Require Python 3.11 and test through 3.14

.github/workflows/tests.yml

@@ -14,9 +14,9 @@ jobs:
     strategy:
       matrix:
         include:
-          - python-version: "3.9"
-            setuptools: "setuptools==77.0.3"
           - python-version: "3.11"
+            setuptools: "setuptools==77.0.3"
+          - python-version: "3.14"
             setuptools: "setuptools"
     steps:
       - uses: actions/checkout@v4
@@ -45,11 +45,19 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - python-version: "3.9"
+          - python-version: "3.11"
             pandas-version: "minimum"
             pyarrow-version: "minimum"
             polars-version: "none"
-          - python-version: "3.10"
+          - python-version: "3.12"
+            pandas-version: "latest"
+            pyarrow-version: "latest"
+            polars-version: "none"
+          - python-version: "3.13"
+            pandas-version: "latest"
+            pyarrow-version: "latest"
+            polars-version: "none"
+          - python-version: "3.14"
             pandas-version: "latest"
             pyarrow-version: "latest"
             polars-version: "none"

AGENTS.md

@@ -29,7 +29,7 @@ Do not tell the user you are "done" or that changes are "complete" until both pa
 
 - Use ruff for linting
 - Configuration is in `pyproject.toml` under `[tool.ruff]`
-- Target Python version: 3.9+ (CI matrix runs 3.9 / 3.10 / 3.11)
+- Target Python version: 3.11+ (CI matrix runs 3.11 through 3.14)
 
 ## Project Shape
 

README.md

@@ -16,7 +16,7 @@ into columns.
 python -m pip install gtfparse
 ```
 
-Python 3.9 or later is required. For optional Polars output, install
+Python 3.11 or later is required. For optional Polars output, install
 `gtfparse[polars]`.
 
 ## Read an annotation and find genes

benchmarks/compare_releases.py

@@ -11,7 +11,7 @@
 import statistics
 import subprocess
 import sys
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 from pathlib import Path
 
 
@@ -120,7 +120,7 @@ def main():
                         )
     result = {
         "description": "Complete production readers; imports/checksums outside wall time; sequential fresh processes",
-        "date": datetime.now(timezone.utc).isoformat(),
+        "date": datetime.now(UTC).isoformat(),
         "threads": args.threads,
         "inputs": {
             path.name: {

docs/index.md

@@ -9,7 +9,7 @@ attribute values such as gene and transcript IDs expanded into columns.
 python -m pip install gtfparse
 ```
 
-Python 3.9 or later is required. For optional Polars output, install
+Python 3.11 or later is required. For optional Polars output, install
 `gtfparse[polars]`.
 
 ## Read an annotation and find genes

gtfparse/__init__.py

@@ -24,7 +24,7 @@
 )
 from .write_gtf import write_gtf
 
-__version__ = "3.0.4"
+__version__ = "3.0.5"
 
 __all__ = [
     "GENCODE_BIOTYPE_ALIASES",

gtfparse/write_gtf.py

@@ -16,7 +16,7 @@
 from collections.abc import Iterable
 from itertools import repeat
 from pathlib import Path
-from typing import TYPE_CHECKING, Optional, Union
+from typing import TYPE_CHECKING, Union
 
 import pandas as pd
 
@@ -74,7 +74,7 @@ def _lines(df):
 def write_gtf(
     df: Union[pd.DataFrame, "polars.DataFrame"],
     path: Union[str, Path],
-    header_lines: Optional[Iterable[str]] = None,
+    header_lines: Iterable[str] | None = None,
 ) -> None:
     """
     Write a DataFrame of genomic features back out to a GTF file.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gtfparse"
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 authors = [ {name="Alex Rubinsteyn", email="alex.rubinsteyn@unc.edu" } ]
 description = "Parsing library for extracting data frames of genomic features from GTF files"
 license = "Apache-2.0"
@@ -16,10 +16,10 @@ 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",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 readme = "README.md"
@@ -46,7 +46,7 @@ dependencies = {file = ["requirements.txt"]}
 packages = ["gtfparse"]
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py311"
 line-length = 100
 src = ["gtfparse", "tests"]
 exclude = [
@@ -78,7 +78,7 @@ ignore = [
     "B008",   # do not perform function calls in argument defaults
     "B905",   # zip() without explicit strict
     "SIM108", # use ternary operator instead of if-else
-    "UP007",  # use X | Y for type unions (need Python 3.10+)
+    "UP007",  # retain the established Union annotation style
     "UP031",  # %-format strings
 ]
 

tasks/todo.md

@@ -521,3 +521,34 @@ PR #93: lint passed, all 213 tests passed, all three executable documentation
 examples passed, and the strict MkDocs build passed.
 PR #95: merged the refreshed parent; version 3.0.4, lint, 213 tests, and the
 strict MkDocs build passed.
+
+# Python 3.11 support floor (#96)
+
+## Specification
+
+Require Python 3.11 or newer with no upper bound. Test Python 3.11–3.14 in CI,
+retaining the existing pandas, PyArrow, and optional Polars compatibility
+combinations. Keep support for both pandas 2 and 3 because this change only
+raises the Python floor. Align package metadata, docs, tooling, and repository
+guidance; bump the patch version to 3.0.5. Preserve parsing behavior.
+
+## Plan
+
+- [x] Read issue, package requirements, CI matrix, repo guidance, and tests.
+- [x] Check plan before implementation: retain compatibility jobs on 3.11 and
+  add 3.12–3.14 jobs with current dependencies; move packaging endpoints to
+  3.11 and 3.14.
+- [x] Update metadata, docs, CI, target version, and package version.
+- [x] Run `./lint.sh` and `./test.sh` in an isolated environment.
+- [x] Verify installed metadata/dependencies and tests on Python 3.11 and 3.14;
+  review the diff.
+- [ ] Open PR, pass CI, merge, deploy from clean master, verify publication.
+
+## Review
+
+`./lint.sh` passed. `./test.sh -W error::DeprecationWarning` passed all 213
+tests with pandas 3.0.6, PyArrow 26, and Polars 2.0.0 on both Python 3.11.12
+and 3.14.6 (97% coverage). Isolated dependency checks passed at both endpoints.
+Installed metadata reports version 3.0.5, `Requires-Python: >=3.11`, and the
+existing pandas 2-compatible dependency floor. Ruff's new Python target enabled
+two safe Python 3.11 syntax updates; no parsing behavior changed.