fix: use default version of pages so links don’t break

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)

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:

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:

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:

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:

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

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:

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/
 publications:
   - 10.1101/2024.11.06.622266
 install:

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:

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:

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:

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:

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:

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

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:

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/en/latest/auto_examples/index.html
+documentation_home: https://pydeseq2.readthedocs.io/
+tutorials_home: https://pydeseq2.readthedocs.io/page/auto_examples/
 install:
   pypi: pydeseq2
 license: MIT

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

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:

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:

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:

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:

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/
 publications:
   - 10.1101/2021.12.16.473007
 install:

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

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:

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:

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:

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

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

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/
 publications:
   - 10.1093/bioadv/vbac016
 install:

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:

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:

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:

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:

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

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

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:

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: