[maint] Deprecate Python 3.9 due to security EOL

CMakeLists.txt

@@ -30,8 +30,8 @@ if (NOT SKBUILD)
 endif()
 
 
-# search for Python >= 3.9 including the Development.Module component required by nanobind
-find_package(Python 3.9 COMPONENTS Interpreter Development.Module REQUIRED)
+# search for Python >= 3.10 including the Development.Module component required by nanobind
+find_package(Python 3.10 COMPONENTS Interpreter Development.Module REQUIRED)
 
 # set the build type to Release by default
 if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)

pyproject.toml

@@ -17,12 +17,11 @@ maintainers = [
 ]
 readme = "README.md"
 keywords = ['beamforming', 'delay and sum', 'ultrasound', 'python', 'cuda']
-requires-python = ">=3.9,<3.14"
+requires-python = ">=3.10,<3.14"
 classifiers = [
     "Intended Audience :: Developers",
     "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",
@@ -146,7 +145,7 @@ build-dir = "build/{wheel_tag}"
 wheel.packages = ["src/mach"]
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 line-length = 120
 fix = true
 
@@ -196,8 +195,6 @@ ignore = [
     "SIM108",
     # Allow assert
     "S101",
-    # Union syntax not available in Python 3.9
-    "UP007",
 ]
 
 [tool.ruff.lint.per-file-ignores]
@@ -226,7 +223,6 @@ testpaths = ["tests"]
 
 [tool.cibuildwheel]
 build = [
-    "cp39-manylinux_x86_64",
     "cp310-manylinux_x86_64",
     "cp311-manylinux_x86_64",
     "cp312-manylinux_x86_64",

src/mach/_array_api.py

@@ -1,7 +1,7 @@
 """Array-API utilities."""
 
 from enum import Enum
-from typing import Any, Protocol, Union, cast, runtime_checkable
+from typing import Any, Protocol, cast, runtime_checkable
 
 from array_api_compat import array_namespace as xpc_array_namespace
 
@@ -112,7 +112,7 @@ def __gt__(self, other: Any) -> "Array": ...
     def __getitem__(self, key: Any) -> "Array": ...
 
 
-def array_namespace(*arrays: Any) -> Union[_ArrayNamespace, _ArrayNamespaceWithLinAlg]:
+def array_namespace(*arrays: Any) -> _ArrayNamespace | _ArrayNamespaceWithLinAlg:
     """Typed wrapper around array_api_compat.array_namespace.
 
     Returns the array namespace for the given arrays with proper type hints.
@@ -137,4 +137,4 @@ def array_namespace(*arrays: Any) -> Union[_ArrayNamespace, _ArrayNamespaceWithL
         ...     # Fallback implementation
         ...     norm = xp.sqrt(xp.sum(arr * arr, axis=-1))
     """
-    return cast(Union[_ArrayNamespace, _ArrayNamespaceWithLinAlg], xpc_array_namespace(*arrays))
+    return cast(_ArrayNamespace | _ArrayNamespaceWithLinAlg, xpc_array_namespace(*arrays))

src/mach/_vis.py

@@ -1,7 +1,6 @@
 """Visualization utilities for test-diagnostics."""
 
 from pathlib import Path
-from typing import Optional, Union
 
 try:
     import matplotlib.pyplot as plt
@@ -61,7 +60,7 @@ def plot_slice(bm_slice, lats, deps, angle):
 
 def save_debug_figures(
     our_result: np.ndarray,
-    reference_result: Optional[np.ndarray],
+    reference_result: np.ndarray | None,
     grid_shape: tuple[int, ...],
     x_axis: np.ndarray,
     z_axis: np.ndarray,
@@ -70,7 +69,7 @@ def save_debug_figures(
     our_label: str = "Our Implementation",
     reference_label: str = "Reference Implementation",
     power_mode: bool = False,
-    main_cmap: Optional[Union[str, Colormap]] = None,
+    main_cmap: str | Colormap | None = None,
     diff_cmap: str = "magma",
 ) -> None:
     """Save debug figures comparing beamforming results.

src/mach/experimental.py

@@ -1,7 +1,7 @@
 """The specific function arguments / names (API) are experimental and may change."""
 
 from enum import Enum
-from typing import Optional, cast
+from typing import cast
 
 from jaxtyping import Num, Real
 
@@ -25,13 +25,13 @@ def beamform(
     rx_coords_m: Real[Array, "n_rx xyz=3"],
     scan_coords_m: Real[Array, "n_points xyz=3"],
     tx_wave_arrivals_s: Real[Array, "n_transmits n_points"],
-    out: Optional[Num[Array, "n_points n_frames"]] = None,
+    out: Num[Array, "n_points n_frames"] | None = None,
     *,
     rx_start_s: float,
     sampling_freq_hz: float,
     f_number: float,
     sound_speed_m_s: float,
-    modulation_freq_hz: Optional[float] = None,
+    modulation_freq_hz: float | None = None,
     tukey_alpha: float = 0.5,
 ) -> Num[Array, "n_points n_frames"]:
     """Wrapper around kernel.beamform that includes coherent compounding.

src/mach/geometry.py

@@ -21,18 +21,17 @@
 
 import math
 import numbers
-from typing import Union
 
 from jaxtyping import Real
 
 from mach._array_api import Array, _ArrayNamespace, array_namespace
 
 
 def ultrasound_angles_to_cartesian(
-    azimuth_rad: Union[Real[Array, " *angles"], float, int],
-    elevation_rad: Union[Real[Array, " *angles"], float, int],
-    radius_m: Union[Real[Array, " *angles"], float, int] = 1,
-) -> Union[Real[Array, "*angles xyz=3"], tuple[float, float, float]]:
+    azimuth_rad: Real[Array, " *angles"] | float | int,
+    elevation_rad: Real[Array, " *angles"] | float | int,
+    radius_m: Real[Array, " *angles"] | float | int = 1,
+) -> Real[Array, "*angles xyz=3"] | tuple[float, float, float]:
     """Convert ultrasound angles (azimuth, elevation, radius) to Cartesian coordinates.
 
     The resulting vectors can be used directly with `mach.wavefront.plane()`.
@@ -87,10 +86,10 @@ def ultrasound_angles_to_cartesian(
 
 
 def spherical_to_cartesian(
-    theta_rad: Union[Real[Array, " *angles"], float, int],
-    phi_rad: Union[Real[Array, " *angles"], float, int],
-    radius_m: Union[Real[Array, " *angles"], float, int] = 1,
-) -> Union[Real[Array, "*angles xyz=3"], tuple[float, float, float]]:
+    theta_rad: Real[Array, " *angles"] | float | int,
+    phi_rad: Real[Array, " *angles"] | float | int,
+    radius_m: Real[Array, " *angles"] | float | int = 1,
+) -> Real[Array, "*angles xyz=3"] | tuple[float, float, float]:
     """Convert standard spherical angle convention to a Cartesian vector.
 
     Uses the physics convention as defined in ISO 80000-2:2019.
@@ -133,8 +132,8 @@ def spherical_to_cartesian(
 
 
 def _prepare_inputs_and_namespace(
-    *inputs: Union[Real[Array, "..."], float, int],
-) -> tuple[Union[type[math], _ArrayNamespace], tuple]:
+    *inputs: Real[Array, "..."] | float | int,
+) -> tuple[type[math] | _ArrayNamespace, tuple]:
     """Prepare inputs and determine the appropriate namespace (math or array).
 
     For scalar inputs, to avoid requiring a specific array library import,

src/mach/io/uff.py

@@ -5,7 +5,7 @@
 https://github.com/magnusdk/pyuff_ustb
 """
 
-from typing import Any, Optional
+from typing import Any
 
 import einops
 import numpy as np
@@ -35,7 +35,7 @@ def extract_wave_directions(sequence: list[Any], xp) -> Array:
 
 
 def compute_tx_wave_arrivals_s(
-    directions: Array, scan_coords_m: Array, speed_of_sound: float, origin: Optional[Array] = None, xp=None
+    directions: Array, scan_coords_m: Array, speed_of_sound: float, origin: Array | None = None, xp=None
 ) -> Array:
     """
     Compute transmit arrival times for plane wave imaging.

src/mach/io/utils.py

@@ -1,7 +1,7 @@
 """General utilities for downloading and caching files with integrity verification.
 
 This module provides:
-- Efficient file hashing compatible with Python 3.9+ (backport of hashlib.file_digest)
+- Efficient file hashing compatible with Python 3.10 (backport of hashlib.file_digest)
 - Robust file downloading with progress bars and integrity verification
 - Smart caching with automatic re-download on corruption
 - Support for multiple hash algorithms (SHA1, SHA256, MD5, etc.)
@@ -18,8 +18,9 @@
 import hashlib
 import sys
 import warnings
+from collections.abc import Callable
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable, Optional, Union
+from typing import TYPE_CHECKING, Any
 
 try:
     import requests
@@ -34,16 +35,16 @@
 try:
     from tqdm import tqdm
 except ImportError:
-    tqdm: Optional[Any] = None
+    tqdm: Any | None = None
 
 CACHE_DIR = Path.home() / ".cache" / "mach"
 
 
-def file_digest(fileobj, digest: Union[str, Callable[[], "hashlib._Hash"]]) -> "hashlib._Hash":
+def file_digest(fileobj, digest: str | Callable[[], "hashlib._Hash"]) -> "hashlib._Hash":
     """Return a digest object that has been updated with contents of file object.
 
     This is a backport-compatible implementation of hashlib.file_digest()
-    that works with Python 3.9+ and follows the same API as Python 3.11+.
+    that works with Python 3.10 and follows the same API as Python 3.11+.
 
     Args:
         fileobj: File-like object opened for reading in binary mode
@@ -91,7 +92,7 @@ def file_digest(fileobj, digest: Union[str, Callable[[], "hashlib._Hash"]]) -> "
 def verify_file_integrity(
     file_path: Path,
     expected_hash: str,
-    digest: Union[str, Callable[[], "hashlib._Hash"]],
+    digest: str | Callable[[], "hashlib._Hash"],
 ) -> bool:
     """Verify file integrity using specified hash algorithm.
 
@@ -114,9 +115,9 @@ def verify_file_integrity(
 
 def _verify_file(
     output_path: Path,
-    expected_size: Optional[int],
-    expected_hash: Optional[str],
-    digest: Optional[Union[str, Callable[[], "hashlib._Hash"]]],
+    expected_size: int | None,
+    expected_hash: str | None,
+    digest: str | Callable[[], "hashlib._Hash"] | None,
 ) -> bool:
     """Verify if existing file meets size and hash requirements.
 
@@ -176,14 +177,14 @@ def _download_with_progress(
 
 def download_file(
     url: str,
-    output_path: Union[str, Path],
+    output_path: str | Path,
     timeout: int = 30,
     chunk_size: int = 1024 * 1024,  # 1MB
     *,
     overwrite: bool = False,
-    expected_hash: Optional[str] = None,
-    digest: Union[None, str, Callable[[], "hashlib._Hash"]] = None,
-    expected_size: Optional[int] = None,
+    expected_hash: str | None = None,
+    digest: None | str | Callable[[], "hashlib._Hash"] = None,
+    expected_size: int | None = None,
     show_progress: bool = (tqdm is not None),
 ) -> Path:
     """Download a file from a URL with optional progress bar and integrity verification.
@@ -240,14 +241,14 @@ def download_file(
 
 def cached_download(
     url: str,
-    cache_dir: Union[str, Path] = CACHE_DIR,
-    filename: Optional[Union[str, Path]] = None,
+    cache_dir: str | Path = CACHE_DIR,
+    filename: str | Path | None = None,
     timeout: int = 30,
     *,
     overwrite: bool = False,
-    expected_size: Optional[int] = None,
-    expected_hash: Optional[str] = None,
-    digest: Union[None, str, Callable[[], "hashlib._Hash"]] = None,
+    expected_size: int | None = None,
+    expected_hash: str | None = None,
+    digest: None | str | Callable[[], "hashlib._Hash"] = None,
     show_progress: bool = (tqdm is not None),
 ) -> Path:
     """Download a file and cache it with optional integrity verification.

src/mach/kernel.py

@@ -1,7 +1,5 @@
 """Python bindings and wrapper for the CUDA kernel."""
 
-from typing import Optional
-
 from array_api_compat import is_writeable_array
 from jaxtyping import Num, Real
 
@@ -24,13 +22,13 @@ def beamform(  # noqa: C901
     rx_coords_m: Real[Array, "n_rx xyz=3"],
     scan_coords_m: Real[Array, "n_scan xyz=3"],
     tx_wave_arrivals_s: Real[Array, " n_scan"],
-    out: Optional[Num[Array, "n_scan n_frames"]] = None,
+    out: Num[Array, "n_scan n_frames"] | None = None,
     *,
     rx_start_s: float,
     sampling_freq_hz: float,
     f_number: float,
     sound_speed_m_s: float,
-    modulation_freq_hz: Optional[float] = None,
+    modulation_freq_hz: float | None = None,
     tukey_alpha: float = 0.5,
     interp_type: InterpolationType = InterpolationType.Linear,
 ) -> Array:

tests/compare/test_pymust.py

@@ -8,7 +8,8 @@
     pytest tests/test_pymust.py --benchmark-histogram --benchmark-sort=mean
 """
 
-from typing import Any, Callable
+from collections.abc import Callable
+from typing import Any
 
 import numpy as np
 import pytest

tests/conftest.py

@@ -1,7 +1,7 @@
 import contextlib
 import hashlib
 from pathlib import Path
-from typing import Optional, cast
+from typing import cast
 
 import pytest
 from pyuff_ustb import ChannelData, Scan, Uff
@@ -79,7 +79,7 @@ def test_data_dir():
 
 
 @pytest.fixture
-def output_dir(request) -> Optional[Path]:
+def output_dir(request) -> Path | None:
     """Output directory for test results.
 
     Returns None if the --save-output flag is not set.

tests/io/test_uff.py

@@ -1,7 +1,6 @@
 """Test the UFF data loader."""
 
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 import pytest
@@ -31,7 +30,7 @@ class Scan(OriginalScan):
 def test_picmus_phantom_resolution(
     picmus_phantom_resolution_channel_data: ChannelData,
     picmus_phantom_resolution_scan: Scan,
-    output_dir: Optional[Path],
+    output_dir: Path | None,
 ):
     """Test the Picmus phantom resolution UFF data."""
     assert picmus_phantom_resolution_channel_data is not None
@@ -63,7 +62,7 @@ def test_picmus_phantom_resolution(
 def test_picmus_phantom_resolution_single_transmit(
     picmus_phantom_resolution_channel_data: ChannelData,
     picmus_phantom_resolution_scan: Scan,
-    output_dir: Optional[Path],
+    output_dir: Path | None,
 ):
     """Test the Picmus phantom resolution UFF data with single transmit (backwards compatibility)."""
     assert picmus_phantom_resolution_channel_data is not None

tests/plot_benchmark.py

@@ -14,7 +14,6 @@
 import argparse
 import json
 from pathlib import Path
-from typing import Optional
 
 import matplotlib.pyplot as plt
 import pandas as pd
@@ -152,7 +151,7 @@ def plot_benchmark_results(
     df: pd.DataFrame,
     data: dict,
     use_points_per_second: bool = False,
-    output_path: Optional[str] = None,
+    output_path: str | None = None,
     show_values: bool = True,
 ) -> None:
     """Create horizontal boxplot of benchmark results."""