Merge branch 'main' into infrastructure-packages

Author: grst

.github/workflows/make-json.yml

@@ -6,7 +6,7 @@ on:
     branches: [main]
 
 concurrency:
-  group: "pages"
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
       - id: trailing-whitespace
       - id: check-case-conflict
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.6.2
+    rev: v3.7.4
     hooks:
       - id: prettier
   # package metadata
@@ -45,7 +45,7 @@ repos:
         exclude: "^packages/.*/(meta.yaml|logo\\..*)$"
   # scripts
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.5
+    rev: v0.14.9
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
@@ -57,15 +57,15 @@ repos:
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/camptocamp/jsonschema-gentypes
-    rev: "2.12.0"
+    rev: "2.13.0"
     hooks:
       - id: jsonschema-gentypes
         args:
           - --json-schema=scripts/src/ecosystem_scripts/schema.json
           - --python=scripts/src/ecosystem_scripts/schema.pyi
         files: ^scripts/.*/schema.json$
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
+    rev: v1.19.1
     hooks:
       - id: mypy
         args: [--config-file=scripts/pyproject.toml, scripts]

packages/DRVI/meta.yaml

@@ -0,0 +1,26 @@
+name: DRVI
+description: |
+  DRVI is a tool for the unsupervised disentanglement and integration of single-cell omics.
+  By providing interpretable latent dimensions, it allows users to identify cellular
+  heterogeneity and biological processes beyond traditional cell types, identify rare cell types,
+  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
+publications:
+  - 10.1101/2024.11.06.622266
+install:
+  pypi: drvi-py
+tags:
+  - disentanglement
+  - interpretability
+  - data integration
+  - variational inference
+  - deep learning
+license: BSD-3-Clause
+version: 0.2.0
+contact:
+  - moinfar
+test_command: uvx hatch run pytest
+category: ecosystem

packages/SnapATAC2/logo.svg

@@ -0,0 +1,24 @@
+name: SnapATAC2
+description: |
+  SnapATAC2 is a scalable and modular pipeline for analyzing single-cell ATAC-seq data,
+  enabling efficient preprocessing, dimensionality reduction, clustering, and integration
+  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
+publications:
+  - 10.1038/s41592-023-02139-9
+install:
+  pypi: snapatac2
+  conda: bioconda::snapatac2
+tags:
+  - ATAC-seq
+  - chromatin accessibility
+  - epigenomics
+license: MIT
+version: 2.5.0
+contact:
+  - kaizhang
+logo: logo.svg
+test_command: pip install ".[test]" && pytest
+category: core-framework

packages/SnapATAC2/meta.yaml

@@ -0,0 +1,17 @@
+name: TreeData
+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/
+install:
+  pypi: treedata
+tags:
+  - lineage-tracing
+license: BSD-3-Clause
+version: v0.2.2
+contact:
+  - colganwi
+test_command: pip install ".[test]" && pytest
+category: ecosystem

packages/TreeData/meta.yaml

@@ -1,12 +1,19 @@
 name: anndata for R
 description: |
-  A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
+  **⚠️ DEPRECATED: This package is deprecated in favor of anndataR. Please use
+  anndataR for new projects.**
+
+  A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way
+  of keeping track of data and learned annotations. Used to read from and write to
+  the h5ad file format.
 project_home: https://github.com/dynverse/anndata
 documentation_home: https://anndata.dynverse.org
 install:
   cran: anndata
 tags:
-  - R package
+  - data structures
+  - interoperability
+  - R
 license: MIT
 version: 0.7.5.5
 contact:

packages/anndata-for-R/meta.yaml

@@ -0,0 +1,24 @@
+name: AnnData
+description: |
+  anndata is a Python package for handling annotated data matrices in memory and on disk,
+  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
+publications:
+  - 10.1101/2021.12.16.473007
+install:
+  pypi: anndata
+  conda: conda-forge::anndata
+tags:
+  - data structure
+  - annotated data
+  - sparse data
+license: BSD-3-Clause
+version: 0.12.4
+contact:
+  - flying-sheep
+  - ilan-gold
+logo: logo.svg
+category: core-datastructure