Drop support for Python 3.9

Author: nsoranzo

.github/workflows/test.yaml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     steps:
       - uses: actions/checkout@v5
         with:
@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
     steps:
       - uses: actions/checkout@v5
         with:

lib/bx/misc/seekbzip2_tests.py

@@ -6,12 +6,11 @@
 import os
 import random
 from codecs import encode
-from typing import Optional
 
 from bx.misc import seekbzip2
 
-F: Optional[str] = None
-T: Optional[str] = None
+F: str | None = None
+T: str | None = None
 
 # F="/Users/james/work/seek-bzip2/test_random.dat.bz2"
 # T="/Users/james/cache/hg18/align/multiz28way/chr10.maf.bz2"

pyproject.toml

@@ -29,7 +29,6 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Operating System :: POSIX",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -38,7 +37,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "numpy",
     "pyparsing",
@@ -52,7 +51,6 @@ Homepage = "https://github.com/bxlab/bx-python"
 [tool.black]
 include = '\.pyi?$'
 line-length = 120
-target-version = ['py39']
 
 [tool.cibuildwheel]
 test-command = """
@@ -116,9 +114,6 @@ EOF
 [tool.darker]
 isort = true
 
-[tool.ruff]
-target-version = "py39"
-
 [tool.ruff.lint]
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
 # flake8-comprehensions (C4), flake8-logging-format (G),

scripts/bed_coverage.py

@@ -12,14 +12,13 @@
 import sys
 from typing import (
     TextIO,
-    Union,
 )
 
 from bx.bitset_builders import binned_bitsets_from_file
 
 bed_filenames = sys.argv[1:]
 if bed_filenames:
-    input: Union[fileinput.FileInput, TextIO] = fileinput.input(bed_filenames)
+    input: fileinput.FileInput | TextIO = fileinput.input(bed_filenames)
 else:
     input = sys.stdin
 

scripts/bed_merge_overlapping.py

@@ -12,14 +12,13 @@
 import sys
 from typing import (
     TextIO,
-    Union,
 )
 
 from bx.bitset_builders import binned_bitsets_from_bed_file
 
 bed_filenames = sys.argv[1:]
 if bed_filenames:
-    input: Union[fileinput.FileInput, TextIO] = fileinput.input(bed_filenames)
+    input: fileinput.FileInput | TextIO = fileinput.input(bed_filenames)
 else:
     input = sys.stdin