try fo fix CI

Author: kaizhang

.github/actions/build-docs/action.yml

@@ -63,7 +63,7 @@ runs:
     shell: bash
     run: |
       #JSON=$(cat ${GITHUB_WORKSPACE}/docs/_static/versions.json)
-      JSON=$(curl -s "https://raw.githubusercontent.com/kaizhang/SnapATAC2/main/docs/_static/versions.json")
+      JSON=$(curl -s "https://raw.githubusercontent.com/scverse/SnapATAC2/main/docs/_static/versions.json")
       VERSION=$(echo "$JSON" | jq -r '.[] | select(.preferred == true) | .version')
       echo "PREFERRED_VERSION=$VERSION" >> $GITHUB_ENV
       echo "Preferred version is $VERSION"

.github/workflows/nightly.yml

@@ -36,7 +36,7 @@ jobs:
   build-wheel:
     needs: check-for-new-commits
     if : ${{ needs.check-for-new-commits.outputs.NEW_COMMITS == 'true' }}
-    uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main
+    uses: scverse/SnapATAC2/.github/workflows/wheels.yml@main
 
   publish:
     needs: build-wheel

.github/workflows/test_python.yml

@@ -35,7 +35,7 @@ jobs:
   build-wheel:
     needs: build-and-test
     if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, '[wheel]') }}
-    uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main
+    uses: scverse/SnapATAC2/.github/workflows/wheels.yml@main
 
   publish:
     needs: build-wheel

README.md

@@ -3,8 +3,8 @@ SnapATAC2: A Python/Rust package for single-cell epigenomics analysis
 
 ![PyPI](https://img.shields.io/pypi/v/snapatac2)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/snapatac2)
-![Continuous integration](https://github.com/kaizhang/SnapATAC2/workflows/test-python-package/badge.svg)
-![GitHub Repo stars](https://img.shields.io/github/stars/kaizhang/SnapATAC2?style=social)
+![Continuous integration](https://github.com/scverse/SnapATAC2/workflows/test-python-package/badge.svg)
+![GitHub Repo stars](https://img.shields.io/github/stars/scverse/SnapATAC2?style=social)
 
 > [!TIP]
 > Got raw fastq files? Check out our new single-cell preprocessing package [precellar](https://github.com/regulatory-genomics/precellar)!
@@ -19,13 +19,12 @@ SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis fram
 - Seamless integration with other single-cell analysis packages such as Scanpy.
 - Implementation of fully backed AnnData.
 
-Resources
----------
+Documentation
+-------------
 
-- **Full Documentation**: https://kzhang.org/SnapATAC2/
-- **Installation instructions**: https://kzhang.org/SnapATAC2/install.html
-- **Tutorial/Demo**: https://kzhang.org/SnapATAC2/tutorials/index.html
-- **Benchmarks**: https://github.com/kaizhang/single-cell-benchmark
+- **Full Documentation**: https://scverse.org/SnapATAC2/
+- **Installation instructions**: https://scverse.org/SnapATAC2/install.html
+- **Tutorial/Demo**: https://scverse.org/SnapATAC2/tutorials/index.html
 
 How to cite
 -----------

docs/conf.py

@@ -28,7 +28,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'SnapATAC2'
-copyright = '2022-2024, Kai Zhang'
+copyright = '2022-2025, Kai Zhang'
 author = 'Kai Zhang'
 
 # -- General configuration ---------------------------------------------------
@@ -128,7 +128,7 @@
         "alt_text": "SnapATAC2",
     },
 
-    "github_url": "https://github.com/kaizhang/SnapATAC2",
+    "github_url": "https://github.com/scverse/SnapATAC2",
     "external_links": [
         {"name": "Learn", "url": "https://kzhang.org/epigenomics-analysis/"}
     ],
@@ -141,12 +141,12 @@
 
     "switcher": {
         "version_match": switcher_version,
-        "json_url": "https://raw.githubusercontent.com/kaizhang/SnapATAC2/main/docs/_static/versions.json", 
+        "json_url": "https://raw.githubusercontent.com/scverse/SnapATAC2/refs/heads/main/docs/_static/versions.json",
     },
 }
 
 commit = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip().decode('ascii')
-code_url = f"https://github.com/kaizhang/SnapATAC2/blob/{commit}"
+code_url = f"https://github.com/scverse/SnapATAC2/blob/{commit}"
 
 # based on numpy doc/source/conf.py
 def linkcode_resolve(domain, info):

docs/install.md

@@ -35,7 +35,7 @@ The nightly build is the build from the latest source codes, which includes the
 latest features, enhancements, and bug fixes that haven't been released. 
 The nightly build can be unstable and include some untested features.
 
-The [nightly release](https://github.com/kaizhang/SnapATAC2/releases/tag/nightly) page
+The [nightly release](https://github.com/scverse/SnapATAC2/releases/tag/nightly) page
 contains wheel files for the nightly build.
 Please download the corresponding wheel file for your platform and use `pip install` to install it.
 For example, if you are using a Linux system with Python 3.8, you can use the following command to install it:
@@ -60,7 +60,7 @@ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
 Once you have the Rust compiler properly installed, you can use pip to install the SnapATAC2 library:
 
 ```
-pip install 'git+https://github.com/kaizhang/SnapATAC2.git#egg=snapatac2&subdirectory=snapatac2-python'
+pip install 'git+https://github.com/scverse/SnapATAC2.git#egg=snapatac2&subdirectory=snapatac2-python'
 ```
 
 Optional dependencies

snapatac2-contrib/setup.py

@@ -14,7 +14,7 @@
     description='SnapATAC2: Single-cell epigenomics analysis pipeline',
     long_description=README,
     long_description_content_type='text/markdown',
-    url='https://kzhang.org/SnapATAC2/', 
+    url='https://scverse.org/SnapATAC2/', 
     license='MIT',
     version=VERSION['__version__'],
     packages=[

snapatac2-python/README.md

@@ -1,4 +1,4 @@
 SnapATAC2
 =========
 
-Please read the [Documentation](https://kzhang.org/SnapATAC2/). 
+Please read the [Documentation](https://scverse.org/SnapATAC2/). 

snapatac2-python/pyproject.toml

@@ -49,11 +49,11 @@ dependencies = [
 ]
 
 [project.urls]
-Homepage = "https://kzhang.org/SnapATAC2/index.html"
-Documentation = "https://kzhang.org/SnapATAC2/index.html"
-Repository = "https://kzhang.org/SnapATAC2/"
-Issues = "https://github.com/kaizhang/SnapATAC2/issues"
-Changelog = "https://kzhang.org/SnapATAC2/version/dev/changelog.html"
+Homepage = "https://scverse.org/SnapATAC2/index.html"
+Documentation = "https://scverse.org/SnapATAC2/index.html"
+Repository = "https://scverse.org/SnapATAC2/"
+Issues = "https://github.com/scverse/SnapATAC2/issues"
+Changelog = "https://scverse.org/SnapATAC2/version/dev/changelog.html"
 
 [project.optional-dependencies]
 recommend = [

snapatac2-python/python/snapatac2/preprocessing/_basic.py

@@ -988,7 +988,7 @@ def select_features(
     various functions to generate submatrices on the fly.
     Features that are zero in all cells will be always removed regardless of the
     filtering criteria.
-    For more discussion about feature selection, see: https://github.com/kaizhang/SnapATAC2/discussions/116.
+    For more discussion about feature selection, see: https://github.com/scverse/SnapATAC2/discussions/116.
 
     Parameters
     ----------
@@ -1021,7 +1021,7 @@ def select_features(
         If greater than 1, this function will perform iterative clustering and feature selection
         based on variable features found using previous clustering results.
         This is similar to the procedure implemented in ArchR, but we do not recommend it,
-        see https://github.com/kaizhang/SnapATAC2/issues/111.
+        see https://github.com/scverse/SnapATAC2/issues/111.
         Default value is 1, which means no iterative clustering is performed.
     inplace
         Perform computation inplace or return result.