Drop Python 3.9, 3.10 is now the new minimum (cctbx#769)

build.py

@@ -13,10 +13,10 @@
 import re
 import sys
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any
 
 
-def get_entry_point(filename: Path, prefix: str, import_path: str) -> List[str]:
+def get_entry_point(filename: Path, prefix: str, import_path: str) -> list[str]:
     """Returns the entry point string for a given path.
 
     This looks for LIBTBX_SET_DISPATCHER_NAME, and a root function
@@ -54,7 +54,7 @@ def get_entry_point(filename: Path, prefix: str, import_path: str) -> List[str]:
     return [f"{prefix}.{filename.stem}={import_path}.{filename.stem}:run"]
 
 
-def enumerate_format_classes(path: Path) -> List[str]:
+def enumerate_format_classes(path: Path) -> list[str]:
     """Find all Format*.py files and contained Format classes in a path"""
     format_classes = []
     for filename in path.glob("Format*.py"):
@@ -81,7 +81,7 @@ def enumerate_format_classes(path: Path) -> List[str]:
     return format_classes
 
 
-def build(setup_kwargs: Dict[str, Any]) -> None:
+def build(setup_kwargs: dict[str, Any]) -> None:
     """Called by setup.py to inject any dynamic configuration"""
     package_path = Path(__file__).parent / "src" / "dxtbx"
     entry_points = setup_kwargs.setdefault("entry_points", {})

cmake/read_env.py

@@ -45,7 +45,7 @@ def _read_obj(obj, prev=None):
         return obj
 
 
-class prop_object(object):
+class prop_object:
     """Object that can convert itself to a dictionary"""
 
     def to_dict(self):
@@ -63,13 +63,13 @@ class _pathed_prop_object(prop_object):
     return _pathed_prop_object
 
 
-class relocatable_path(object):
+class relocatable_path:
     def __repr__(self):
         _all_relocatable_paths.add(self)
         return os.path.normpath(os.path.join(str(self._anchor), self.relocatable))
 
 
-class absolute_path(object):
+class absolute_path:
     def __init__(self, path):
         # This init not used by unpickle - only for rewriting in here
         self._path = str(path)

newsfragments/769.removal

@@ -0,0 +1 @@
+Python 3.10 is now the minimum required

src/dxtbx/__init__.py

@@ -45,9 +45,7 @@ class IncorrectFormatError(RuntimeError):
     """
 
     def __init__(self, format_instance, filename):
-        super().__init__(
-            "Could not open {} as {}".format(filename, str(format_instance))
-        )
+        super().__init__(f"Could not open {filename} as {str(format_instance)}")
         self.args = (format_instance, filename)
 
 

src/dxtbx/dxtbx_format_nexus_ext.pyi

@@ -1,9 +1,9 @@
 from __future__ import annotations
 
-from typing import Any, Tuple
+from typing import Any
 
 from scitbx.array_family import flex
 
-def dataset_as_flex_double(dataset_id: Any, selection: Tuple[slice]) -> flex.double: ...
-def dataset_as_flex_float(dataset_id: Any, selection: Tuple[slice]) -> flex.float: ...
-def dataset_as_flex_int(dataset_id: Any, selection: Tuple[slice]) -> flex.int: ...
+def dataset_as_flex_double(dataset_id: Any, selection: tuple[slice]) -> flex.double: ...
+def dataset_as_flex_float(dataset_id: Any, selection: tuple[slice]) -> flex.float: ...
+def dataset_as_flex_int(dataset_id: Any, selection: tuple[slice]) -> flex.int: ...

src/dxtbx/dxtbx_imageset_ext.pyi

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any, Tuple, Union
+from typing import Any, Union
 
 from scitbx.array_family import flex
 
@@ -71,7 +71,7 @@ class ImageSet:
     def get_mask(self, int) -> Any: ...
     def get_path(self, int) -> Any: ...
     def get_pedestal(self, int) -> Any: ...
-    def get_raw_data(self, index: int) -> Tuple[ImageData]: ...
+    def get_raw_data(self, index: int) -> tuple[ImageData]: ...
     def get_scan(self) -> Any: ...
     def has_dynamic_mask(self) -> Any: ...
     def indices(self) -> Any: ...

src/dxtbx/dxtbx_masking_ext.pyi

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any, Tuple
+from typing import Any
 
 from scitbx.array_family import flex
 
@@ -31,7 +31,7 @@ class GoniometerShadowMasker:
     def project_extrema(
         self, detector: Detector, scan_angle: float
     ) -> flex.vec2_double: ...
-    def get_mask(self, detector: Detector, scan_angle: float) -> Tuple[flex.bool]: ...
+    def get_mask(self, detector: Detector, scan_angle: float) -> tuple[flex.bool]: ...
 
 class SmarGonShadowMasker(GoniometerShadowMasker):
     def __init__(self, goniometer: MultiAxisGoniometer) -> None: ...

src/dxtbx/dxtbx_model_ext.pyi

@@ -1,14 +1,9 @@
 from __future__ import annotations
 
+from collections.abc import Iterator, Sequence
 from enum import Enum
 from typing import (
     Any,
-    Dict,
-    Iterator,
-    List,
-    Optional,
-    Sequence,
-    Tuple,
     TypeVar,
     Union,
     overload,
@@ -33,12 +28,12 @@ TExperimentModel = TypeVar(
     "TExperimentModel", BeamBase, Detector, Goniometer, Scan, CrystalBase, object
 )
 
-Vec2Float = Tuple[float, float]
-Vec3Float = Tuple[float, float, float]
-Vec6Float = Tuple[float, float, float, float, float, float]
-Vec9Float = Tuple[float, float, float, float, float, float, float, float, float]
-Vec2Int = Tuple[int, int]
-Vec4Int = Tuple[int, int, int, int]
+Vec2Float = tuple[float, float]
+Vec3Float = tuple[float, float, float]
+Vec6Float = tuple[float, float, float, float, float, float]
+Vec9Float = tuple[float, float, float, float, float, float, float, float, float]
+Vec2Int = tuple[int, int]
+Vec4Int = tuple[int, int, int, int]
 ScanPropertyTypes = Union[
     flex.int,
     flex.double,
@@ -65,7 +60,7 @@ class BeamBase:
     def get_s0_at_scan_point(self, index: int) -> Vec3Float: ...
     def get_s0_at_scan_points(self) -> flex.vec3_double: ...
     def set_s0_at_scan_points(
-        self, points: Union[Tuple[Vec3Float], List[Vec3Float]]
+        self, points: tuple[Vec3Float] | list[Vec3Float]
     ) -> None: ...
     def get_sample_to_source_direction(self) -> Vec3Float: ...
     def get_sample_to_source_distance(self) -> float: ...
@@ -144,8 +139,8 @@ class Beam(BeamBase):
         deg: bool = ...,
     ) -> None: ...
     @staticmethod
-    def from_dict(data: Dict) -> Beam: ...
-    def to_dict(self) -> Dict: ...
+    def from_dict(data: dict) -> Beam: ...
+    def to_dict(self) -> dict: ...
     @staticmethod
     def get_probe_from_name(name: str) -> Probe: ...
 
@@ -179,8 +174,8 @@ class PolychromaticBeam(Beam):
     def set_wavelength_range(self, wavelength_range: Vec2Float) -> None: ...
     def get_wavelength_range(self) -> Vec2Float: ...
     @staticmethod
-    def from_dict(data: Dict) -> PolychromaticBeam: ...
-    def to_dict(self) -> Dict: ...
+    def from_dict(data: dict) -> PolychromaticBeam: ...
+    def to_dict(self) -> dict: ...
 
 class CrystalBase:
     @property
@@ -205,7 +200,7 @@ class CrystalBase:
     def get_real_space_vectors(self) -> flex.vec3_double: ...
     def get_recalculated_cell_parameter_sd(self) -> Vec6Float: ...
     def get_recalculated_cell_volume_sd(self) -> float: ...
-    def get_recalculated_unit_cell(self) -> Optional[unit_cell]: ...
+    def get_recalculated_unit_cell(self) -> unit_cell | None: ...
     def get_unit_cell(self) -> unit_cell: ...
     def get_space_group(self) -> space_group: ...
     def get_unit_cell_at_scan_point(self, index: int) -> unit_cell: ...
@@ -222,11 +217,9 @@ class CrystalBase:
         self, axis: Vec3Float, angle: float, deg: bool = ...
     ) -> Any: ...
     def set_A_at_scan_points(
-        self, value: Union[List[Vec9Float], Tuple[Vec9Float], flex.mat3_double]
-    ) -> None: ...
-    def set_B_covariance(
-        self, covariance: Union[Tuple[float, ...], flex.double]
+        self, value: list[Vec9Float] | tuple[Vec9Float] | flex.mat3_double
     ) -> None: ...
+    def set_B_covariance(self, covariance: tuple[float, ...] | flex.double) -> None: ...
     def set_B_covariance_at_scan_points(self, data: flex.double) -> None: ...
     def set_recalculated_cell_parameter_sd(self, value: Vec6Float) -> None: ...
     def set_recalculated_cell_volume_sd(self, volume: float) -> None: ...
@@ -306,13 +299,13 @@ class Detector:
     @overload
     def add_panel(self, panel: Panel) -> Panel: ...
     @staticmethod
-    def from_dict(data: Dict) -> Detector: ...
-    def to_dict(self) -> Dict: ...
+    def from_dict(data: dict) -> Detector: ...
+    def to_dict(self) -> dict: ...
     def get_max_inscribed_resolution(self, s0: Vec3Float) -> float: ...
     def get_max_resolution(self, s0: Vec3Float) -> float: ...
     def get_names(self) -> flex.std_string: ...
     def get_panel_intersection(self, s1: Vec3Float) -> int: ...
-    def get_ray_intersection(self, s1: Vec3Float) -> Tuple[int, Vec2Float]: ...
+    def get_ray_intersection(self, s1: Vec3Float) -> tuple[int, Vec2Float]: ...
     def has_projection_2d(self) -> bool: ...
     def is_similar_to(
         self,
@@ -380,10 +373,10 @@ class ExperimentList:
     def __contains__(self, obj: TExperimentModel) -> bool: ...
     def replace(self, obj: TExperimentModel, withobj: TExperimentModel) -> None: ...
     def indices(
-        self, obj: Union[TExperimentModel, FlexPlain[TExperimentModel]]
+        self, obj: TExperimentModel | FlexPlain[TExperimentModel]
     ) -> flex.size_t: ...
-    def remove_on_experiment_identifiers(self, identifiers: List[str]) -> None: ...
-    def select_on_experiment_identifiers(self, identifiers: List[str]) -> None: ...
+    def remove_on_experiment_identifiers(self, identifiers: list[str]) -> None: ...
+    def select_on_experiment_identifiers(self, identifiers: list[str]) -> None: ...
     def where(
         self,
         beam: BeamBase,
@@ -419,7 +412,7 @@ class Goniometer(GoniometerBase):
     @property
     def num_scan_points(self) -> int: ...
     @staticmethod
-    def from_dict(data: Dict) -> Goniometer: ...
+    def from_dict(data: dict) -> Goniometer: ...
     def get_fixed_rotation(self) -> Vec9Float: ...
     def get_num_scan_points(self) -> int: ...
     def get_rotation_axis(self) -> Vec3Float: ...
@@ -444,9 +437,9 @@ class Goniometer(GoniometerBase):
     def set_setting_rotation(self, rotation: Vec9Float) -> None: ...
     def set_setting_rotation_at_scan_points(
         self,
-        setting_rotations: Union[List[Vec9Float], Tuple[Vec9Float], flex.mat3_double],
+        setting_rotations: list[Vec9Float] | tuple[Vec9Float] | flex.mat3_double,
     ) -> Any: ...
-    def to_dict(self) -> Dict: ...
+    def to_dict(self) -> dict: ...
 
 class KappaDirection(Enum):
     PlusY = ...
@@ -498,8 +491,8 @@ class MultiAxisGoniometer(Goniometer):
         scan_axis: int,
     ) -> None: ...
     @staticmethod
-    def from_dict(data: Dict) -> MultiAxisGoniometer: ...
-    def to_dict(self) -> Dict: ...
+    def from_dict(data: dict) -> MultiAxisGoniometer: ...
+    def to_dict(self) -> dict: ...
     def get_angles(self) -> flex.double: ...
     def set_angles(self, angles: flex.double) -> None: ...
     def get_axes(self) -> flex.vec3_double: ...
@@ -601,7 +594,7 @@ class Panel(PanelData):
         slow_axis: Vec3Float,
         origin: Vec3Float,
         pixel_size: Vec2Float,
-        image_size: Tuple[int, int],
+        image_size: tuple[int, int],
         trusted_range: Vec2Float,
         thickness: float,
         material: str,
@@ -617,7 +610,7 @@ class Panel(PanelData):
         slow_axis: Vec3Float,
         origin: Vec3Float,
         pixel_size: Vec2Float,
-        image_size: Tuple[int, int],
+        image_size: tuple[int, int],
         trusted_range: Vec2Float,
         thickness: float,
         material: str,
@@ -627,10 +620,10 @@ class Panel(PanelData):
     ) -> None: ...
     @staticmethod
     @overload
-    def from_dict(data: Dict) -> Panel: ...
+    def from_dict(data: dict) -> Panel: ...
     @staticmethod
     @overload
-    def from_dict(data: Dict, dx: flex.double, dy: flex.double) -> Panel: ...
+    def from_dict(data: dict, dx: flex.double, dy: flex.double) -> Panel: ...
     def get_beam_centre_px(self, s0: Vec3Float) -> Vec2Float: ...
     def get_bidirectional_ray_intersection_px(self, s1: Vec3Float) -> Vec2Float: ...
     def get_cos2_two_theta_array(self, s0: Vec3Float) -> flex.double: ...
@@ -652,7 +645,7 @@ class Panel(PanelData):
     def get_normal_origin_px(self) -> Vec2Float: ...
     def get_pedestal(self) -> float: ...
     def get_pixel_lab_coord(self, px: Vec2Float) -> Vec3Float: ...
-    def get_projection_2d(self) -> Union[Tuple[Vec4Int, Vec2Int], Tuple[()]]: ...
+    def get_projection_2d(self) -> tuple[Vec4Int, Vec2Int] | tuple[()]: ...
     def get_px_mm_strategy(self) -> PxMmStrategy: ...
     def get_ray_intersection_px(self, s1: Vec3Float) -> Vec2Float: ...
     @overload
@@ -663,9 +656,7 @@ class Panel(PanelData):
     def get_resolution_at_pixel(
         self, beam: PolychromaticBeam, xy: Vec2Float
     ) -> float: ...
-    def get_trusted_range_mask(
-        self, image: Union[flex.int, flex.double]
-    ) -> flex.bool: ...
+    def get_trusted_range_mask(self, image: flex.int | flex.double) -> flex.bool: ...
     def get_two_theta_array(self, s0: Vec3Float) -> flex.double: ...
     def get_two_theta_at_pixel(self, s0: Vec3Float, xy: Vec2Float) -> float: ...
     def get_untrusted_rectangle_mask(self) -> flex.bool: ...
@@ -689,7 +680,7 @@ class Panel(PanelData):
     def set_pedestal(self, pedestal: float) -> None: ...
     def set_projection_2d(self, rotation: Vec4Int, translation: Vec2Int) -> None: ...
     def set_px_mm_strategy(self, strategy: PxMmStrategy) -> None: ...
-    def to_dict(self) -> Dict: ...
+    def to_dict(self) -> dict: ...
 
 class DetectorNode(Panel):
     @overload
@@ -780,13 +771,13 @@ class Scan(ScanBase):
     def __init__(
         self,
         image_range: Vec2Int,
-        properties_table: Dict,
+        properties_table: dict,
         batch_offset: int,
         deg: bool = ...,
     ) -> None: ...
     def append(self, other: Scan, scan_tolerance: float) -> None: ...
     @staticmethod
-    def from_dict(data: Dict) -> Scan: ...
+    def from_dict(data: dict) -> Scan: ...
     @overload
     def get_angle_from_array_index(self, index: float, deg: bool = ...) -> float: ...
     @overload
@@ -825,8 +816,8 @@ class Scan(ScanBase):
     def get_oscillation(self, deg: bool = ...) -> Vec2Float: ...
     def set_oscillation(self, oscillation: Vec2Float, deg: bool = ...) -> None: ...
     def get_oscillation_range(self, deg: bool = ...) -> Vec2Float: ...
-    def get_valid_image_ranges(self, i: str) -> List[Vec2Int]: ...
-    def set_valid_image_ranges(self, i: str, ranges: List[Vec2Int]) -> None: ...
+    def get_valid_image_ranges(self, i: str) -> list[Vec2Int]: ...
+    def set_valid_image_ranges(self, i: str, ranges: list[Vec2Int]) -> None: ...
     def get_properties(self) -> dict: ...
     def set_properties(self, properties: dict) -> None: ...
     def has_property(self, key: str) -> bool: ...
@@ -852,8 +843,8 @@ class Scan(ScanBase):
     def is_image_index_valid(self, index: int) -> bool: ...
     def is_still(self) -> bool: ...
     def swap(self, other: Scan) -> None: ...
-    def to_dict(self) -> Dict: ...
-    def __getitem__(self, index: Union[int, slice]) -> Scan: ...
+    def to_dict(self) -> dict: ...
+    def __getitem__(self, index: int | slice) -> Scan: ...
     def __len__(self) -> int: ...
     def __add__(self, other: Scan) -> Scan: ...
     def __iadd__(self, other: Scan) -> Scan: ...
@@ -868,15 +859,15 @@ class Spectrum:
     @overload
     def __init__(self, energies: flex.double, weights: flex.double) -> None: ...
     @staticmethod
-    def from_dict(data: Dict) -> Spectrum: ...
+    def from_dict(data: dict) -> Spectrum: ...
     def get_emax_eV(self) -> float: ...
     def get_emin_eV(self) -> float: ...
     def get_energies_eV(self) -> flex.double: ...
     def get_weighted_energy_eV(self) -> float: ...
     def get_weighted_energy_variance(self) -> float: ...
     def get_weighted_wavelength(self) -> float: ...
     def get_weights(self) -> flex.double: ...
-    def to_dict(self) -> Dict: ...
+    def to_dict(self) -> dict: ...
 
 class flex_Beam(FlexPlain[Beam]):
     pass

src/dxtbx/format/Format.py

@@ -12,8 +12,9 @@
 import bz2
 import functools
 import os
+from collections.abc import Callable
 from io import IOBase
-from typing import Callable, ClassVar
+from typing import ClassVar
 
 import libtbx