Add support for Python 3.13

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]
@@ -22,27 +22,28 @@ classifiers = [
     "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 >= 0.60.0; python_version < '3.13'",
+    "tensorflow >= 2.17.0; python_version < '3.13'",
+    "wfdb >= 4.1.2",
 ]
 
 dev = [  # everything needed for development
@@ -52,20 +53,18 @@ dev = [  # everything needed for development
     "pre-commit >= 2.13.0",
     "pytest >= 6.2.0",
     "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 >= 0.60.0; python_version < '3.13'",
+    "wfdb >= 4.1.2",
 ]
 
 [project.urls]

readthedocs.yml

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

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_heartbeats.py

@@ -4,6 +4,8 @@
 
 """Tests for heartbeat detection and detector evaluation."""
 
+import sys
+
 import numpy as np
 import pytest
 
@@ -30,7 +32,19 @@ def mitdb_234_MLII():
     return next(read_mitdb(records_pattern="234"))
 
 
-@pytest.mark.parametrize("backend", ["c", "numba", "python"])
+@pytest.mark.parametrize(
+    "backend",
+    [
+        "c",
+        pytest.param(
+            "numba",
+            marks=pytest.mark.skipif(
+                sys.version_info >= (3, 13), reason="numba does not support Python 3.13"
+            ),
+        ),
+        "python",
+    ],
+)
 def test_detect_heartbeats(mitdb_234_MLII, backend):
     """Test heartbeat detection on mitdb:234:MLII."""
     record = mitdb_234_MLII