Add support for Python 3.13 (#241)

* Add support for Python 3.13

* Fix imports

* Skip numba test for >= 3.13

* Use numpy >= 2 only in build-system

* Revert scipy

* Bump wfdb

* Remove Python 3.9

* Fix style

* Fix Python version badge

* Add pytest-cov dependency

* Add changelog entry

.github/workflows/cibuildwheel.yml

@@ -90,10 +90,8 @@ jobs:
       - run: ls -al dist
       - name: Triage dependencies
         run: |
-          if [[ "${{ matrix.python-version }}" != "3.13" ]]; then
-            echo "PIP_EXTRA=wfdb numpy<2 numba pytest-error-for-skips" | tee -a $GITHUB_ENV
-            echo "PYTEST_EXTRA=--error-for-skips" | tee -a $GITHUB_ENV
-          fi
+          echo "PIP_EXTRA=wfdb numba pytest-error-for-skips" | tee -a $GITHUB_ENV
+          echo "PYTEST_EXTRA=--error-for-skips" | tee -a $GITHUB_ENV
       - run: python -m pip install ./dist/*.whl pytest pytest-cov edfio $PIP_EXTRA --only-binary="numpy,numba,edfio"
       - run: pytest -rfEXs --cov=sleepecg --cov-report=xml --tb=short --cov-branch --color=yes $PYTEST_EXTRA tests/
       - uses: codecov/codecov-action@v5

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.5
+    rev: v0.9.2
     hooks:
       - id: ruff
         args: [ --fix ]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.14.1
     hooks:
     - id: mypy
       exclude: ^tests|^examples
-      args: [--python-version=3.9]
+      args: [--python-version=3.10]
       additional_dependencies:
       - types-PyYAML
       - types-requests

CHANGELOG.md

@@ -6,6 +6,9 @@
 ### Changed
 - Split `get_config` function into `get_config` and `get_config_value` to get the entire configuration (as a dictionary) or an individual configuration key, respectively ([#229](https://github.com/cbrnr/sleepecg/pull/225) by [Clemens Brunner](https://github.com/cbrnr))
 
+### Removed
+- Remove Python 3.9 support ([#241](https://github.com/cbrnr/sleepecg/pull/241) by [Clemens Brunner](https://github.com/cbrnr))
+
 ### Fixed
 - Fix `plot_ecg` for newer versions of Matplotlib ([#225](https://github.com/cbrnr/sleepecg/pull/225) by [Clemens Brunner](https://github.com/cbrnr))
 

README.md

@@ -1,4 +1,4 @@
-![Python](https://img.shields.io/pypi/pyversions/sleepecg.svg?logo=python&logoColor=white)
+![Python](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fcbrnr%2Fsleepecg%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&logo=python&logoColor=white)
 [![PyPI](https://img.shields.io/pypi/v/sleepecg)](https://pypi.org/project/sleepecg/)
 [![Docs](https://readthedocs.org/projects/sleepecg/badge/?version=latest)](https://sleepecg.readthedocs.io/en/stable/index.html)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05411/status.svg)](https://doi.org/10.21105/joss.05411)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "setuptools-scm", "wheel", "numpy>=2,<3"]
+requires = ["setuptools", "setuptools-scm", "wheel", "numpy>=2"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -11,38 +11,38 @@ authors = [
     {name = "Clemens Brunner", email = "[email protected]"},
 ]
 readme = "README.md"
-requires-python = ">= 3.9"
+requires-python = ">= 3.10"
 classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS :: MacOS X",
     "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 :: Implementation :: CPython",
     "Typing :: Typed",
 ]
 keywords = ["sleep", "ecg", "qrs", "peak"]
 dependencies = [
-    "numpy >= 1.25.0, < 3.0.0",
-    "PyYAML >= 5.4.0",
-    "requests >= 2.25.0",
-    "scipy >= 1.7.0",
-    "tqdm >= 4.60.0",
+    "numpy >= 1.26.0",
+    "pyyaml >= 6.0.0",
+    "requests >= 2.32.3",
+    "scipy >= 1.13.0",
+    "tqdm >= 4.66.0",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 full = [  # complete package functionality
-    "edfio >= 0.4.0",
-    "joblib >= 1.0.0",
-    "matplotlib >= 3.5.0",
-    "numba >= 0.59.1",
-    "tensorflow >= 2.16.1",
-    "wfdb >= 3.4.0",
+    "edfio >= 0.4.4",
+    "joblib >= 1.4.2",
+    "matplotlib >= 3.9.2",
+    "numba >= 0.61.0",
+    "tensorflow >= 2.17.0; python_version < '3.13'",
+    "wfdb >= 4.2.0",
 ]
 
 dev = [  # everything needed for development
@@ -51,21 +51,20 @@ dev = [  # everything needed for development
     "mypy >= 0.991",
     "pre-commit >= 2.13.0",
     "pytest >= 6.2.0",
+    "pytest-cov >= 6.0.0",
     "ruff >= 0.4.0",
-    "setuptools >= 56.0.0",
+    "setuptools >= 72.1.0",
 ]
 
 doc = [  # RTD uses this when building the documentation
-    "mkdocs-material >= 8.4.0",
-    "mkdocstrings-python >= 0.8.2",
+    "mkdocs-material >= 9.5.0",
+    "mkdocstrings-python >= 1.11.1",
 ]
 
 cibw = [  # cibuildwheel uses this for running the test suite
-    "edfio >= 0.4.0",
-    "numba >= 0.59.1",
-    "wfdb >= 3.4.0",
-    # https://github.com/MIT-LCP/wfdb-python/pull/511
-    "numpy < 2.0.0",  # TODO: just for wfdb!
+    "edfio >= 0.4.4",
+    "numba >= 0.61.0",
+    "wfdb >= 4.2.0",
 ]
 
 [project.urls]
@@ -79,7 +78,7 @@ test-requires = "pytest"
 test-extras = "cibw"
 test-command = "pytest {package}"
 skip = 'pp* *musllinux*'
-build = "cp39-*"  # abi3
+build = "cp310-*"  # abi3
 
 [[tool.cibuildwheel.overrides]]
 select = "*"

readthedocs.yml

@@ -6,7 +6,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 mkdocs:
   configuration: mkdocs.yml

setup.py

@@ -4,18 +4,17 @@
 
 # Following https://github.com/joerick/python-abi3-package-sample
 
-
-# Currently set to 3.9. If this is bumped for example to 3.10, the hex
-# in the Extension needs to change to 0x030A0000, and the cibuildwheel `build`
-# selector needs to change in pyproject.toml
+# Currently set to 3.10. If this is bumped for example to 3.11, the hex in the Extension
+# needs to change to 0x030B0000, and the cibuildwheel `build` selector needs to change
+# in pyproject.toml.
 
 class bdist_wheel_abi3(bdist_wheel):
     def get_tag(self) -> tuple:
         python, abi, plat = super().get_tag()
 
         if python.startswith("cp"):
             # on CPython, our wheels are abi3 and compatible back to 3.6
-            return "cp39", "abi3", plat
+            return "cp310", "abi3", plat
 
         return python, abi, plat
 
@@ -26,7 +25,7 @@ def get_tag(self) -> tuple:
             "sleepecg._heartbeat_detection",
             ["src/sleepecg/_heartbeat_detection.c"],
             include_dirs=[np.get_include()],
-            define_macros=[("Py_LIMITED_API", "0x03090000")],
+            define_macros=[("Py_LIMITED_API", "0x030A0000")],
             py_limited_api=True,
         ),
     ],

src/sleepecg/utils.py

@@ -6,9 +6,9 @@
 
 import datetime
 import warnings
-from collections.abc import Iterable
+from collections.abc import Callable, Iterable
 from pathlib import Path
-from typing import Any, Callable, TypeVar
+from typing import Any, TypeVar
 
 import numpy as np
 

tests/test_sleep_readers.py

@@ -68,7 +68,7 @@ def _dummy_nsrr_xml(filename: str, hours: float, random_state: int):
             start += epoch_duration
 
         xml_file.write(
-            "</ScoredEvents>\n" "</PSGAnnotation>\n",
+            "</ScoredEvents>\n</PSGAnnotation>\n",
         )