stable/index.html
+documentation_home: https://moscot.readthedocs.io/page/index.html
 publications:
   - 10.1101/2023.05.11.540374
 install:
diff --git a/packages/mudata/meta.yaml b/packages/mudata/meta.yaml
index 9f32d916..a5436a4c 100644
--- a/packages/mudata/meta.yaml
+++ b/packages/mudata/meta.yaml
@@ -4,8 +4,8 @@ description: |
   by an AnnData object. MuData's reference implementation is in Python, and the cross-language
   functionality is achieved via HDF5-based .h5mu files with libraries in R and Julia.
 project_home: https://github.com/scverse/mudata
-documentation_home: https://mudata.readthedocs.io/en/latest/
-tutorials_home: https://mudata.readthedocs.io/en/latest/notebooks/quickstart_mudata.html
+documentation_home: https://mudata.readthedocs.io/
+tutorials_home: https://mudata.readthedocs.io/page/notebooks/quickstart_mudata.html
 publications:
   - 10.1186/s13059-021-02577-8
 install:
diff --git a/packages/muon/meta.yaml b/packages/muon/meta.yaml
index 8b6a41da..a9b3ddc9 100644
--- a/packages/muon/meta.yaml
+++ b/packages/muon/meta.yaml
@@ -3,8 +3,8 @@ description: |
   muon is a Python framework for multimodal omics analysis. It provides functionality
   for working with multimodal data, including preprocessing, integration, and visualization.
 project_home: https://github.com/scverse/muon
-documentation_home: https://muon.readthedocs.io/en/latest/
-tutorials_home: https://muon-tutorials.readthedocs.io/en/latest/
+documentation_home: https://muon.readthedocs.io/
+tutorials_home: https://muon-tutorials.readthedocs.io/
 publications:
   - 10.1186/s13059-021-02577-8
 install:
diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml
index 17f2b343..b58507f5 100644
--- a/packages/panpipes/meta.yaml
+++ b/packages/panpipes/meta.yaml
@@ -2,8 +2,8 @@ name: Panpipes
 description: |
   A pipeline for multiomic single-cell and spatial transcriptomic data analysis
 project_home: https://github.com/DendrouLab/panpipes
-documentation_home: https://panpipes-pipelines.readthedocs.io/en/latest/index.html
-tutorials_home: https://panpipes-pipelines.readthedocs.io/en/latest/tutorials/index.html
+documentation_home: https://panpipes-pipelines.readthedocs.io/page/index.html
+tutorials_home: https://panpipes-pipelines.readthedocs.io/page/tutorials/index.html
 publications:
   - 10.1101/2023.03.11.532085
 install:
diff --git a/packages/pegasus/meta.yaml b/packages/pegasus/meta.yaml
index a56b5f1d..1f9f676a 100644
--- a/packages/pegasus/meta.yaml
+++ b/packages/pegasus/meta.yaml
@@ -2,8 +2,8 @@ name: pegasus
 description: |
   Pegasus is a tool for analyzing transcriptomes of millions of single cells.
 project_home: https://github.com/lilab-bcb/pegasus
-documentation_home: https://pegasus.readthedocs.io/en/stable/
-tutorials_home: https://pegasus.readthedocs.io/en/stable/tutorials.html
+documentation_home: https://pegasus.readthedocs.io/
+tutorials_home: https://pegasus.readthedocs.io/page/tutorials.html
 publications:
   - 10.1038/s41592-020-0905-x
 install:
diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml
index d4c23e5b..33f0e9f2 100644
--- a/packages/pertpy/meta.yaml
+++ b/packages/pertpy/meta.yaml
@@ -4,8 +4,8 @@ description: |
   It harmonizes datasets, automates metadata annotation, calculates perturbation distances,
   and analyzes cellular responses to genetic modifications, drugs, and environmental changes.
 project_home: https://github.com/scverse/pertpy
-documentation_home: https://pertpy.readthedocs.io/en/stable/
-tutorials_home: https://pertpy.readthedocs.io/en/stable/tutorials.html
+documentation_home: https://pertpy.readthedocs.io/
+tutorials_home: https://pertpy.readthedocs.io/page/tutorials.html
 publications:
   - 10.1101/2024.08.04.606516
 install:
diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml
index 5793656b..8ff69ec9 100644
--- a/packages/popV/meta.yaml
+++ b/packages/popV/meta.yaml
@@ -2,7 +2,7 @@ name: popV
 description: |
   p(opular)V(oting) is a consensus tool for transfering labels from an annotated reference dataset to an unannotated query dataset. Consensus calling allows interpretable scores that quantify certainty.
 project_home: https://github.com/YosefLab/popV
-documentation_home: https://popv.readthedocs.io/en/latest/
+documentation_home: https://popv.readthedocs.io/
 install:
   pypi: popv
 tags:
diff --git a/packages/pySCENIC/meta.yaml b/packages/pySCENIC/meta.yaml
index b98dac82..d03c644b 100644
--- a/packages/pySCENIC/meta.yaml
+++ b/packages/pySCENIC/meta.yaml
@@ -5,8 +5,8 @@ description: |
   biologists to infer transcription factors, gene regulatory networks and
   cell types from single-cell RNA-seq data.
 project_home: https://github.com/aertslab/pySCENIC
-documentation_home: https://pyscenic.readthedocs.io/en/latest/
-tutorials_home: https://pyscenic.readthedocs.io/en/latest/tutorial.html
+documentation_home: https://pyscenic.readthedocs.io/
+tutorials_home: https://pyscenic.readthedocs.io/page/tutorial.html
 publications:
   - 10.1038/nmeth.4463
   - 10.1371/journal.pone.0012776
diff --git a/packages/pyUCell/meta.yaml b/packages/pyUCell/meta.yaml
index 9865f231..943b27d3 100644
--- a/packages/pyUCell/meta.yaml
+++ b/packages/pyUCell/meta.yaml
@@ -7,8 +7,8 @@ description: |
   processing of large datasets in a few minutes even on machines with limited
   computing power.
 project_home: https://github.com/carmonalab/pyucell
-documentation_home: https://pyucell.readthedocs.io/en/latest
-tutorials_home: https://pyucell.readthedocs.io/en/latest/notebooks/basic.html
+documentation_home: https://pyucell.readthedocs.io/
+tutorials_home: https://pyucell.readthedocs.io/page/notebooks/basic.html
 publications:
   - 10.1016/j.csbj.2021.06.043
 install:
diff --git a/packages/pycea/meta.yaml b/packages/pycea/meta.yaml
index aa526fab..5b633cfc 100644
--- a/packages/pycea/meta.yaml
+++ b/packages/pycea/meta.yaml
@@ -2,8 +2,8 @@ name: pycea
 description: |
   Pycea is a Python toolkit for single-cell lineage tracing analysis and visualization.
 project_home: https://github.com/YosefLab/pycea
-documentation_home: https://pycea.readthedocs.io/en/latest/
-tutorials_home: https://pycea.readthedocs.io/en/latest/
+documentation_home: https://pycea.readthedocs.io/
+tutorials_home: https://pycea.readthedocs.io/
 install:
   pypi: pycea-lineage
 tags:
diff --git a/packages/pychromVAR/meta.yaml b/packages/pychromVAR/meta.yaml
index 1ca7a414..eaefa9b8 100644
--- a/packages/pychromVAR/meta.yaml
+++ b/packages/pychromVAR/meta.yaml
@@ -2,8 +2,8 @@ name: pychromVAR
 description: |
   A python pacakge for chromVAR.
 project_home: https://github.com/lzj1769/pychromVAR
-documentation_home: https://pychromvar.readthedocs.io/en/latest/
-tutorials_home: https://pychromvar.readthedocs.io/en/latest/
+documentation_home: https://pychromvar.readthedocs.io/
+tutorials_home: https://pychromvar.readthedocs.io/
 install:
   pypi: pychromvar
 tags:
diff --git a/packages/pytximport/meta.yaml b/packages/pytximport/meta.yaml
index 424627bd..2d48fc45 100644
--- a/packages/pytximport/meta.yaml
+++ b/packages/pytximport/meta.yaml
@@ -2,8 +2,8 @@ name: pytximport
 description: |
   A Python port of the `tximport` R package for importing transcript-level quantification data from various RNA-seq quantification tools such as `salmon` and `kallisto` and summarizing it to the gene level.
 project_home: https://github.com/complextissue/pytximport
-documentation_home: https://pytximport.readthedocs.io/en/latest/
-tutorials_home: https://pytximport.readthedocs.io/en/latest/
+documentation_home: https://pytximport.readthedocs.io/
+tutorials_home: https://pytximport.readthedocs.io/
 install:
   pypi: pytximport
 tags:
diff --git a/packages/rapids-singlecell/meta.yaml b/packages/rapids-singlecell/meta.yaml
index ce2c2e99..75097b62 100644
--- a/packages/rapids-singlecell/meta.yaml
+++ b/packages/rapids-singlecell/meta.yaml
@@ -3,8 +3,8 @@ description: |
   rapids-singlecell is a GPU-accelerated single-cell analysis library that serves as a
   drop-in replacement for scanpy, squidpy, and decoupler.
 project_home: https://github.com/scverse/rapids_singlecell
-documentation_home: https://rapids-singlecell.readthedocs.io/en/latest/
-tutorials_home: https://rapids-singlecell.readthedocs.io/en/latest/notebooks.html
+documentation_home: https://rapids-singlecell.readthedocs.io/
+tutorials_home: https://rapids-singlecell.readthedocs.io/page/notebooks.html
 install:
   pypi: rapids-singlecell
 tags:
diff --git a/packages/scFates/meta.yaml b/packages/scFates/meta.yaml
index ea8f7189..68923196 100644
--- a/packages/scFates/meta.yaml
+++ b/packages/scFates/meta.yaml
@@ -2,8 +2,8 @@ name: scFates
 description: |
   A scalable python package for tree inference and advanced pseudotime analysis from scRNAseq data.
 project_home: https://github.com/LouisFaure/scFates
-documentation_home: https://scfates.readthedocs.io/en/latest/
-tutorials_home: https://scfates.readthedocs.io/en/latest/Tree_Analysis_Bone_marrow_fates.html
+documentation_home: https://scfates.readthedocs.io/
+tutorials_home: https://scfates.readthedocs.io/page/Tree_Analysis_Bone_marrow_fates.html
 publications:
   - 10.1093/bioinformatics/btac746
 install:
diff --git a/packages/scGen/meta.yaml b/packages/scGen/meta.yaml
index 4e760fcd..19ac78bf 100644
--- a/packages/scGen/meta.yaml
+++ b/packages/scGen/meta.yaml
@@ -3,8 +3,8 @@ description: |
   scGen is a generative model to predict single-cell perturbation response
   across cell types, studies and species.
 project_home: https://github.com/theislab/scgen
-documentation_home: https://scgen.readthedocs.io/en/stable/
-tutorials_home: https://scgen.readthedocs.io/en/stable/tutorials/index.html
+documentation_home: https://scgen.readthedocs.io/
+tutorials_home: https://scgen.readthedocs.io/page/tutorials/index.html
 publications:
   - 10.1038/s41592-019-0494-8
 install:
diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml
index b0665c65..d8b41c6a 100644
--- a/packages/scXpand/meta.yaml
+++ b/packages/scXpand/meta.yaml
@@ -3,8 +3,8 @@ description: |
   scXpand is a machine learning framework for pan-cancer detection of T-cell clonal expansion
   directly from single-cell RNA sequencing (scRNA-seq), without paired T-cell receptor (TCR) sequencing.
 project_home: https://github.com/yizhak-lab-ccg/scXpand
-documentation_home: https://scxpand.readthedocs.io/en/latest/
-tutorials_home: https://scxpand.readthedocs.io/en/latest/
+documentation_home: https://scxpand.readthedocs.io/
+tutorials_home: https://scxpand.readthedocs.io/
 publications:
   - 10.1101/2025.09.14.676069
 install:
diff --git a/packages/scanpro/meta.yaml b/packages/scanpro/meta.yaml
index 8aec480f..a91d6abe 100644
--- a/packages/scanpro/meta.yaml
+++ b/packages/scanpro/meta.yaml
@@ -2,7 +2,7 @@ name: scanpro
 description: robust cell proportion analysis for single cell data
 project_home: https://github.com/loosolab/scanpro
 documentation_home: https://scanpro.readthedocs.io
-tutorials_home: https://scanpro.readthedocs.io/en/latest/proportion_analysis.html
+tutorials_home: https://scanpro.readthedocs.io/page/proportion_analysis.html
 publications:
   - 10.1101/2023.08.14.553234
 install:
diff --git a/packages/scanpy/meta.yaml b/packages/scanpy/meta.yaml
index 292bbeed..c799c640 100644
--- a/packages/scanpy/meta.yaml
+++ b/packages/scanpy/meta.yaml
@@ -5,8 +5,8 @@ description: |
   and differential expression testing. The Python-based implementation efficiently deals
   with datasets of more than one million cells.
 project_home: https://github.com/scverse/scanpy
-documentation_home: https://scanpy.readthedocs.io/en/latest/
-tutorials_home: https://scanpy.readthedocs.io/en/latest/tutorials.html
+documentation_home: https://scanpy.readthedocs.io/
+tutorials_home: https://scanpy.readthedocs.io/page/tutorials.html
 publications:
   - 10.1186/s13059-017-1382-0
 install:
diff --git a/packages/schist/meta.yaml b/packages/schist/meta.yaml
index 1f6a49eb..6582ecec 100644
--- a/packages/schist/meta.yaml
+++ b/packages/schist/meta.yaml
@@ -2,7 +2,7 @@ name: schist
 description: schist applies Stochastic Block Models (SBM) to the analysis of single cell data, in particular to identify cell populations
 project_home: https://github.com/dawe/schist
 documentation_home: https://schist.readthedocs.io
-tutorials_home: https://schist.readthedocs.io/en/latest/tutorials.html
+tutorials_home: https://schist.readthedocs.io/page/tutorials.html
 install:
   conda: conda-forge::schist
 license: BSD-3-Clause
diff --git a/packages/scirpy/meta.yaml b/packages/scirpy/meta.yaml
index a12d5396..1c1b0dc2 100644
--- a/packages/scirpy/meta.yaml
+++ b/packages/scirpy/meta.yaml
@@ -5,7 +5,7 @@ description: |
   various modules for data import, analysis and visualization.
 project_home: https://github.com/scverse/scirpy
 documentation_home: https://scirpy.scverse.org/
-tutorials_home: https://scirpy.scverse.org/en/latest/tutorials.html
+tutorials_home: https://scirpy.scverse.org/page/tutorials.html
 publications:
   - 10.1093/bioinformatics/btaa611
 install:
diff --git a/packages/sctriangulate/meta.yaml b/packages/sctriangulate/meta.yaml
index 4ded158e..5b31e45e 100644
--- a/packages/sctriangulate/meta.yaml
+++ b/packages/sctriangulate/meta.yaml
@@ -2,8 +2,8 @@ name: scTriangulate
 description: |
   Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
 project_home: https://github.com/frankligy/scTriangulate
-documentation_home: https://sctriangulate.readthedocs.io/en/latest/get_started.html
-tutorials_home: https://sctriangulate.readthedocs.io/en/latest/tutorial.html
+documentation_home: https://sctriangulate.readthedocs.io/page/get_started.html
+tutorials_home: https://sctriangulate.readthedocs.io/page/tutorial.html
 publications:
   - 10.1101/2021.10.16.464640
 install:
diff --git a/packages/scverse-tutorials/meta.yaml b/packages/scverse-tutorials/meta.yaml
index 509c448f..9e72106c 100644
--- a/packages/scverse-tutorials/meta.yaml
+++ b/packages/scverse-tutorials/meta.yaml
@@ -2,8 +2,8 @@ name: scverse-tutorials
 description: |
   Tutorials and tutorials registry for scverse.org/learn.
 project_home: https://github.com/scverse/scverse-tutorials
-documentation_home: https://scverse-tutorials.readthedocs.io/en/latest/
-tutorials_home: https://scverse-tutorials.readthedocs.io/en/latest/
+documentation_home: https://scverse-tutorials.readthedocs.io/
+tutorials_home: https://scverse-tutorials.readthedocs.io/
 tags:
   - tutorials
   - education
diff --git a/packages/scvi-tools/meta.yaml b/packages/scvi-tools/meta.yaml
index 56c55d56..90ab25e9 100644
--- a/packages/scvi-tools/meta.yaml
+++ b/packages/scvi-tools/meta.yaml
@@ -6,8 +6,8 @@ description: |
   scvi-tools also contains easy-to-use implementations of more than 14 state-of-the-art
   probabilistic models in the field.
 project_home: https://github.com/scverse/scvi-tools
-documentation_home: https://docs.scvi-tools.org/en/stable/
-tutorials_home: https://docs.scvi-tools.org/en/stable/tutorials/index.html
+documentation_home: https://docs.scvi-tools.org/
+tutorials_home: https://docs.scvi-tools.org/page/tutorials/index.html
 publications:
   - 10.1038/s41587-021-01206-w # Scvi-tools library paper, NBT 2022
   - 10.1038/s41587-022-01272-8 # DestVI
diff --git a/packages/sincei/meta.yaml b/packages/sincei/meta.yaml
index 79fa5e21..cf562e29 100644
--- a/packages/sincei/meta.yaml
+++ b/packages/sincei/meta.yaml
@@ -6,7 +6,7 @@ description: |
   - Perform dimensionality reduction and clustering of various types of single-cell data (open chromatin, histone marks, methylation etc..).
   - Create coverage files (bigwigs) for visualization.
 project_home: https://github.com/bhardwaj-lab/sincei
-documentation_home: https://sincei.readthedocs.io/en/latest/
+documentation_home: https://sincei.readthedocs.io/
 publications:
   - 10.1101/2024.07.27.605424
 install:
diff --git a/packages/spatial-eggplant/meta.yaml b/packages/spatial-eggplant/meta.yaml
index d09db477..932a8f8f 100644
--- a/packages/spatial-eggplant/meta.yaml
+++ b/packages/spatial-eggplant/meta.yaml
@@ -2,8 +2,8 @@ name: spatial-eggplant
 description: |
   Python package designed to transfer information from multiple spatial-transcriptomics data sets to a single reference representing a Common Coordinate Framework (CCF).
 project_home: https://github.com/almaan/eggplant
-documentation_home: https://spatial-eggplant.readthedocs.io/en/latest/index.html
-tutorials_home: https://spatial-eggplant.readthedocs.io/en/latest/index.html
+documentation_home: https://spatial-eggplant.readthedocs.io/page/index.html
+tutorials_home: https://spatial-eggplant.readthedocs.io/page/index.html
 publications:
   - 10.1101/2021.11.11.468178
 install:
diff --git a/packages/spatialdata/meta.yaml b/packages/spatialdata/meta.yaml
index 95d0b825..b1f6e126 100644
--- a/packages/spatialdata/meta.yaml
+++ b/packages/spatialdata/meta.yaml
@@ -4,8 +4,8 @@ description: |
   python libraries for performant access, alignment, and processing of uni- and multi-modal
   spatial omics datasets.
 project_home: https://github.com/scverse/spatialdata
-documentation_home: https://spatialdata.scverse.org/en/latest/
-tutorials_home: https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks.html
+documentation_home: https://spatialdata.scverse.org/
+tutorials_home: https://spatialdata.scverse.org/page/tutorials/notebooks/notebooks.html
 publications:
   - 10.1038/s41592-024-02212-x
 install:
diff --git a/packages/squidpy/meta.yaml b/packages/squidpy/meta.yaml
index fae640b3..8e0ac1e8 100644
--- a/packages/squidpy/meta.yaml
+++ b/packages/squidpy/meta.yaml
@@ -6,7 +6,7 @@ description: |
   if available.
 project_home: https://github.com/scverse/squidpy
 documentation_home: https://squidpy.readthedocs.io/
-tutorials_home: https://squidpy.readthedocs.io/en/latest/notebooks/tutorials/index.html
+tutorials_home: https://squidpy.readthedocs.io/page/notebooks/tutorials/index.html
 publications:
   - 10.1038/s41592-021-01358-2
 install:
diff --git a/packages/tangram/meta.yaml b/packages/tangram/meta.yaml
index 4a01dc5f..a27e65f5 100644
--- a/packages/tangram/meta.yaml
+++ b/packages/tangram/meta.yaml
@@ -2,8 +2,8 @@ name: tangram
 description: |
   Spatial alignment and gene expression mapping of single cell transcriptomic data.
 project_home: https://github.com/broadinstitute/Tangram
-documentation_home: https://tangram-sc.readthedocs.io/en/latest/index.html
-tutorials_home: https://tangram-sc.readthedocs.io/en/latest/tutorials.html
+documentation_home: https://tangram-sc.readthedocs.io/page/index.html
+tutorials_home: https://tangram-sc.readthedocs.io/page/tutorials.html
 publications:
   - 10.1038/s41592-021-01264-7
 install:
diff --git a/packages/wsidata/meta.yaml b/packages/wsidata/meta.yaml
index cdddab0b..bee8e6f8 100644
--- a/packages/wsidata/meta.yaml
+++ b/packages/wsidata/meta.yaml
@@ -2,7 +2,7 @@ name: wsidata
 description: |
   wsidata is a data-structure for efficient IO of Whole Slide Images based on spatialdata.
 project_home: https://github.com/rendeirolab/wsidata
-documentation_home: https://wsidata.readthedocs.io/en/latest/
+documentation_home: https://wsidata.readthedocs.io/
 install:
   pypi: wsidata
 tags:

From 79babce65cf850483f529fa17b49b2dfd2c14e74 Mon Sep 17 00:00:00 2001
From: "Philipp A." <flying-sheep@web.de>
Date: Tue, 27 Jan 2026 10:08:09 +0100
Subject: [PATCH 2/2] unify

---
 packages/DRVI/meta.yaml             | 2 +-
 packages/Mowgli/meta.yaml           | 2 +-
 packages/PyDESeq2/meta.yaml         | 4 ++--
 packages/Rectangle/meta.yaml        | 2 +-
 packages/SnapATAC2/meta.yaml        | 2 +-
 packages/anndata/meta.yaml          | 2 +-
 packages/biolord/meta.yaml          | 4 ++--
 packages/decoupler/meta.yaml        | 2 +-
 packages/moscot/meta.yaml           | 2 +-
 packages/palantir/meta.yaml         | 2 +-
 packages/panpipes/meta.yaml         | 4 ++--
 packages/pyLemur/meta.yaml          | 2 +-
 packages/scCellFie/meta.yaml        | 4 ++--
 packages/scGen/meta.yaml            | 2 +-
 packages/scanpro/meta.yaml          | 2 +-
 packages/schist/meta.yaml           | 2 +-
 packages/scib/meta.yaml             | 2 +-
 packages/scvelo/meta.yaml           | 2 +-
 packages/scvi-tools/meta.yaml       | 2 +-
 packages/sift-sc/meta.yaml          | 4 ++--
 packages/spatial-eggplant/meta.yaml | 4 ++--
 packages/squidpy/meta.yaml          | 2 +-
 packages/tangram/meta.yaml          | 2 +-
 23 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/packages/DRVI/meta.yaml b/packages/DRVI/meta.yaml
index c4011935..f2700ee6 100644
--- a/packages/DRVI/meta.yaml
+++ b/packages/DRVI/meta.yaml
@@ -7,7 +7,7 @@ description: |
   set of utility functions for interacting with latent dimensions.
 project_home: https://github.com/theislab/DRVI
 documentation_home: https://drvi.readthedocs.io/
-tutorials_home: https://drvi.readthedocs.io/page/tutorials/index.html
+tutorials_home: https://drvi.readthedocs.io/page/tutorials/
 publications:
   - 10.1101/2024.11.06.622266
 install:
diff --git a/packages/Mowgli/meta.yaml b/packages/Mowgli/meta.yaml
index 02e96f77..1009d028 100644
--- a/packages/Mowgli/meta.yaml
+++ b/packages/Mowgli/meta.yaml
@@ -2,7 +2,7 @@ name: Mowgli
 description: |
   Paired single-cell multi-omics data integration with Optimal Transport-flavored Nonnegative Matrix Factorization
 project_home: https://github.com/cantinilab/mowgli
-documentation_home: https://mowgli.readthedocs.io
+documentation_home: https://mowgli.readthedocs.io/
 publications:
   - 10.1101/2023.02.02.526825
 install:
diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml
index a84b4aee..246b7894 100644
--- a/packages/PyDESeq2/meta.yaml
+++ b/packages/PyDESeq2/meta.yaml
@@ -3,8 +3,8 @@ description: |
   PyDESeq2 is a python package for bulk RNA-seq differential expression analysis. It is a re-implementation
   from scratch of the main features of the R package DESeq2 (Love et al. 2014).
 project_home: https://github.com/owkin/PyDESeq2
-documentation_home: https://pydeseq2.readthedocs.io
-tutorials_home: https://pydeseq2.readthedocs.io/page/auto_examples/index.html
+documentation_home: https://pydeseq2.readthedocs.io/
+tutorials_home: https://pydeseq2.readthedocs.io/page/auto_examples/
 install:
   pypi: pydeseq2
 license: MIT
diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml
index 10456308..b6b6a1bc 100644
--- a/packages/Rectangle/meta.yaml
+++ b/packages/Rectangle/meta.yaml
@@ -3,7 +3,7 @@ description: |
   Rectangle is a python package for computational deconvolution.
   Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing, an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
 project_home: https://github.com/ComputationalBiomedicineGroup/Rectangle
-documentation_home: https://rectanglepy.readthedocs.io
+documentation_home: https://rectanglepy.readthedocs.io/
 tutorials_home: https://rectanglepy.readthedocs.io/notebooks/example.html
 install:
   pypi: rectanglepy
diff --git a/packages/SnapATAC2/meta.yaml b/packages/SnapATAC2/meta.yaml
index dd9fa019..b39c0e8a 100644
--- a/packages/SnapATAC2/meta.yaml
+++ b/packages/SnapATAC2/meta.yaml
@@ -5,7 +5,7 @@ description: |
   with single-cell RNA-seq.
 project_home: https://github.com/scverse/SnapATAC2
 documentation_home: https://scverse.org/SnapATAC2/
-tutorials_home: https://scverse.org/SnapATAC2/tutorials/index.html
+tutorials_home: https://scverse.org/SnapATAC2/tutorials/
 publications:
   - 10.1038/s41592-023-02139-9
 install:
diff --git a/packages/anndata/meta.yaml b/packages/anndata/meta.yaml
index fddef4c9..578f75d9 100644
--- a/packages/anndata/meta.yaml
+++ b/packages/anndata/meta.yaml
@@ -5,7 +5,7 @@ description: |
   efficient features including, among others, sparse data support, lazy operations, and GPU support.
 project_home: https://github.com/scverse/anndata
 documentation_home: https://anndata.readthedocs.io/
-tutorials_home: https://anndata.readthedocs.io/page/tutorials/index.html
+tutorials_home: https://anndata.readthedocs.io/page/tutorials/
 publications:
   - 10.1101/2021.12.16.473007
 install:
diff --git a/packages/biolord/meta.yaml b/packages/biolord/meta.yaml
index 646dffa3..390bd05d 100644
--- a/packages/biolord/meta.yaml
+++ b/packages/biolord/meta.yaml
@@ -2,8 +2,8 @@ name: biolord
 description: |
   biolord (biological representation disentanglement) is a deep generative framework for disentangling known and unknown attributes in single-cell data.
 project_home: https://github.com/nitzanlab/biolord
-documentation_home: https://biolord.readthedocs.io
-tutorials_home: https://biolord.readthedocs.io
+documentation_home: https://biolord.readthedocs.io/
+tutorials_home: https://biolord.readthedocs.io/
 install:
   pypi: biolord
 tags:
diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml
index 468e5720..a32a87a9 100644
--- a/packages/decoupler/meta.yaml
+++ b/packages/decoupler/meta.yaml
@@ -4,7 +4,7 @@ description: |
   biologically driven scores from omics data within a unified framework.
 project_home: https://github.com/scverse/decoupler
 documentation_home: https://decoupler.readthedocs.io/
-tutorials_home: https://decoupler.readthedocs.io/page/notebooks/index.html
+tutorials_home: https://decoupler.readthedocs.io/page/notebooks/
 publications:
   - 10.1093/bioadv/vbac016
 install:
diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml
index fb1f9ebe..5ccb5a1d 100644
--- a/packages/moscot/meta.yaml
+++ b/packages/moscot/meta.yaml
@@ -2,7 +2,7 @@ name: moscot
 description: |
   moscot is a scalable toolbox for multiomics single-cell optimal transport applications.
 project_home: https://github.com/theislab/moscot
-documentation_home: https://moscot.readthedocs.io/page/index.html
+documentation_home: https://moscot.readthedocs.io/page/
 publications:
   - 10.1101/2023.05.11.540374
 install:
diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml
index 17bb6419..417bffc0 100644
--- a/packages/palantir/meta.yaml
+++ b/packages/palantir/meta.yaml
@@ -8,7 +8,7 @@ description: |
   Palantir has been designed to work with multidimensional single cell data from
   diverse technologies such as Mass cytometry and single cell RNA-seq.
 project_home: https://github.com/dpeerlab/Palantir
-documentation_home: https://palantir.readthedocs.io
+documentation_home: https://palantir.readthedocs.io/
 publications:
   - 10.1038/s41587-019-0068-4
 install:
diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml
index b58507f5..8cda09a2 100644
--- a/packages/panpipes/meta.yaml
+++ b/packages/panpipes/meta.yaml
@@ -2,8 +2,8 @@ name: Panpipes
 description: |
   A pipeline for multiomic single-cell and spatial transcriptomic data analysis
 project_home: https://github.com/DendrouLab/panpipes
-documentation_home: https://panpipes-pipelines.readthedocs.io/page/index.html
-tutorials_home: https://panpipes-pipelines.readthedocs.io/page/tutorials/index.html
+documentation_home: https://panpipes-pipelines.readthedocs.io/
+tutorials_home: https://panpipes-pipelines.readthedocs.io/page/tutorials/
 publications:
   - 10.1101/2023.03.11.532085
 install:
diff --git a/packages/pyLemur/meta.yaml b/packages/pyLemur/meta.yaml
index 499e2607..6053cf09 100644
--- a/packages/pyLemur/meta.yaml
+++ b/packages/pyLemur/meta.yaml
@@ -2,7 +2,7 @@ name: pyLemur
 description: |
   Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data..
 project_home: https://github.com/const-ae/pyLemur
-documentation_home: https://pyLemur.readthedocs.io
+documentation_home: https://pyLemur.readthedocs.io/
 tutorials_home: https://pylemur.readthedocs.io/page/notebooks/Tutorial.html
 publications:
   - 10.1101/2023.03.06.531268
diff --git a/packages/scCellFie/meta.yaml b/packages/scCellFie/meta.yaml
index 8a63145e..f49538bd 100644
--- a/packages/scCellFie/meta.yaml
+++ b/packages/scCellFie/meta.yaml
@@ -2,8 +2,8 @@ name: scCellFie
 description: |
   scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.
 project_home: https://github.com/earmingol/scCellFie
-documentation_home: https://sccellfie.readthedocs.io
-tutorials_home: https://sccellfie.readthedocs.io
+documentation_home: https://sccellfie.readthedocs.io/
+tutorials_home: https://sccellfie.readthedocs.io/
 install:
   pypi: sccellfie
 tags:
diff --git a/packages/scGen/meta.yaml b/packages/scGen/meta.yaml
index 19ac78bf..a15f822d 100644
--- a/packages/scGen/meta.yaml
+++ b/packages/scGen/meta.yaml
@@ -4,7 +4,7 @@ description: |
   across cell types, studies and species.
 project_home: https://github.com/theislab/scgen
 documentation_home: https://scgen.readthedocs.io/
-tutorials_home: https://scgen.readthedocs.io/page/tutorials/index.html
+tutorials_home: https://scgen.readthedocs.io/page/tutorials/
 publications:
   - 10.1038/s41592-019-0494-8
 install:
diff --git a/packages/scanpro/meta.yaml b/packages/scanpro/meta.yaml
index a91d6abe..76ef198c 100644
--- a/packages/scanpro/meta.yaml
+++ b/packages/scanpro/meta.yaml
@@ -1,7 +1,7 @@
 name: scanpro
 description: robust cell proportion analysis for single cell data
 project_home: https://github.com/loosolab/scanpro
-documentation_home: https://scanpro.readthedocs.io
+documentation_home: https://scanpro.readthedocs.io/
 tutorials_home: https://scanpro.readthedocs.io/page/proportion_analysis.html
 publications:
   - 10.1101/2023.08.14.553234
diff --git a/packages/schist/meta.yaml b/packages/schist/meta.yaml
index 6582ecec..5fde688f 100644
--- a/packages/schist/meta.yaml
+++ b/packages/schist/meta.yaml
@@ -1,7 +1,7 @@
 name: schist
 description: schist applies Stochastic Block Models (SBM) to the analysis of single cell data, in particular to identify cell populations
 project_home: https://github.com/dawe/schist
-documentation_home: https://schist.readthedocs.io
+documentation_home: https://schist.readthedocs.io/
 tutorials_home: https://schist.readthedocs.io/page/tutorials.html
 install:
   conda: conda-forge::schist
diff --git a/packages/scib/meta.yaml b/packages/scib/meta.yaml
index a470e0c5..17f91009 100644
--- a/packages/scib/meta.yaml
+++ b/packages/scib/meta.yaml
@@ -2,7 +2,7 @@ name: scib
 description: |
   Evaluating single-cell data integration methods
 project_home: https://github.com/theislab/scib
-documentation_home: https://scib.readthedocs.io
+documentation_home: https://scib.readthedocs.io/
 publications:
   - 10.1038/s41592-021-01336-8
 install:
diff --git a/packages/scvelo/meta.yaml b/packages/scvelo/meta.yaml
index a359f1d2..94344866 100644
--- a/packages/scvelo/meta.yaml
+++ b/packages/scvelo/meta.yaml
@@ -2,7 +2,7 @@ name: scVelo
 description: |
   scVelo is a scalable toolkit for RNA velocity analysis in single cells, based on [Bergen et al., Nature Biotech, 2020](https://doi.org/10.1038/s41587-020-0591-3).
 project_home: https://github.com/theislab/scvelo
-documentation_home: https://scvelo.readthedocs.io
+documentation_home: https://scvelo.readthedocs.io/
 publications:
   - 10.1038/s41587-020-0591-3
 install:
diff --git a/packages/scvi-tools/meta.yaml b/packages/scvi-tools/meta.yaml
index 90ab25e9..f96dbe9a 100644
--- a/packages/scvi-tools/meta.yaml
+++ b/packages/scvi-tools/meta.yaml
@@ -7,7 +7,7 @@ description: |
   probabilistic models in the field.
 project_home: https://github.com/scverse/scvi-tools
 documentation_home: https://docs.scvi-tools.org/
-tutorials_home: https://docs.scvi-tools.org/page/tutorials/index.html
+tutorials_home: https://docs.scvi-tools.org/page/tutorials/
 publications:
   - 10.1038/s41587-021-01206-w # Scvi-tools library paper, NBT 2022
   - 10.1038/s41587-022-01272-8 # DestVI
diff --git a/packages/sift-sc/meta.yaml b/packages/sift-sc/meta.yaml
index 77af9977..6be22aac 100644
--- a/packages/sift-sc/meta.yaml
+++ b/packages/sift-sc/meta.yaml
@@ -3,8 +3,8 @@ description: |
   SiFT is a computational framework which aims to uncover the underlying structure by filtering out previously exposed biological signals.
   SiFT can be applied to a wide range of tasks, from (i) the removal of unwanted variation as a pre-processing step, through (ii) revealing hidden biological structure by utilizing prior knowledge with respect to existing signal, to (iii) uncovering trajectories of interest using reference data to remove unwanted variation.
 project_home: https://github.com/nitzanlab/sift-sc
-documentation_home: https://sift-sc.readthedocs.io
-tutorials_home: https://sift-sc.readthedocs.io
+documentation_home: https://sift-sc.readthedocs.io/
+tutorials_home: https://sift-sc.readthedocs.io/
 install:
   pypi: sift-sc
 tags:
diff --git a/packages/spatial-eggplant/meta.yaml b/packages/spatial-eggplant/meta.yaml
index 932a8f8f..26cd1cb0 100644
--- a/packages/spatial-eggplant/meta.yaml
+++ b/packages/spatial-eggplant/meta.yaml
@@ -2,8 +2,8 @@ name: spatial-eggplant
 description: |
   Python package designed to transfer information from multiple spatial-transcriptomics data sets to a single reference representing a Common Coordinate Framework (CCF).
 project_home: https://github.com/almaan/eggplant
-documentation_home: https://spatial-eggplant.readthedocs.io/page/index.html
-tutorials_home: https://spatial-eggplant.readthedocs.io/page/index.html
+documentation_home: https://spatial-eggplant.readthedocs.io/
+tutorials_home: https://spatial-eggplant.readthedocs.io/
 publications:
   - 10.1101/2021.11.11.468178
 install:
diff --git a/packages/squidpy/meta.yaml b/packages/squidpy/meta.yaml
index 8e0ac1e8..2f525b81 100644
--- a/packages/squidpy/meta.yaml
+++ b/packages/squidpy/meta.yaml
@@ -6,7 +6,7 @@ description: |
   if available.
 project_home: https://github.com/scverse/squidpy
 documentation_home: https://squidpy.readthedocs.io/
-tutorials_home: https://squidpy.readthedocs.io/page/notebooks/tutorials/index.html
+tutorials_home: https://squidpy.readthedocs.io/page/notebooks/tutorials/
 publications:
   - 10.1038/s41592-021-01358-2
 install:
diff --git a/packages/tangram/meta.yaml b/packages/tangram/meta.yaml
index a27e65f5..9081c8ce 100644
--- a/packages/tangram/meta.yaml
+++ b/packages/tangram/meta.yaml
@@ -2,7 +2,7 @@ name: tangram
 description: |
   Spatial alignment and gene expression mapping of single cell transcriptomic data.
 project_home: https://github.com/broadinstitute/Tangram
-documentation_home: https://tangram-sc.readthedocs.io/page/index.html
+documentation_home: https://tangram-sc.readthedocs.io/
 tutorials_home: https://tangram-sc.readthedocs.io/page/tutorials.html
 publications:
   - 10.1038/s41592-021-01264-7