Drop Python 3.9

Try removing Windows cbgen restriction

Fix quotes

.github/workflows/benchmark.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
-          python-version: '3.9'
+          python-version: ["3.10"]
       - name: Install dependencies
         run: |
           sudo apt update -y

.github/workflows/build-gpu.yml

@@ -17,7 +17,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10"]
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/docs.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
-        python-version: '3.10'
+        python-version: ["3.10"]
     - name: Install dependencies
       run: |
         sudo apt update -y

.github/workflows/wheels.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@v2
@@ -46,7 +46,7 @@ jobs:
       matrix:
         # don't use macos-latest as it uses M1 which doesn't work
         os: [ubuntu-latest, macos-12]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
     runs-on: ${{ matrix.os }}
     steps:
       # checkout repo to subdirectory to get access to scripts
@@ -76,7 +76,7 @@ jobs:
     needs: ['build']
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
     steps:
       # checkout repo to subdirectory to get access to scripts
       - uses: actions/checkout@v2

.github/workflows/windows.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@v2

.mergify.yml

@@ -2,10 +2,9 @@ queue_rules:
   - name: default
     conditions:
       - base=main
-      - status-success=build (3.9)
       - status-success=build (3.10)
       - status-success=build (3.11)
-      - status-success=win_build (3.9)
+      - status-success=win_build (3.10)
       - approved-reviews-by=@sgkit-dev/committers
       - "#approved-reviews-by>=1"
       - label=auto-merge
@@ -14,10 +13,9 @@ pull_request_rules:
   - name: automatic merge
     conditions:
       - base=main
-      - status-success=build (3.9)
       - status-success=build (3.10)
       - status-success=build (3.11)
-      - status-success=win_build (3.9)
+      - status-success=win_build (3.10)
       - approved-reviews-by=@sgkit-dev/committers
       - "#approved-reviews-by>=1"
       - label=auto-merge

docs/changelog.rst

@@ -21,6 +21,9 @@ Breaking changes
   and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages instead.
   (:user:`tomwhite`, :pr:`1264`)
 
+- Drop support for Python 3.9.
+  (:user:`tomwhite`, :pr:`1276`)
+
 .. Deprecations
 .. ~~~~~~~~~~~~
 

docs/getting_started.rst

@@ -10,7 +10,7 @@ Getting Started
 Installation
 ------------
 
-You can install sgkit with pip. Python 3.9, 3.10, or 3.11 is required::
+You can install sgkit with pip. Python 3.10, 3.11, or 3.12 is required::
 
     $ pip install sgkit
 

requirements-dev.txt

@@ -12,8 +12,7 @@ scikit-learn
 partd
 bed-reader
 rechunker
-cbgen < 1.0.5; platform_system != "Windows"
-cbgen == 1.0.1; platform_system == "Windows"
+cbgen < 1.0.5
 bio2zarr; platform_system != "Windows"
 yarl
 matplotlib

requirements-numpy2-dev.txt

@@ -12,8 +12,7 @@ scikit-learn
 partd
 bed-reader
 rechunker
-cbgen > 1.0.5; platform_system != "Windows"
-cbgen == 1.0.1; platform_system == "Windows"
+cbgen > 1.0.5
 yarl
 matplotlib
 asv

setup.cfg

@@ -16,7 +16,6 @@ classifiers =
     Intended Audience :: Science/Research
     Programming Language :: Python
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
@@ -26,7 +25,7 @@ classifiers =
 packages = sgkit
 zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.html
 include_package_data = True
-python_requires = >=3.9
+python_requires = >=3.10
 install_requires =
     numpy < 2
     xarray
@@ -62,8 +61,7 @@ plink =
     bed-reader
 bgen =
     rechunker
-    cbgen < 1.0.5; platform_system != "Windows"
-    cbgen == 1.0.1; platform_system == "Windows"
+    cbgen < 1.0.5
 
 [coverage:report]
 fail_under = 100