Drop Python 3.9 support

Author: benjeffery

.github/workflows/cd.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/ci.yml

@@ -25,7 +25,7 @@ jobs:
         # Use macos-13 because pip binary packages for ARM aren't
         # available for many dependencies
         os: [macos-13, macos-14, ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         exclude:
           # Just run macos tests on one Python version
           - os: macos-13
@@ -34,8 +34,6 @@ jobs:
             python-version: "3.11"
           - os: macos-13
             python-version: "3.12"
-          - os: macos-14
-            python-version: "3.9"
           - os: macos-14
             python-version: "3.10"
           - os: macos-14

bio2zarr/core.py

@@ -7,10 +7,8 @@
 import multiprocessing
 import os
 import os.path
-import sys
 import threading
 import time
-import warnings
 
 import humanfriendly
 import numcodecs
@@ -256,22 +254,6 @@ def setup_progress_counter(counter):
     _progress_counter = counter
 
 
-def warn_py39_mac():
-    if sys.platform == "darwin" and sys.version_info[:2] == (3, 9):
-        warnings.warn(
-            "There is a known issue with bio2zarr on MacOS Python 3.9 "
-            "in which OS-level named semaphores are leaked. "
-            "You will also probably see warnings like 'There appear to be N "
-            "leaked semaphore objects at shutdown'. "
-            "While this is likely harmless for a few runs, it could lead to "
-            "issues if you do a lot of conversion. To get prevent this issue "
-            "either: (1) use --worker-processes=0 or (2) upgrade to a newer "
-            "Python version. See https://github.com/sgkit-dev/bio2zarr/issues/209 "
-            "for more details.",
-            stacklevel=2,
-        )
-
-
 class ParallelWorkManager(contextlib.AbstractContextManager):
     def __init__(self, worker_processes=1, progress_config=None):
         # Need to specify this explicitly to suppport Macs and
@@ -284,7 +266,6 @@ def __init__(self, worker_processes=1, progress_config=None):
             # production. See note on the SynchronousExecutor class.
             self.executor = SynchronousExecutor()
         else:
-            warn_py39_mac()
             self.executor = cf.ProcessPoolExecutor(
                 max_workers=worker_processes,
                 mp_context=ctx,

pyproject.toml

@@ -26,7 +26,7 @@ dependencies = [
   "cyvcf2",
   "bed_reader",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
   "Development Status :: 4 - Beta",
   "License :: OSI Approved :: Apache Software License",
@@ -37,7 +37,6 @@ 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",
@@ -76,8 +75,8 @@ testpaths = "tests"
 addopts = "--cov=bio2zarr --cov-report term-missing"
 
 [tool.ruff]
-# Assume Python 3.9
-target-version = "py39"
+# Assume Python 3.10
+target-version = "py310"
 
 # Same as Black.
 line-length = 88