pystatgen to sgkit-dev rename

.github/scripts/test_sgkit_bgen.py

@@ -4,7 +4,7 @@
 
 if __name__ == "__main__":
     urllib.request.urlretrieve(
-        "https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/bgen/data/example.bgen",
+        "https://github.com/sgkit-dev/sgkit/raw/main/sgkit/tests/io/bgen/data/example.bgen",
         "example.bgen",
     )
     ds = read_bgen("example.bgen")

.github/scripts/test_sgkit_plink.py

@@ -5,7 +5,7 @@
 if __name__ == "__main__":
     for ext in (".bed", ".bim", ".fam"):
         urllib.request.urlretrieve(
-            f"https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/plink/data/plink_sim_10s_100v_10pmiss{ext}",
+            f"https://github.com/sgkit-dev/sgkit/raw/main/sgkit/tests/io/plink/data/plink_sim_10s_100v_10pmiss{ext}",
             f"plink_sim_10s_100v_10pmiss{ext}",
         )
     ds = read_plink(path="plink_sim_10s_100v_10pmiss")

.github/scripts/test_sgkit_vcf.py

@@ -7,7 +7,7 @@
 if __name__ == "__main__":
     for ext in (".gz", ".gz.tbi"):
         urllib.request.urlretrieve(
-            f"https://github.com/pystatgen/sgkit/raw/main/sgkit/tests/io/vcf/data/sample.vcf{ext}",
+            f"https://github.com/sgkit-dev/sgkit/raw/main/sgkit/tests/io/vcf/data/sample.vcf{ext}",
             f"sample.vcf{ext}",
         )
     vcf_to_zarr("sample.vcf.gz", "out")

.github/workflows/benchmark.yml

@@ -7,14 +7,14 @@ on:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
-  BENCHMARKS_REPO: pystatgen/sgkit-benchmarks-asv
+  BENCHMARKS_REPO: sgkit-dev/sgkit-benchmarks-asv
   ASV_CONFIG: benchmarks/asv.conf.json
   MACHINE_NAME: github-actions  # to identify github actions machine as hostname changes everytime
 
 jobs:
   build:
     # This workflow only runs on the origin org
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -62,7 +62,7 @@ jobs:
         run: |
           cd ~/$BENCHMARKS_REPO
           git add .
-          git config --global user.email "project@pystatgen.org"
+          git config --global user.email "project@sgkit-dev.org"
           git config --global user.name "sgkit benchmark bot"
           git commit -m "Update benchmarks"
           git push origin main

.github/workflows/build.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   build:
     # Scheduled runs only on the origin org
-    if: (github.event_name == 'schedule' && github.repository_owner == 'pystatgen') || (github.event_name != 'schedule')
+    if: (github.event_name == 'schedule' && github.repository_owner == 'sgkit-dev') || (github.event_name != 'schedule')
     runs-on: ubuntu-latest
     strategy:
       matrix:

.github/workflows/check-docs.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   build:
     # Scheduled runs only on the origin org
-    if: (github.event_name == 'schedule' && github.repository_owner == 'pystatgen') || (github.event_name != 'schedule')
+    if: (github.event_name == 'schedule' && github.repository_owner == 'sgkit-dev') || (github.event_name != 'schedule')
     runs-on: ubuntu-latest
     strategy:
       matrix:

.github/workflows/docs.yml

@@ -28,7 +28,7 @@ jobs:
         make html SPHINXOPTS="-W --keep-going -n"
     - name: Commit documentation changes to gh-pages branch
       run: |
-        git clone https://github.com/pystatgen/sgkit.git --branch gh-pages --single-branch gh-pages
+        git clone https://github.com/sgkit-dev/sgkit.git --branch gh-pages --single-branch gh-pages
         mkdir -p gh-pages/latest
         cp -r docs/_build/html/* gh-pages/latest
         cd gh-pages

.github/workflows/upstream.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   build:
     # This workflow only runs on the origin org
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
     strategy:
       matrix:

.github/workflows/validation.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   validation_suite:
     # This workflow only runs on the origin org
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v2

.github/workflows/wheels.yml

@@ -13,7 +13,7 @@ on:
 jobs:
   build:
     # This workflow only runs on the origin org
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -40,7 +40,7 @@ jobs:
 
   unix-test:
     # This workflow only runs on the origin org
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     needs: ['build']
     strategy:
       matrix:
@@ -72,7 +72,7 @@ jobs:
   # Windows doesn't support vcf
   windows-test:
     # This workflow only runs on the origin org
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     runs-on: windows-latest
     needs: ['build']
     strategy:
@@ -100,7 +100,7 @@ jobs:
           python sgkit-copy/.github/scripts/test_sgkit_plink.py
 
   pypi-upload:
-    if: github.repository_owner == 'pystatgen'
+    if: github.repository_owner == 'sgkit-dev'
     runs-on: ubuntu-latest
     needs: ['unix-test', 'windows-test']
     steps:

.github/workflows/windows.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   win_build:
     # Scheduled runs only on the origin org
-    if: (github.event_name == 'schedule' && github.repository_owner == 'pystatgen') || (github.event_name != 'schedule')
+    if: (github.event_name == 'schedule' && github.repository_owner == 'sgkit-dev') || (github.event_name != 'schedule')
     runs-on: windows-latest
     strategy:
       matrix:

.mergify.yml

@@ -6,7 +6,7 @@ queue_rules:
       - status-success=build (3.10)
       - status-success=build (3.11)
       - status-success=win_build (3.9)
-      - approved-reviews-by=@pystatgen/committers
+      - approved-reviews-by=@sgkit-dev/committers
       - "#approved-reviews-by>=1"
       - label=auto-merge
 
@@ -18,7 +18,7 @@ pull_request_rules:
       - status-success=build (3.10)
       - status-success=build (3.11)
       - status-success=win_build (3.9)
-      - approved-reviews-by=@pystatgen/committers
+      - approved-reviews-by=@sgkit-dev/committers
       - "#approved-reviews-by>=1"
       - label=auto-merge
     actions:

CONTRIBUTING.md

@@ -1,3 +1,3 @@
 All contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome.
 
-For general information on how to contribute see https://pystatgen.github.io/sgkit/latest/contributing.html.
+For general information on how to contribute see https://sgkit-dev.github.io/sgkit/latest/contributing.html.

GOVERNANCE.md

@@ -1 +1 @@
-Please see our [code of conduct](https://github.com/pystatgen/.github/blob/master/CODE_OF_CONDUCT.md) for more information.
+Please see our [code of conduct](https://github.com/sgkit-dev/.github/blob/master/CODE_OF_CONDUCT.md) for more information.

README.md

@@ -1,17 +1,17 @@
 # sgkit: Statistical genetics toolkit in Python
-[![Build status](https://github.com/pystatgen/sgkit/workflows/Build/badge.svg?branch=main)](https://github.com/pystatgen/sgkit/actions?query=workflow%3A%22Build%22+branch%3Amain)
-[![Windows build status](https://github.com/pystatgen/sgkit/workflows/Windows/badge.svg?branch=main)](https://github.com/pystatgen/sgkit/actions?query=workflow%3A%22Windows%22+branch%3Amain)
-[![Documentation status](https://github.com/pystatgen/sgkit/workflows/Docs/badge.svg?branch=main)](https://pystatgen.github.io/sgkit/)
-[![Validation status](https://github.com/pystatgen/sgkit/workflows/Validation/badge.svg?branch=main)](https://github.com/pystatgen/sgkit/actions?query=workflow%3A%22Validation%22+branch%3Amain)
-[![Upstream status](https://github.com/pystatgen/sgkit/workflows/Upstream/badge.svg?branch=main)](https://github.com/pystatgen/sgkit/actions?query=workflow%3A%22Upstream%22+branch%3Amain)
-[![asv](https://img.shields.io/badge/Benchmarked%20by-asv-green.svg?style=flat)](https://pystatgen.github.io/sgkit-benchmarks-asv/)
+[![Build status](https://github.com/sgkit-dev/sgkit/workflows/Build/badge.svg?branch=main)](https://github.com/sgkit-dev/sgkit/actions?query=workflow%3A%22Build%22+branch%3Amain)
+[![Windows build status](https://github.com/sgkit-dev/sgkit/workflows/Windows/badge.svg?branch=main)](https://github.com/sgkit-dev/sgkit/actions?query=workflow%3A%22Windows%22+branch%3Amain)
+[![Documentation status](https://github.com/sgkit-dev/sgkit/workflows/Docs/badge.svg?branch=main)](https://sgkit-dev.github.io/sgkit/)
+[![Validation status](https://github.com/sgkit-dev/sgkit/workflows/Validation/badge.svg?branch=main)](https://github.com/sgkit-dev/sgkit/actions?query=workflow%3A%22Validation%22+branch%3Amain)
+[![Upstream status](https://github.com/sgkit-dev/sgkit/workflows/Upstream/badge.svg?branch=main)](https://github.com/sgkit-dev/sgkit/actions?query=workflow%3A%22Upstream%22+branch%3Amain)
+[![asv](https://img.shields.io/badge/Benchmarked%20by-asv-green.svg?style=flat)](https://sgkit-dev.github.io/sgkit-benchmarks-asv/)
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](http://numfocus.org)
 
 Sgkit is a Python package that provides a variety of analytical genetics methods through the use of
 general-purpose frameworks such as [Xarray](http://xarray.pydata.org/en/stable/), [Pandas](https://pandas.pydata.org/docs/),
 [Dask](https://docs.dask.org/en/latest/) and [Zarr](https://zarr.readthedocs.io/en/stable/).
 
-For more information on using sgkit, see the [documentation](https://pystatgen.github.io/sgkit/).
+For more information on using sgkit, see the [documentation](https://sgkit-dev.github.io/sgkit/).
 
 [//]: # (numfocus-fiscal-sponsor-attribution)
 

benchmarks/asv.conf.json

@@ -7,7 +7,7 @@
     "project": "sgkit",
 
     // The project's homepage
-    "project_url": "https://pystatgen.github.io/sgkit/",
+    "project_url": "https://sgkit-dev.github.io/sgkit/",
 
     // The URL or local path of the source code repository for the
     // project being benchmarked
@@ -55,7 +55,7 @@
     //"install_timeout": 600,
 
     // the base URL to show a commit for the project.
-     "show_commit_url": "http://github.com/pystatgen/sgkit/commit/",
+     "show_commit_url": "http://github.com/sgkit-dev/sgkit/commit/",
 
     // The Pythons you'd like to test against.  If not provided, defaults
     // to the current version of Python used to run `asv`.

docs/_static/switcher.json

@@ -1,37 +1,37 @@
 [
     {
         "version": "latest",
-        "url": "https://pystatgen.github.io/sgkit/latest/"
+        "url": "https://sgkit-dev.github.io/sgkit/latest/"
     },
     {
         "name": "0.7.0 (stable)",
         "version": "0.7.0",
-        "url": "https://pystatgen.github.io/sgkit/0.7.0/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.7.0/"
     },
     {
         "name": "0.6.0",
         "version": "0.6.0",
-        "url": "https://pystatgen.github.io/sgkit/0.6.0/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.6.0/"
     },
     {
         "name": "0.5.0",
         "version": "0.5.0",
-        "url": "https://pystatgen.github.io/sgkit/0.5.0/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.5.0/"
     },
     {
         "version": "0.4.0",
-        "url": "https://pystatgen.github.io/sgkit/0.4.0/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.4.0/"
     },
     {
         "version": "0.3.0",
-        "url": "https://pystatgen.github.io/sgkit/0.3.0/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.3.0/"
     },
     {
         "version": "0.2.0a1",
-        "url": "https://pystatgen.github.io/sgkit/0.2.0a1/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.2.0a1/"
     },
     {
         "version": "0.1.0a1",
-        "url": "https://pystatgen.github.io/sgkit/0.1.0a1/"
+        "url": "https://sgkit-dev.github.io/sgkit/0.1.0a1/"
     }
 ]

docs/conf.py

@@ -66,8 +66,8 @@
 ]
 
 extlinks = {
-    "issue": ("https://github.com/pystatgen/sgkit/issues/%s", "GH %s"),
-    "pr": ("https://github.com/pystatgen/sgkit/pull/%s", "PR %s"),
+    "issue": ("https://github.com/sgkit-dev/sgkit/issues/%s", "GH %s"),
+    "pr": ("https://github.com/sgkit-dev/sgkit/pull/%s", "PR %s"),
     "user": ("https://github.com/%s", "%s"),
 }
 
@@ -96,7 +96,7 @@ def filter(self, record: pylogging.LogRecord) -> bool:
 
 html_context = dict(
     display_github=False,  # Integrate GitHub
-    github_user="pystatgen",  # Username
+    github_user="sgkit-dev",  # Username
     github_repo="sgkit",  # Repo name
     github_version="main",  # Version
     conf_py_path="/docs/",  # Path in the checkout to the docs root
@@ -142,7 +142,7 @@ def filter(self, record: pylogging.LogRecord) -> bool:
 
 # https://pydata-sphinx-theme.readthedocs.io/en/latest/user_guide/configuring.html
 html_theme_options = {
-    "github_url": "https://github.com/pystatgen/sgkit",
+    "github_url": "https://github.com/sgkit-dev/sgkit",
     "logo": {
         "image_light": "sgkit_trnsprnt.png",
         "image_dark": "sgkit_blue_trnsprnt.png",