Merge branch 'main' into add-flashdeconv

Author: flying-sheep

.pre-commit-config.yaml

@@ -18,18 +18,18 @@ repos:
       - id: trailing-whitespace
       - id: check-case-conflict
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.7.4
+    rev: v3.8.1
     hooks:
       - id: prettier
   # package metadata
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.0
+    rev: 0.36.2
     hooks:
       - id: check-jsonschema
         files: "scripts/src/ecosystem_scripts/schema.json"
         args: ["--check-metaschema"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.0
+    rev: 0.36.2
     hooks:
       - id: check-jsonschema
         files: "packages/.*/meta.yaml"
@@ -45,15 +45,15 @@ repos:
         exclude: "^packages/.*/(meta.yaml|logo\\..*)$"
   # scripts
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.1
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
         files: ^scripts/.*$
       - id: ruff-format
         files: ^scripts/.*$
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.11.1
+    rev: v2.16.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/camptocamp/jsonschema-gentypes

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: