pystatgen to sgkit-dev rename

Author: hammer

.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: