From 8e3db4ba52de514e7364880866b14f18b45276ad Mon Sep 17 00:00:00 2001 From: Ken Kroenlein Date: Wed, 14 Oct 2026 13:50:20 -0600 Subject: [PATCH 1/7] Drop Python 3.9 support for gemd 3.0.0 - Require Python 3.10 and remove the 3.9 classifier and dependency pins - Remove the typing_extensions fallback for TypeAlias - Remove the deprecated "clean" unit format, scheduled for removal in 3.0.0 - Replace typing.ByteString, removed in Python 3.14, with (bytes, bytearray) - Remove the private _cached_isinstance alias - Move PR tests to the common-gh-actions v3 matrix, which skips 3.9 and adds 3.14 - Raise numpy and pandas lower bounds on 3.14 to the first releases with wheels Co-Authored-By: Claude Opus 5.5 --- .github/workflows/pr-tests.yml | 4 +--- gemd/__version__.py | 2 +- gemd/units/impl.py | 41 ++-------------------------------- gemd/util/impl.py | 15 ++++++------- pyproject.toml | 17 ++++++-------- requirements.txt | 1 - test_requirements.txt | 9 +++----- tests/units/test_parser.py | 19 ---------------- 8 files changed, 21 insertions(+), 87 deletions(-) diff --git a/.github/workflows/pr-tests.yml b/.github/workflows/pr-tests.yml index d824f7a..7542fce 100644 --- a/.github/workflows/pr-tests.yml +++ b/.github/workflows/pr-tests.yml @@ -12,8 +12,6 @@ on: jobs: pr-tests: - uses: CitrineInformatics/common-gh-actions/.github/workflows/run-tests.yml@v1.1 + uses: CitrineInformatics/common-gh-actions/.github/workflows/matrix-tests.yml@v3 with: src: gemd - skip_38: true - include_313: true diff --git a/gemd/__version__.py b/gemd/__version__.py index ef6497d..528787c 100644 --- a/gemd/__version__.py +++ b/gemd/__version__.py @@ -1 +1 @@ -__version__ = "2.3.2" +__version__ = "3.0.0" diff --git a/gemd/units/impl.py b/gemd/units/impl.py index 3bcd789..ce61de2 100644 --- a/gemd/units/impl.py +++ b/gemd/units/impl.py @@ -6,18 +6,10 @@ from importlib.resources import files from pathlib import Path from tempfile import TemporaryDirectory -from typing import Any, Generator, List, Tuple, Union - -from deprecation import deprecated - -try: - from typing import TypeAlias # Python 3.10+ -except ImportError: # pragma nocover - from typing_extensions import TypeAlias # Python 3.9 - from tokenize import ERRORTOKEN, NAME, NUMBER, OP, TokenInfo +from typing import Any, Generator, List, Tuple, TypeAlias, Union -from pint import UnitRegistry, register_unit_format +from pint import UnitRegistry from pint.errors import DefinitionSyntaxError, UndefinedUnitError # alias the error that is thrown when units are incompatible @@ -296,35 +288,6 @@ def convert_units(value: float, starting_unit: str, final_unit: str) -> float: return resolved_value.to(resolved_final_unit).magnitude -@register_unit_format("clean") -@deprecated(deprecated_in="2.1.0", removed_in="3.0.0", details="Scaling factor clean-up ") -def _format_clean(unit, registry, **options): - """DEPRECATED Formatter that turns scaling-factor-units into numbers again. - - Responsibility for this piece of clean-up has been shifted to a custom class. - - """ - try: # Informal route changed in 0.22 - from pint.formatting import _FORMATTERS - - formatter = _FORMATTERS["D"] # pragma: no cover - except ImportError: # pragma: no cover - from pint import Unit - - formatter_obj = registry.formatter._formatters["D"] - - def _surrogate_formatter(unit, registry, **options): - try: - parsed = Unit(unit) - return formatter_obj.format_unit(parsed) - except ValueError: - return formatter_obj.format_quantity(unit) - - formatter = _surrogate_formatter - - return formatter(unit, registry, **options) - - @functools.lru_cache(maxsize=1024) def parse_units( units: Union[str, UnitRegistry.Unit, None], *, return_unit: bool = False diff --git a/gemd/util/impl.py b/gemd/util/impl.py index 590f235..5f4a565 100644 --- a/gemd/util/impl.py +++ b/gemd/util/impl.py @@ -4,7 +4,6 @@ import uuid from typing import ( Any, - ByteString, Callable, Iterable, List, @@ -69,10 +68,6 @@ def cached_isinstance(obj: object, class_or_tuple: Union[Type, Tuple[Type]]) -> return _cached_issubclass(obj_type, class_or_tuple) -# Older unreleased versions of citrine-python referenced the private method directly -_cached_isinstance = cached_isinstance - - @functools.lru_cache(maxsize=1024) def _cached_issubclass(cls: Type, class_or_tuple: Union[Type, Tuple[Type]]) -> bool: """Emulate issubclass builtin to take advantage of functools caching. @@ -181,7 +176,7 @@ def _key(obj): return None elif obj.__hash__ is not None: return obj - elif cached_isinstance(obj, Iterable) and not cached_isinstance(obj, ByteString): + elif cached_isinstance(obj, Iterable) and not cached_isinstance(obj, (bytes, bytearray)): return id(obj) else: return None # pragma: no cover Fallback for caution's sake @@ -448,7 +443,9 @@ def recursive_foreach( elif cached_isinstance(this, DictSerializable): for k, x in this.__dict__.items(): queue.append(x) - elif cached_isinstance(this, Iterable) and not cached_isinstance(this, (str, ByteString)): + elif cached_isinstance(this, Iterable) and not cached_isinstance( + this, (str, bytes, bytearray) + ): for x in this: queue.append(x) @@ -511,7 +508,9 @@ def recursive_flatmap( queue.append(x) elif cached_isinstance(this, Reversible): queue.extend(reversed(this)) # Preserve order of the list/tuple - elif cached_isinstance(this, Iterable) and not cached_isinstance(this, (str, ByteString)): + elif cached_isinstance(this, Iterable) and not cached_isinstance( + this, (str, bytes, bytearray) + ): queue.extend(this) # No control over order return res diff --git a/pyproject.toml b/pyproject.toml index 9037979..99db244 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,9 +4,8 @@ dynamic = ["version"] dependencies = [ "pint>=0.24.4,<0.25", "deprecation>=2.1.0,<3", - "typing_extensions>=4.8,<5; python_version<'3.10'", ] -requires-python = ">=3.9" +requires-python = ">=3.10" authors = [ {name = "Citrine Informatics"} ] @@ -15,7 +14,6 @@ readme = "README.md" license-files = ["LICENSE"] classifiers = [ "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", @@ -48,12 +46,11 @@ dev = [ "ruff==0.16.6", "flake8==7.0.0", "flake8-docstrings==1.7.0", - "numpy>=1.24.4; python_version<'3.10'", - "pandas>=2.0.3; python_version<'3.10'", - "numpy>=2.0.2,<3; python_version>='3.10'", - "pandas>=2.3.0,<4; python_version>='3.10'", - "pytest==8.4.2; python_version<'3.10'", - "pytest==9.0.3; python_version>='3.10'", + "numpy>=2.0.2,<3; python_version<'3.14'", + "numpy>=2.3.2,<3; python_version>='3.14'", # first release with 3.14 wheels + "pandas>=2.3.0,<4; python_version<'3.14'", + "pandas>=2.3.3,<4; python_version>='3.14'", # first release with 3.14 wheels + "pytest==9.0.3", "pytest-cov==7.0.0", "derp==0.1.1", "tomli>=2.2.1", @@ -77,7 +74,7 @@ omit = [ [tool.ruff] line-length = 99 -target-version = "py39" +target-version = "py310" [tool.ruff.lint] # Mirror the flake8 configuration in tox.ini so both linters agree. diff --git a/requirements.txt b/requirements.txt index 0af944d..23cfe0c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,2 @@ pint==0.24.4 deprecation==2.1.0 -typing_extensions>=4.8,<5; python_version<'3.10' diff --git a/test_requirements.txt b/test_requirements.txt index 7115aba..d79cc99 100644 --- a/test_requirements.txt +++ b/test_requirements.txt @@ -1,10 +1,7 @@ flake8==7.0.0 flake8-docstrings==1.7.0 -numpy==1.24.4; python_version<'3.10' -pandas==2.0.3; python_version<'3.10' -numpy>=2.0.2,<=2.1.0; python_version>='3.10' -pandas==2.3.0; python_version>='3.10' -pytest==8.4.2; python_version<'3.10' -pytest==9.0.3; python_version>='3.10' +numpy>=2.0.2,<=2.1.0 +pandas==2.3.0 +pytest==9.0.3 pytest-cov==7.0.0 derp==0.1.1 diff --git a/tests/units/test_parser.py b/tests/units/test_parser.py index 031bc24..2c0743b 100644 --- a/tests/units/test_parser.py +++ b/tests/units/test_parser.py @@ -3,7 +3,6 @@ from importlib.resources import files import pytest -from deprecation import DeprecatedWarning from pint import UnitRegistry from gemd.units import ( @@ -242,21 +241,3 @@ def test__scientific_notation_preprocessor(): assert "1e" not in parse_units("F* kg * 10 cm") assert "-3.07e2" in parse_units("F* -3.07 * 10 ** 2") assert "11e2" in parse_units("F* 11*10^2") - - -def test_deprecation(): - """Make sure deprecated things warn correctly.""" - megapascals = parse_units("MPa", return_unit=True) - with pytest.warns(DeprecatedWarning): - stringified = f"{megapascals:clean}" - assert megapascals == parse_units(stringified, return_unit=False) - - from pint import Quantity - - with pytest.warns(DeprecatedWarning): - assert f"{Quantity('5 MPa'):clean}" == f"5 {stringified}" - - from pint import Unit - - with pytest.warns(DeprecatedWarning): - assert f"{Unit('MPa'):clean}" == stringified From ed509756779a2633dc4a75ee7b18fee74b34886f Mon Sep 17 00:00:00 2001 From: Ken Kroenlein Date: Thu, 15 Oct 2026 08:23:58 -0600 Subject: [PATCH 2/7] Adopt Python 3.10 syntax with pyupgrade Apply ruff's pyupgrade fixes for a 3.10 target: PEP 604 unions, builtin generics, and collections.abc imports. Convert module-level type aliases by hand and unquote two test annotations whose names are imported. Co-Authored-By: Claude Opus 5.5 --- gemd/builders/impl.py | 27 ++++++++------- gemd/demo/strehlow_and_cook.py | 2 +- gemd/entity/attribute/base_attribute.py | 20 +++++------ gemd/entity/attribute/condition.py | 4 +-- gemd/entity/attribute/parameter.py | 4 +-- gemd/entity/attribute/property.py | 4 +-- .../attribute/property_and_conditions.py | 8 ++--- gemd/entity/base_entity.py | 17 +++++----- gemd/entity/bounds/base_bounds.py | 8 ++--- gemd/entity/bounds/categorical_bounds.py | 17 +++++----- gemd/entity/bounds/composition_bounds.py | 11 ++++--- gemd/entity/bounds/integer_bounds.py | 8 ++--- .../bounds/molecular_structure_bounds.py | 10 +++--- gemd/entity/bounds/real_bounds.py | 8 ++--- gemd/entity/dict_serializable.py | 23 +++++++------ gemd/entity/has_dependencies.py | 4 +-- gemd/entity/object/base_object.py | 8 ++--- gemd/entity/object/has_conditions.py | 10 +++--- gemd/entity/object/has_material.py | 7 ++-- gemd/entity/object/has_parameters.py | 10 +++--- gemd/entity/object/has_process.py | 7 ++-- gemd/entity/object/has_properties.py | 10 +++--- gemd/entity/object/has_quantities.py | 2 +- gemd/entity/object/has_source.py | 2 +- gemd/entity/object/has_spec.py | 13 ++++---- gemd/entity/object/has_template.py | 11 +++---- .../object/has_template_check_generator.py | 5 +-- gemd/entity/object/ingredient_run.py | 27 +++++++-------- gemd/entity/object/ingredient_spec.py | 20 +++++------ gemd/entity/object/material_run.py | 21 ++++++------ gemd/entity/object/material_spec.py | 24 +++++++------- gemd/entity/object/measurement_run.py | 20 +++++------ gemd/entity/object/measurement_spec.py | 12 +++---- gemd/entity/object/process_run.py | 19 ++++++----- gemd/entity/object/process_spec.py | 19 ++++++----- gemd/entity/setters.py | 9 ++--- gemd/entity/template/base_template.py | 10 +++--- .../template/has_condition_templates.py | 15 +++++---- .../template/has_parameter_templates.py | 15 +++++---- .../entity/template/has_property_templates.py | 17 +++++----- gemd/entity/util.py | 4 +-- gemd/entity/valid_list.py | 7 ++-- gemd/entity/value/discrete_categorical.py | 6 ++-- gemd/enumeration/base_enumeration.py | 9 +++-- gemd/json/gemd_json.py | 10 +++--- gemd/units/impl.py | 19 ++++++----- gemd/util/impl.py | 33 +++++++------------ tests/builders/test_builders.py | 6 ++-- tests/util/test_cached_isinstance.py | 6 ++-- 49 files changed, 286 insertions(+), 302 deletions(-) diff --git a/gemd/builders/impl.py b/gemd/builders/impl.py index b55420a..e00ebae 100644 --- a/gemd/builders/impl.py +++ b/gemd/builders/impl.py @@ -1,5 +1,4 @@ # Tools to help build GEMD objects -from typing import List, Union from gemd.entity.attribute import Condition, Parameter, Property, PropertyAndConditions from gemd.entity.attribute.base_attribute import BaseAttribute @@ -104,10 +103,10 @@ def add_edge( output_material: MaterialRun, *, name: str = None, - mass_fraction: Union[float, ContinuousValue] = None, - number_fraction: Union[float, ContinuousValue] = None, - volume_fraction: Union[float, ContinuousValue] = None, - absolute_quantity: Union[int, float, ContinuousValue] = None, + mass_fraction: float | ContinuousValue = None, + number_fraction: float | ContinuousValue = None, + volume_fraction: float | ContinuousValue = None, + absolute_quantity: int | float | ContinuousValue = None, absolute_units: str = None, ) -> IngredientRun: """Connect two material-process spec-run quadruples with ingredients. @@ -209,7 +208,7 @@ def add_measurement( *, name: str = None, template: MeasurementTemplate = None, - attributes: List[BaseAttribute] = None, + attributes: list[BaseAttribute] = None, ) -> MeasurementRun: """Add a measurement run-spec set to a :class:`~gemd.entity.object.material_run.MaterialRun`. @@ -264,10 +263,10 @@ def add_measurement( def add_attribute( - target: Union[HasProperties, HasConditions, HasParameters], - template: Union[PropertyTemplate, ConditionTemplate, ParameterTemplate], - value: Union[BaseValue, str, float, int], -) -> Union[Property, Condition, Parameter]: + target: HasProperties | HasConditions | HasParameters, + template: PropertyTemplate | ConditionTemplate | ParameterTemplate, + value: BaseValue | str | float | int, +) -> Property | Condition | Parameter: """Generate an attribute, and then add it attribute to a GEMD object. Parameters @@ -314,9 +313,9 @@ def add_attribute( def make_attribute( - template: Union[PropertyTemplate, ConditionTemplate, ParameterTemplate], - value: Union[BaseValue, str, float, int], -) -> Union[Property, Condition, Parameter]: + template: PropertyTemplate | ConditionTemplate | ParameterTemplate, + value: BaseValue | str | float | int, +) -> Property | Condition | Parameter: """Generate an Attribute and the contained Value. Parameters @@ -350,7 +349,7 @@ def make_attribute( return attribute -def make_value(value: Union[str, float, int], bounds: BaseBounds) -> BaseValue: +def make_value(value: str | float | int, bounds: BaseBounds) -> BaseValue: """Generate a Value object based upon a number or string and a particular bounds. Parameters diff --git a/gemd/demo/strehlow_and_cook.py b/gemd/demo/strehlow_and_cook.py index aa8f529..9339339 100644 --- a/gemd/demo/strehlow_and_cook.py +++ b/gemd/demo/strehlow_and_cook.py @@ -1,6 +1,6 @@ """Demo representing Strehlow & Cook bandgap data with data concepts.""" -from typing import Iterable +from collections.abc import Iterable from gemd.entity.attribute.condition import Condition from gemd.entity.attribute.property import Property diff --git a/gemd/entity/attribute/base_attribute.py b/gemd/entity/attribute/base_attribute.py index 0b43652..062bc90 100644 --- a/gemd/entity/attribute/base_attribute.py +++ b/gemd/entity/attribute/base_attribute.py @@ -1,5 +1,5 @@ from abc import abstractmethod -from typing import Iterable, List, Optional, Type, Union +from collections.abc import Iterable from gemd.entity.bounds_validation import WarningLevel, get_validation_level from gemd.entity.dict_serializable import DictSerializable, logger @@ -37,11 +37,11 @@ def __init__( self, name: str, *, - template: Union[AttributeTemplate, LinkByUID, None] = None, - origin: Union[Origin, str] = Origin.UNKNOWN, + template: AttributeTemplate | LinkByUID | None = None, + origin: Origin | str = Origin.UNKNOWN, value: BaseValue = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): self.name = name self.notes = notes @@ -85,12 +85,12 @@ def value(self, value: BaseValue): raise TypeError(f"value must be a BaseValue: {value}") @property - def template(self) -> Optional[Union[AttributeTemplate, LinkByUID]]: + def template(self) -> AttributeTemplate | LinkByUID | None: """Get the template.""" return self._template @template.setter - def template(self, template: Optional[Union[AttributeTemplate, LinkByUID]]): + def template(self, template: AttributeTemplate | LinkByUID | None): """Set the template.""" if template is None: self._template = None @@ -103,7 +103,7 @@ def template(self, template: Optional[Union[AttributeTemplate, LinkByUID]]): @staticmethod @abstractmethod - def _template_type() -> Type: + def _template_type() -> type: """Get the expected type of template for this object (property of child).""" @property @@ -112,18 +112,18 @@ def origin(self) -> Origin: return self._origin @origin.setter - def origin(self, origin: Union[Origin, str]): + def origin(self, origin: Origin | str): """Set the origin.""" if origin is None: raise ValueError("origin must be specified (but may be `unknown`)") self._origin = Origin.from_str(origin, exception=True) @property - def file_links(self) -> List[FileLink]: + def file_links(self) -> list[FileLink]: """Get the file links.""" return self._file_links @file_links.setter - def file_links(self, file_links: Optional[Union[Iterable[FileLink], FileLink]]): + def file_links(self, file_links: Iterable[FileLink] | FileLink | None): """Set the file links.""" self._file_links = validate_list(file_links, FileLink) diff --git a/gemd/entity/attribute/condition.py b/gemd/entity/attribute/condition.py index b714373..4050c89 100644 --- a/gemd/entity/attribute/condition.py +++ b/gemd/entity/attribute/condition.py @@ -1,5 +1,3 @@ -from typing import Type - from gemd.entity.attribute.base_attribute import BaseAttribute from gemd.entity.template import ConditionTemplate @@ -32,5 +30,5 @@ class Condition(BaseAttribute, typ="condition"): """ @staticmethod - def _template_type() -> Type: + def _template_type() -> type: return ConditionTemplate diff --git a/gemd/entity/attribute/parameter.py b/gemd/entity/attribute/parameter.py index fea5dd6..850175c 100644 --- a/gemd/entity/attribute/parameter.py +++ b/gemd/entity/attribute/parameter.py @@ -1,5 +1,3 @@ -from typing import Type - from gemd.entity.attribute.base_attribute import BaseAttribute from gemd.entity.template import ParameterTemplate @@ -33,5 +31,5 @@ class Parameter(BaseAttribute, typ="parameter"): """ @staticmethod - def _template_type() -> Type: + def _template_type() -> type: return ParameterTemplate diff --git a/gemd/entity/attribute/property.py b/gemd/entity/attribute/property.py index fab30a5..695eaea 100644 --- a/gemd/entity/attribute/property.py +++ b/gemd/entity/attribute/property.py @@ -1,5 +1,3 @@ -from typing import Type - from gemd.entity.attribute.base_attribute import BaseAttribute from gemd.entity.template import PropertyTemplate @@ -32,5 +30,5 @@ class Property(BaseAttribute, typ="property"): """ @staticmethod - def _template_type() -> Type: + def _template_type() -> type: return PropertyTemplate diff --git a/gemd/entity/attribute/property_and_conditions.py b/gemd/entity/attribute/property_and_conditions.py index 3fb96b9..9f4d117 100644 --- a/gemd/entity/attribute/property_and_conditions.py +++ b/gemd/entity/attribute/property_and_conditions.py @@ -1,4 +1,4 @@ -from typing import Iterable, List, Optional, Union +from collections.abc import Iterable from gemd.entity.attribute.condition import Condition from gemd.entity.attribute.property import Property @@ -26,7 +26,7 @@ class PropertyAndConditions(DictSerializable, typ="property_and_conditions"): """ def __init__( - self, property: Property = None, conditions: Union[Iterable[Condition], Condition] = None + self, property: Property = None, conditions: Iterable[Condition] | Condition = None ): self._property = None self.property = property @@ -34,7 +34,7 @@ def __init__( self.conditions = conditions @property - def conditions(self) -> List[Condition]: + def conditions(self) -> list[Condition]: """Get conditions.""" return self._conditions @@ -49,7 +49,7 @@ def name(self) -> str: return self.property.name @property - def template(self) -> Optional[Union[PropertyTemplate, LinkByUID]]: + def template(self) -> PropertyTemplate | LinkByUID | None: """Get template of attribute (use template of property).""" return self.property.template diff --git a/gemd/entity/base_entity.py b/gemd/entity/base_entity.py index 870aafb..6367491 100644 --- a/gemd/entity/base_entity.py +++ b/gemd/entity/base_entity.py @@ -1,6 +1,7 @@ """Base class for all entities.""" -from typing import Dict, FrozenSet, Iterable, List, MutableMapping, Optional, Set, TypeVar, Union +from collections.abc import Iterable, MutableMapping +from typing import TypeVar from gemd.entity.case_insensitive_dict import CaseInsensitiveDict from gemd.entity.dict_serializable import DictSerializable @@ -28,7 +29,7 @@ def __init__(self, uids: MutableMapping[str, str], tags: Iterable[str]): self.uids = uids @property - def tags(self) -> List[str]: + def tags(self) -> list[str]: """A collection of structured labels. `Tags `_ @@ -43,7 +44,7 @@ def tags(self, tags: Iterable[str]): self._tags = validate_list(tags, str) @property - def uids(self) -> Dict[str, str]: + def uids(self) -> dict[str, str]: """A collection of unique IDs. Requirements for and the value of unique IDs are discussed @@ -76,9 +77,7 @@ def add_uid(self, scope: str, uid: str): """ self.uids[scope] = uid - def to_link( - self, scope: Optional[str] = None, *, allow_fallback: bool = False - ) -> LinkByUIDType: + def to_link(self, scope: str | None = None, *, allow_fallback: bool = False) -> LinkByUIDType: """Generate a ~gemd.entity.link_by_uid.LinkByUID for this object. Parameters @@ -107,7 +106,7 @@ def to_link( return LinkByUID(scope=scope, id=uid) - def all_dependencies(self) -> Set[Union[BaseEntityType, LinkByUIDType]]: + def all_dependencies(self) -> set[BaseEntityType | LinkByUIDType]: """Return a set of all immediate dependencies (no recursion).""" result = set() queue = [type(self)] @@ -121,8 +120,8 @@ def all_dependencies(self) -> Set[Union[BaseEntityType, LinkByUIDType]]: @staticmethod def _cached_equals( - this: "BaseEntity", that: "BaseEntity", *, cache: Dict[FrozenSet, Optional[bool]] = None - ) -> Optional[bool]: + this: "BaseEntity", that: "BaseEntity", *, cache: dict[frozenset, bool | None] = None + ) -> bool | None: """Compute and stash whether two Base Entities are equal in a recursive sense. The cache uses ternary logic to communicate state. True or False indicate a completed diff --git a/gemd/entity/bounds/base_bounds.py b/gemd/entity/bounds/base_bounds.py index f236b65..93f1bc9 100644 --- a/gemd/entity/bounds/base_bounds.py +++ b/gemd/entity/bounds/base_bounds.py @@ -1,7 +1,7 @@ """Base class for all bounds.""" from abc import abstractmethod -from typing import TypeVar, Union +from typing import TypeVar from gemd.entity.dict_serializable import DictSerializable @@ -14,7 +14,7 @@ class BaseBounds(DictSerializable): """Base class for bounds, including RealBounds and CategoricalBounds.""" @abstractmethod - def contains(self, bounds: Union[BaseBoundsType, BaseValueType]): + def contains(self, bounds: BaseBoundsType | BaseValueType): """Check if another bounds is contained within this bounds. Parameters @@ -41,7 +41,7 @@ def contains(self, bounds: Union[BaseBoundsType, BaseValueType]): raise TypeError(f"{bounds} is not a Bounds object") @abstractmethod - def union(self, *others: Union[BaseBoundsType, BaseValueType]) -> BaseBoundsType: + def union(self, *others: BaseBoundsType | BaseValueType) -> BaseBoundsType: """Return the union of this bounds and other bounds. The others list must also be the same class (e.g., categorical, real...). @@ -61,7 +61,7 @@ def union(self, *others: Union[BaseBoundsType, BaseValueType]) -> BaseBoundsType """ @abstractmethod - def update(self, *others: Union[BaseBoundsType, BaseValueType]): + def update(self, *others: BaseBoundsType | BaseValueType): """Update this bounds to include other bounds. The others list must also be the same class (e.g., categorical, real...). diff --git a/gemd/entity/bounds/categorical_bounds.py b/gemd/entity/bounds/categorical_bounds.py index ada26d8..4e20f11 100644 --- a/gemd/entity/bounds/categorical_bounds.py +++ b/gemd/entity/bounds/categorical_bounds.py @@ -1,4 +1,5 @@ -from typing import Any, Dict, Iterable, Optional, Set, TypeVar, Union +from collections.abc import Iterable +from typing import Any, TypeVar from gemd.entity.bounds.base_bounds import BaseBounds from gemd.entity.util import array_like @@ -19,17 +20,17 @@ class CategoricalBounds(BaseBounds, typ="categorical_bounds"): """ - def __init__(self, categories: Optional[Iterable[str]] = None): + def __init__(self, categories: Iterable[str] | None = None): self._categories = None self.categories = categories @property - def categories(self) -> Set[str]: + def categories(self) -> set[str]: """The collection of allowed categories.""" return self._categories @categories.setter - def categories(self, categories: Optional[Iterable[str]]): + def categories(self, categories: Iterable[str] | None): if categories is None: self._categories = set() elif isinstance(categories, array_like()): @@ -42,7 +43,7 @@ def categories(self, categories: Optional[Iterable[str]]): if not all(isinstance(x, str) for x in self.categories): raise ValueError("All the categories must be strings") - def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: + def contains(self, bounds: BaseBounds | BaseValueType) -> bool: """Check if another bounds object or value object is contained by this bounds. The other object must also be Categorical and its allowed categories must be a @@ -74,7 +75,7 @@ def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: return bounds.categories.issubset(self.categories) def union( - self, *others: Union[CategoricalBoundsType, CategoricalValueType] + self, *others: CategoricalBoundsType | CategoricalValueType ) -> CategoricalBoundsType: """Return the union of this bounds and other bounds. @@ -111,7 +112,7 @@ def union( result.update(bounds.categories) return CategoricalBounds(result) - def update(self, *others: Union[CategoricalBoundsType, CategoricalValueType]): + def update(self, *others: CategoricalBoundsType | CategoricalValueType): """Update this bounds to include other bounds. The others list must also be Categorical Bounds or Values. @@ -126,7 +127,7 @@ def update(self, *others: Union[CategoricalBoundsType, CategoricalValueType]): """ self.categories = self.union(*others).categories - def as_dict(self) -> Dict[str, Any]: + def as_dict(self) -> dict[str, Any]: """Convert bounds to a dictionary. Returns diff --git a/gemd/entity/bounds/composition_bounds.py b/gemd/entity/bounds/composition_bounds.py index 7060127..62e52cc 100644 --- a/gemd/entity/bounds/composition_bounds.py +++ b/gemd/entity/bounds/composition_bounds.py @@ -1,6 +1,7 @@ """Bounds a composition to have a specified set of components.""" -from typing import Iterable, Set, TypeVar, Union +from collections.abc import Iterable +from typing import TypeVar from gemd.entity.bounds.base_bounds import BaseBounds from gemd.entity.util import array_like @@ -26,7 +27,7 @@ def __init__(self, components=None): self.components = components @property - def components(self) -> Set[str]: + def components(self) -> set[str]: """Get the collection of the components that are allowed in the composition.""" return self._components @@ -45,7 +46,7 @@ def components(self, value: Iterable[str]): if not all(isinstance(x, str) for x in self.components): raise ValueError("All the components must be strings") - def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: + def contains(self, bounds: BaseBounds | BaseValueType) -> bool: """Check if another bounds or value object is contained by this bounds. The other object must also be a Composition and its components must be a subset of @@ -76,7 +77,7 @@ def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: return bounds.components.issubset(self.components) def union( - self, *others: Union[CompositionBoundsType, CompositionValueType] + self, *others: CompositionBoundsType | CompositionValueType ) -> CompositionBoundsType: """Return the union of this bounds and other bounds. @@ -113,7 +114,7 @@ def union( result.update(bounds.components) return CompositionBounds(result) - def update(self, *others: Union[CompositionBoundsType, CompositionValueType]): + def update(self, *others: CompositionBoundsType | CompositionValueType): """Update this bounds to include other bounds. The others list must also be Composition Bounds or Values. diff --git a/gemd/entity/bounds/integer_bounds.py b/gemd/entity/bounds/integer_bounds.py index 5c7acd2..fcc3731 100644 --- a/gemd/entity/bounds/integer_bounds.py +++ b/gemd/entity/bounds/integer_bounds.py @@ -1,7 +1,7 @@ """Bounds an integer to be between two values.""" from math import isfinite -from typing import TypeVar, Union +from typing import TypeVar from gemd.entity.bounds.base_bounds import BaseBounds @@ -64,7 +64,7 @@ def upper_bound(self, value: int): ) self._upper_bound = int(value) - def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: + def contains(self, bounds: BaseBounds | BaseValueType) -> bool: """Check if another bounds or value object is a subset of this range. The other object must also be an Integer and its lower and upper bound must *both* @@ -94,7 +94,7 @@ def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: return bounds.lower_bound >= self.lower_bound and bounds.upper_bound <= self.upper_bound - def union(self, *others: Union[IntegerBoundsType, IntegerValueType]) -> IntegerBoundsType: + def union(self, *others: IntegerBoundsType | IntegerValueType) -> IntegerBoundsType: """Return the union of this bounds and other bounds. The others list must also be Integer Bounds or Values. @@ -132,7 +132,7 @@ def union(self, *others: Union[IntegerBoundsType, IntegerValueType]) -> IntegerB upper = bounds.upper_bound return IntegerBounds(lower_bound=lower, upper_bound=upper) - def update(self, *others: Union[IntegerBoundsType, IntegerValueType]): + def update(self, *others: IntegerBoundsType | IntegerValueType): """Update this bounds to include other bounds. The others list must also be Integer Bounds or Values. diff --git a/gemd/entity/bounds/molecular_structure_bounds.py b/gemd/entity/bounds/molecular_structure_bounds.py index 7b5b2e9..63f5be6 100644 --- a/gemd/entity/bounds/molecular_structure_bounds.py +++ b/gemd/entity/bounds/molecular_structure_bounds.py @@ -3,7 +3,7 @@ In the future, this may include substructural restrictions. """ -from typing import TypeVar, Union +from typing import TypeVar from gemd.entity.bounds.base_bounds import BaseBounds @@ -16,7 +16,7 @@ class MolecularStructureBounds(BaseBounds, typ="molecular_structure_bounds"): """Molecular bounds, with no component or substructural restrictions (yet).""" - def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: + def contains(self, bounds: BaseBounds | BaseValueType) -> bool: """Check if another bounds or value object is contained by this bounds. The other object must also be or type Molecular. There are no other @@ -46,9 +46,7 @@ def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: return True - def union( - self, *others: Union[MolecularBoundsType, MolecularValueType] - ) -> MolecularBoundsType: + def union(self, *others: MolecularBoundsType | MolecularValueType) -> MolecularBoundsType: """Return the union of this bounds and other bounds. The others list must also be Molecular Structure Bounds or Values. @@ -79,7 +77,7 @@ def union( ) return MolecularStructureBounds() - def update(self, *others: Union[MolecularBoundsType, MolecularValueType]): + def update(self, *others: MolecularBoundsType | MolecularValueType): """Update this bounds to include other bounds. The others list must also be Molecular Structure Bounds or Values. diff --git a/gemd/entity/bounds/real_bounds.py b/gemd/entity/bounds/real_bounds.py index e3dfdd7..fe3e32d 100644 --- a/gemd/entity/bounds/real_bounds.py +++ b/gemd/entity/bounds/real_bounds.py @@ -1,7 +1,7 @@ """Bound a real number to be between two values.""" from math import isfinite -from typing import TypeVar, Union +from typing import TypeVar import gemd.units as units from gemd.entity.bounds.base_bounds import BaseBounds @@ -85,7 +85,7 @@ def default_units(self, default_units: str): ) self._default_units = units.parse_units(default_units, return_unit=False) - def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: + def contains(self, bounds: BaseBounds | BaseValueType) -> bool: """Check if another bounds or value object is a subset of this range. The other object must also be Real and its lower and upper bound must *both* @@ -121,7 +121,7 @@ def contains(self, bounds: Union[BaseBounds, BaseValueType]) -> bool: return bounds.lower_bound >= lower and bounds.upper_bound <= upper - def union(self, *others: Union[RealBoundsType, ContinuousValueType]) -> RealBoundsType: + def union(self, *others: RealBoundsType | ContinuousValueType) -> RealBoundsType: """Return the union of this bounds and other bounds. The others list must also be Real Bounds or Values. @@ -163,7 +163,7 @@ def union(self, *others: Union[RealBoundsType, ContinuousValueType]) -> RealBoun upper = bnd_hi return RealBounds(lower_bound=lower, upper_bound=upper, default_units=unit_) - def update(self, *others: Union[RealBoundsType, ContinuousValueType]): + def update(self, *others: RealBoundsType | ContinuousValueType): """Update this bounds to include other bounds. The others list must also be Real Bounds or Values. diff --git a/gemd/entity/dict_serializable.py b/gemd/entity/dict_serializable.py index 7ed208b..ca5dc1f 100644 --- a/gemd/entity/dict_serializable.py +++ b/gemd/entity/dict_serializable.py @@ -1,8 +1,9 @@ import functools import inspect from abc import ABC, ABCMeta +from collections.abc import Iterable, Mapping from logging import getLogger -from typing import Any, Dict, Iterable, List, Mapping, Set, TypeVar, Union +from typing import Any, TypeVar __all__ = ["DictSerializable"] @@ -16,7 +17,7 @@ class DictSerializableMeta(ABCMeta): """Metaclass for tracking DictSerializable type string to class mappings.""" - _class: Dict[str, type] = {} + _class: dict[str, type] = {} def __new__( mcs, @@ -24,12 +25,12 @@ def __new__( bases, *args, # noqa: D102 typ: str = None, - skip: Set[str] = frozenset(), + skip: set[str] = frozenset(), **kwargs, ): return super().__new__(mcs, name, bases, *args, **kwargs) - def __init__(cls, name, bases, *args, typ: str = None, skip: Set[str] = frozenset(), **kwargs): + def __init__(cls, name, bases, *args, typ: str = None, skip: set[str] = frozenset(), **kwargs): super().__init__(name, bases, *args, **kwargs) if typ is not None: if typ in cls._class and not issubclass(cls, cls._class.get(typ)): @@ -44,7 +45,7 @@ def __init__(cls, name, bases, *args, typ: str = None, skip: Set[str] = frozense cls.skip = {x for b in bases for x in getattr(b, "skip", {})} | skip @property - def class_mapping(cls) -> Dict[str, type]: + def class_mapping(cls) -> dict[str, type]: """Return class typ string -> class map for DictSerializable and its descendants. Note that is actually returns a copy of the internal dict to avoid accidental breakage. @@ -90,13 +91,13 @@ def from_dict(cls, d: Mapping[str, Any]) -> DictSerializableType: @classmethod @functools.lru_cache(maxsize=1024) - def _init_sig(cls) -> List[str]: + def _init_sig(cls) -> list[str]: """Internal method for generating the argument names for the class init method.""" expected_arg_names = inspect.getfullargspec(cls.__init__).args expected_arg_names += inspect.getfullargspec(cls.__init__).kwonlyargs return expected_arg_names - def as_dict(self) -> Dict[str, Any]: + def as_dict(self) -> dict[str, Any]: """Convert the object to a dictionary. Returns @@ -110,7 +111,7 @@ def as_dict(self) -> Dict[str, Any]: attributes["type"] = self.typ return attributes - def dump(self) -> Dict[str, Any]: + def dump(self) -> dict[str, Any]: """Convert the object to a JSON dictionary, so that every entry is serialized. Uses the json encoder client, so objects with uids are converted to LinkByUID dictionaries. @@ -160,9 +161,7 @@ def __repr__(self) -> str: object_dict[key] = self._name_repr(skipped_field) return str(object_dict) - def _name_repr( - self, entity: Union[Iterable[DictSerializableType], DictSerializableType] - ) -> str: + def _name_repr(self, entity: Iterable[DictSerializableType] | DictSerializableType) -> str: """A representation of an object or a list of objects that uses the name and type. This is used to represent soft-linked objects without inundating the user with @@ -188,7 +187,7 @@ def _name_repr( name = getattr(entity, "name", "") return f"<{type(entity).__name__} '{name}'>" - def _dict_for_compare(self) -> Dict[str, Any]: + def _dict_for_compare(self) -> dict[str, Any]: """Which fields & values are relevant to an equality test.""" return self.as_dict() diff --git a/gemd/entity/has_dependencies.py b/gemd/entity/has_dependencies.py index d911c0a..dbc8ed1 100644 --- a/gemd/entity/has_dependencies.py +++ b/gemd/entity/has_dependencies.py @@ -1,7 +1,7 @@ """For entities that have dependencies.""" from abc import ABC, abstractmethod -from typing import Set, TypeVar, Union +from typing import TypeVar __all__ = ["HasDependencies"] BaseEntityType = TypeVar("BaseEntityType", bound="BaseEntity") # noqa: F821 @@ -12,5 +12,5 @@ class HasDependencies(ABC): """Mix-in trait for objects that reference other objects.""" @abstractmethod - def _local_dependencies(self) -> Set[Union[BaseEntityType, LinkByUIDType]]: + def _local_dependencies(self) -> set[BaseEntityType | LinkByUIDType]: """All dependencies (objects) that this class introduces.""" diff --git a/gemd/entity/object/base_object.py b/gemd/entity/object/base_object.py index 4d7a433..632df4a 100644 --- a/gemd/entity/object/base_object.py +++ b/gemd/entity/object/base_object.py @@ -1,5 +1,5 @@ import functools -from typing import Iterable, List, Mapping, Optional, Union +from collections.abc import Iterable, Mapping from gemd.entity.base_entity import BaseEntity from gemd.entity.file_link import FileLink @@ -39,7 +39,7 @@ def __init__( uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): BaseEntity.__init__(self, uids, tags) self.notes = notes @@ -71,10 +71,10 @@ def name(self, name: str): self._name = validate_str(name) @property - def file_links(self) -> List[FileLink]: + def file_links(self) -> list[FileLink]: """Links to associated files, with resource paths into the files API.""" return self._file_links @file_links.setter - def file_links(self, file_links: Union[Iterable[FileLink], FileLink]): + def file_links(self, file_links: Iterable[FileLink] | FileLink): self._file_links = validate_list(file_links, FileLink) diff --git a/gemd/entity/object/has_conditions.py b/gemd/entity/object/has_conditions.py index 61e0a7d..dedff08 100644 --- a/gemd/entity/object/has_conditions.py +++ b/gemd/entity/object/has_conditions.py @@ -1,7 +1,7 @@ """For entities that have conditions.""" from abc import ABC -from typing import Iterable, List, Set, Union +from collections.abc import Iterable from gemd.entity.attribute.condition import Condition from gemd.entity.base_entity import BaseEntity @@ -17,21 +17,21 @@ class HasConditions(HasTemplateCheckGenerator, HasDependencies, ABC): """Mixin-trait for entities that include conditions.""" - def __init__(self, conditions: Union[Condition, Iterable[Condition]]): + def __init__(self, conditions: Condition | Iterable[Condition]): self._conditions = None self.conditions = conditions @property - def conditions(self) -> List[Condition]: + def conditions(self) -> list[Condition]: """A list of conditions associated with this entity.""" return self._conditions @conditions.setter - def conditions(self, conditions: Union[Condition, Iterable[Condition]]): + def conditions(self, conditions: Condition | Iterable[Condition]): """Set the list of conditions.""" checker = self._generate_template_check(HasConditionTemplates.validate_condition) self._conditions = validate_list(conditions, Condition, trigger=checker) - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {cond.template for cond in self.conditions if cond.template is not None} diff --git a/gemd/entity/object/has_material.py b/gemd/entity/object/has_material.py index 4f5484b..26c1aa5 100644 --- a/gemd/entity/object/has_material.py +++ b/gemd/entity/object/has_material.py @@ -1,7 +1,6 @@ """For entities that have specs.""" from abc import ABC, abstractmethod -from typing import Set, Union from gemd.entity.base_entity import BaseEntity from gemd.entity.has_dependencies import HasDependencies @@ -16,14 +15,14 @@ class HasMaterial(HasDependencies, ABC): @property @abstractmethod - def material(self) -> Union[BaseObject, LinkByUID]: + def material(self) -> BaseObject | LinkByUID: """Get the material.""" @material.setter @abstractmethod - def material(self, spec: Union[BaseObject, LinkByUID]): + def material(self, spec: BaseObject | LinkByUID): """Set the material.""" - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {self.material} if self.material is not None else set() diff --git a/gemd/entity/object/has_parameters.py b/gemd/entity/object/has_parameters.py index 196ddd0..6bf3c32 100644 --- a/gemd/entity/object/has_parameters.py +++ b/gemd/entity/object/has_parameters.py @@ -1,7 +1,7 @@ """For entities that have parameters.""" from abc import ABC -from typing import Iterable, List, Set, Union +from collections.abc import Iterable from gemd.entity.attribute.parameter import Parameter from gemd.entity.base_entity import BaseEntity @@ -17,21 +17,21 @@ class HasParameters(HasTemplateCheckGenerator, HasDependencies, ABC): """Mixin-trait for entities that include parameters.""" - def __init__(self, parameters: Union[Parameter, Iterable[Parameter]]): + def __init__(self, parameters: Parameter | Iterable[Parameter]): self._parameters = None self.parameters = parameters @property - def parameters(self) -> List[Parameter]: + def parameters(self) -> list[Parameter]: """A list of parameters associated with this entity.""" return self._parameters @parameters.setter - def parameters(self, parameters: Union[Parameter, Iterable[Parameter]]): + def parameters(self, parameters: Parameter | Iterable[Parameter]): """Set the list of parameters.""" checker = self._generate_template_check(HasParameterTemplates.validate_parameter) self._parameters = validate_list(parameters, Parameter, trigger=checker) - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {param.template for param in self.parameters if param.template is not None} diff --git a/gemd/entity/object/has_process.py b/gemd/entity/object/has_process.py index 5fdbbfa..bc5b261 100644 --- a/gemd/entity/object/has_process.py +++ b/gemd/entity/object/has_process.py @@ -1,7 +1,6 @@ """For entities that have specs.""" from abc import abstractmethod -from typing import Set, Union from gemd.entity.base_entity import BaseEntity from gemd.entity.has_dependencies import HasDependencies @@ -16,14 +15,14 @@ class HasProcess(HasDependencies): @property @abstractmethod - def process(self) -> Union[BaseObject, LinkByUID]: + def process(self) -> BaseObject | LinkByUID: """Get the process.""" @process.setter @abstractmethod - def process(self, process: Union[BaseObject, LinkByUID]): + def process(self, process: BaseObject | LinkByUID): """Set the process.""" - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {self.process} if self.process is not None else set() diff --git a/gemd/entity/object/has_properties.py b/gemd/entity/object/has_properties.py index 3c44dfd..e5d69d2 100644 --- a/gemd/entity/object/has_properties.py +++ b/gemd/entity/object/has_properties.py @@ -1,7 +1,7 @@ """For entities that have properties.""" from abc import ABC -from typing import Iterable, List, Set, Union +from collections.abc import Iterable from gemd.entity.attribute.property import Property from gemd.entity.base_entity import BaseEntity @@ -17,21 +17,21 @@ class HasProperties(HasTemplateCheckGenerator, HasDependencies, ABC): """Mixin-trait for entities that include properties.""" - def __init__(self, properties: Union[Property, Iterable[Property]]): + def __init__(self, properties: Property | Iterable[Property]): self._properties = None self.properties = properties @property - def properties(self) -> List[Property]: + def properties(self) -> list[Property]: """A list of properties associated with this entity.""" return self._properties @properties.setter - def properties(self, properties: Union[Property, Iterable[Property]]): + def properties(self, properties: Property | Iterable[Property]): """Set the list of properties.""" checker = self._generate_template_check(HasPropertyTemplates.validate_property) self._properties = validate_list(properties, Property, trigger=checker) - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {prop.template for prop in self.properties if prop.template is not None} diff --git a/gemd/entity/object/has_quantities.py b/gemd/entity/object/has_quantities.py index c06c2ba..f5e0ef6 100644 --- a/gemd/entity/object/has_quantities.py +++ b/gemd/entity/object/has_quantities.py @@ -11,7 +11,7 @@ __all__ = ["HasQuantities"] -class HasQuantities(object): +class HasQuantities: """Mixin-trait that includes the mass, volume, number fraction, and absolute quantity.""" def __init__( diff --git a/gemd/entity/object/has_source.py b/gemd/entity/object/has_source.py index 666e557..343ea3a 100644 --- a/gemd/entity/object/has_source.py +++ b/gemd/entity/object/has_source.py @@ -5,7 +5,7 @@ __all__ = ["HasSource"] -class HasSource(object): +class HasSource: """Mixin-trait for entities that include sources (data provenance).""" def __init__(self, source: PerformedSource): diff --git a/gemd/entity/object/has_spec.py b/gemd/entity/object/has_spec.py index 76c7389..9ac4798 100644 --- a/gemd/entity/object/has_spec.py +++ b/gemd/entity/object/has_spec.py @@ -1,7 +1,6 @@ """For entities that have specs.""" from abc import abstractmethod -from typing import Optional, Set, Type, Union from gemd.entity.base_entity import BaseEntity from gemd.entity.has_dependencies import HasDependencies @@ -15,17 +14,17 @@ class HasSpec(HasDependencies): """Mix-in trait for objects that can be assigned specs.""" - def __init__(self, spec: Union[HasTemplate, LinkByUID] = None): + def __init__(self, spec: HasTemplate | LinkByUID = None): self._spec = None self.spec = spec @property - def spec(self) -> Union[HasTemplate, LinkByUID]: + def spec(self) -> HasTemplate | LinkByUID: """A spec, which expresses the anticipated or aspirational behavior of this object.""" return self._spec @spec.setter - def spec(self, spec: Union[HasTemplate, LinkByUID]): + def spec(self, spec: HasTemplate | LinkByUID): """Set the spec.""" if spec is None: self._spec = None @@ -38,17 +37,17 @@ def spec(self, spec: Union[HasTemplate, LinkByUID]): @staticmethod @abstractmethod - def _spec_type() -> Type: + def _spec_type() -> type: """Child must report implementation details.""" @property - def template(self) -> Optional[Union[BaseTemplate, LinkByUID]]: + def template(self) -> BaseTemplate | LinkByUID | None: """Get the template associated with the spec.""" if isinstance(self.spec, HasTemplate): return self.spec.template else: return None - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {self.spec} if self.spec is not None else set() diff --git a/gemd/entity/object/has_template.py b/gemd/entity/object/has_template.py index 8a73254..25bf48f 100644 --- a/gemd/entity/object/has_template.py +++ b/gemd/entity/object/has_template.py @@ -1,7 +1,6 @@ """For entities that have templates.""" from abc import abstractmethod -from typing import Optional, Set, Type, Union from gemd.entity.base_entity import BaseEntity from gemd.entity.has_dependencies import HasDependencies @@ -14,22 +13,22 @@ class HasTemplate(HasDependencies): """Mix-in trait for objects that can be assigned templates.""" - def __init__(self, template: Optional[Union[BaseTemplate, LinkByUID]] = None): + def __init__(self, template: BaseTemplate | LinkByUID | None = None): self._template = None self.template = template @staticmethod @abstractmethod - def _template_type() -> Type: + def _template_type() -> type: """Child must report implementation details.""" @property - def template(self) -> Optional[Union[BaseTemplate, LinkByUID]]: + def template(self) -> BaseTemplate | LinkByUID | None: """A template that defines the allowed values.""" return self._template @template.setter - def template(self, template: Optional[Union[BaseTemplate, LinkByUID]]): + def template(self, template: BaseTemplate | LinkByUID | None): """Set the template.""" if template is None: self._template = None @@ -40,6 +39,6 @@ def template(self, template: Optional[Union[BaseTemplate, LinkByUID]]): f"Template must be a {self._template_type()} or LinkByUID, not {type(template)}" ) - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {self.template} if self.template is not None else set() diff --git a/gemd/entity/object/has_template_check_generator.py b/gemd/entity/object/has_template_check_generator.py index bea344f..f22984c 100644 --- a/gemd/entity/object/has_template_check_generator.py +++ b/gemd/entity/object/has_template_check_generator.py @@ -1,8 +1,9 @@ """For entities that have specs.""" from abc import ABC, abstractmethod +from collections.abc import Callable from inspect import getmembers, getmodule, isclass, signature -from typing import Callable, TypeVar, Union +from typing import TypeVar from gemd.entity.bounds_validation import WarningLevel, get_validation_level from gemd.entity.dict_serializable import logger @@ -19,7 +20,7 @@ class HasTemplateCheckGenerator(ABC): @property @abstractmethod - def template(self) -> Union[BaseTemplate, LinkByUID]: + def template(self) -> BaseTemplate | LinkByUID: """Get the object template associated with this object.""" def _generate_template_check( diff --git a/gemd/entity/object/ingredient_run.py b/gemd/entity/object/ingredient_run.py index f7f068a..ea2d20e 100644 --- a/gemd/entity/object/ingredient_run.py +++ b/gemd/entity/object/ingredient_run.py @@ -1,4 +1,5 @@ -from typing import Any, Iterable, List, Mapping, Optional, Type, Union +from collections.abc import Iterable, Mapping +from typing import Any from gemd.entity.dict_serializable import DictSerializable from gemd.entity.file_link import FileLink @@ -58,17 +59,17 @@ class IngredientRun( def __init__( self, *, - material: Union[MaterialRun, LinkByUID] = None, - process: Union[ProcessRun, LinkByUID] = None, + material: MaterialRun | LinkByUID = None, + process: ProcessRun | LinkByUID = None, mass_fraction: ContinuousValue = None, volume_fraction: ContinuousValue = None, number_fraction: ContinuousValue = None, absolute_quantity: ContinuousValue = None, - spec: Union[IngredientSpec, LinkByUID] = None, + spec: IngredientSpec | LinkByUID = None, uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): BaseObject.__init__( self, name=None, uids=uids, tags=tags, notes=notes, file_links=file_links @@ -100,7 +101,7 @@ def name(self) -> str: return super().name @property - def labels(self) -> List[str]: + def labels(self) -> list[str]: """Get labels.""" from gemd.entity.object.ingredient_spec import IngredientSpec @@ -110,12 +111,12 @@ def labels(self) -> List[str]: return self._labels @property - def material(self) -> Union[MaterialRun, LinkByUID]: + def material(self) -> MaterialRun | LinkByUID: """Get the material.""" return self._material @material.setter - def material(self, material: Union[MaterialRun, LinkByUID]): + def material(self, material: MaterialRun | LinkByUID): if material is None: self._material = None elif isinstance(material, (MaterialRun, LinkByUID)): @@ -126,12 +127,12 @@ def material(self, material: Union[MaterialRun, LinkByUID]): ) @property - def process(self) -> Union[ProcessRun, LinkByUID]: + def process(self) -> ProcessRun | LinkByUID: """Get the material.""" return self._process @process.setter - def process(self, process: Union[ProcessRun, LinkByUID]): + def process(self, process: ProcessRun | LinkByUID): if isinstance(self._process, ProcessRun): # This could throw an exception if it's not in the list, but then something else broke self._process.ingredients.remove(self) @@ -144,17 +145,17 @@ def process(self, process: Union[ProcessRun, LinkByUID]): raise TypeError(f"IngredientRun.process must be a ProcessRun or LinkByUID: {process}") @staticmethod - def _spec_type() -> Type: + def _spec_type() -> type: """Required method to satisfy HasTemplates mix-in.""" return IngredientSpec @property - def spec(self) -> Union[IngredientSpec, LinkByUID]: + def spec(self) -> IngredientSpec | LinkByUID: """Get the spec.""" return super().spec @spec.setter - def spec(self, spec: Union[IngredientSpec, LinkByUID]): + def spec(self, spec: IngredientSpec | LinkByUID): """Set the spec.""" if isinstance(self.spec, IngredientSpec): # Store values if you had them self._name = self.spec.name diff --git a/gemd/entity/object/ingredient_spec.py b/gemd/entity/object/ingredient_spec.py index 2dc0138..a885e8b 100644 --- a/gemd/entity/object/ingredient_spec.py +++ b/gemd/entity/object/ingredient_spec.py @@ -1,4 +1,4 @@ -from typing import Iterable, List, Mapping, Optional, Type, Union +from collections.abc import Iterable, Mapping from gemd.entity.file_link import FileLink from gemd.entity.link_by_uid import LinkByUID @@ -59,8 +59,8 @@ def __init__( self, name: str, *, - material: Union[MaterialSpec, LinkByUID] = None, - process: Union[ProcessSpec, LinkByUID] = None, + material: MaterialSpec | LinkByUID = None, + process: ProcessSpec | LinkByUID = None, labels: Iterable[str] = None, mass_fraction: ContinuousValue = None, volume_fraction: ContinuousValue = None, @@ -69,7 +69,7 @@ def __init__( uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): BaseObject.__init__( @@ -92,7 +92,7 @@ def __init__( self.process = process @property - def labels(self) -> List[str]: + def labels(self) -> list[str]: """Get labels.""" return self._labels @@ -101,12 +101,12 @@ def labels(self, labels: Iterable[str]): self._labels = validate_list(labels, str) @property - def material(self) -> Union[MaterialSpec, LinkByUID]: + def material(self) -> MaterialSpec | LinkByUID: """Get the material spec.""" return self._material @material.setter - def material(self, material: Union[MaterialSpec, LinkByUID]): + def material(self, material: MaterialSpec | LinkByUID): """Set the material spec.""" if material is None: self._material = None @@ -116,12 +116,12 @@ def material(self, material: Union[MaterialSpec, LinkByUID]): raise TypeError("IngredientSpec.material must be a MaterialSpec or LinkByUID") @property - def process(self) -> Union[ProcessSpec, LinkByUID]: + def process(self) -> ProcessSpec | LinkByUID: """Get the process.""" return self._process @process.setter - def process(self, process: Union[ProcessSpec, LinkByUID]): + def process(self, process: ProcessSpec | LinkByUID): """Set the process.""" if isinstance(self._process, ProcessSpec): # This could throw an exception if it's not in the list, but then something else broke @@ -147,6 +147,6 @@ def template(self, template): raise AttributeError("Ingredients do not support a template.") @staticmethod - def _template_type() -> Type: + def _template_type() -> type: """Required method to satisfy HasTemplates mix-in.""" return type(None) diff --git a/gemd/entity/object/material_run.py b/gemd/entity/object/material_run.py index 4469828..5002988 100644 --- a/gemd/entity/object/material_run.py +++ b/gemd/entity/object/material_run.py @@ -1,4 +1,5 @@ -from typing import Any, Iterable, List, Mapping, Optional, Type, TypeVar, Union +from collections.abc import Iterable, Mapping +from typing import Any, TypeVar from gemd.entity.file_link import FileLink from gemd.entity.link_by_uid import LinkByUID @@ -49,13 +50,13 @@ def __init__( self, name: str, *, - spec: Union[MaterialSpec, LinkByUID] = None, - process: Union[ProcessRun, LinkByUID] = None, - sample_type: Union[SampleType, str] = "unknown", + spec: MaterialSpec | LinkByUID = None, + process: ProcessRun | LinkByUID = None, + sample_type: SampleType | str = "unknown", uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): from gemd.entity.object.measurement_run import MeasurementRun @@ -71,12 +72,12 @@ def __init__( self.sample_type = sample_type @property - def process(self) -> Union[ProcessRun, LinkByUID]: + def process(self) -> ProcessRun | LinkByUID: """Get the originating process run.""" return self._process @process.setter - def process(self, process: Union[ProcessRun, LinkByUID]): + def process(self, process: ProcessRun | LinkByUID): if self.process is not None and isinstance(self.process, ProcessRun): self.process._output_material = None if process is None: @@ -90,7 +91,7 @@ def process(self, process: Union[ProcessRun, LinkByUID]): raise TypeError(f"process must be a ProcessRun or LinkByUID: {process}") @property - def measurements(self) -> List[MeasurementRunType]: + def measurements(self) -> list[MeasurementRunType]: """Measurements performed on this material. The link is established by creating the measurement run and settings its @@ -105,11 +106,11 @@ def sample_type(self) -> SampleType: return self._sample_type @sample_type.setter - def sample_type(self, sample_type: Union[SampleType, str]): + def sample_type(self, sample_type: SampleType | str): self._sample_type = SampleType.from_str(sample_type, exception=True) @staticmethod - def _spec_type() -> Type: + def _spec_type() -> type: """Required method to satisfy HasTemplates mix-in.""" return MaterialSpec diff --git a/gemd/entity/object/material_spec.py b/gemd/entity/object/material_spec.py index f0d4ba9..7c825ca 100644 --- a/gemd/entity/object/material_spec.py +++ b/gemd/entity/object/material_spec.py @@ -1,4 +1,4 @@ -from typing import Iterable, List, Mapping, Optional, Set, Type, Union +from collections.abc import Iterable, Mapping from gemd.entity.attribute.property_and_conditions import PropertyAndConditions from gemd.entity.file_link import FileLink @@ -51,13 +51,13 @@ def __init__( self, name: str, *, - template: Optional[Union[MaterialTemplate, LinkByUID]] = None, - process: Union[ProcessSpec, LinkByUID] = None, - properties: Union[Iterable[PropertyAndConditions], PropertyAndConditions] = None, + template: MaterialTemplate | LinkByUID | None = None, + process: ProcessSpec | LinkByUID = None, + properties: Iterable[PropertyAndConditions] | PropertyAndConditions = None, uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): BaseObject.__init__( self, name=name, uids=uids, tags=tags, notes=notes, file_links=file_links @@ -69,25 +69,23 @@ def __init__( self.process = process @property - def properties(self) -> List[PropertyAndConditions]: + def properties(self) -> list[PropertyAndConditions]: """Get the list of property-and-conditions.""" return self._properties @properties.setter - def properties( - self, properties: Union[Iterable[PropertyAndConditions], PropertyAndConditions] - ): + def properties(self, properties: Iterable[PropertyAndConditions] | PropertyAndConditions): """Set the list of property-and-conditions.""" checker = self._generate_template_check(HasPropertyTemplates.validate_property) self._properties = validate_list(properties, PropertyAndConditions, trigger=checker) @property - def process(self) -> Union[ProcessSpec, LinkByUID]: + def process(self) -> ProcessSpec | LinkByUID: """Get the originating process spec.""" return self._process @process.setter - def process(self, process: Union[ProcessSpec, LinkByUID]): + def process(self, process: ProcessSpec | LinkByUID): """Link to the ProcessSpec that creates this MaterialSpec. If the input, process, is not an instance of ProcessSpec, raise an error. @@ -113,11 +111,11 @@ def process(self, process: Union[ProcessSpec, LinkByUID]): ) @staticmethod - def _template_type() -> Type: + def _template_type() -> type: """Communicate expected template type to parent class.""" return MaterialTemplate - def _local_dependencies(self) -> Set[Union[BaseEntity, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntity | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" result = set() for attr in self.properties: diff --git a/gemd/entity/object/measurement_run.py b/gemd/entity/object/measurement_run.py index 9e5a22f..4d59a85 100644 --- a/gemd/entity/object/measurement_run.py +++ b/gemd/entity/object/measurement_run.py @@ -1,4 +1,4 @@ -from typing import Iterable, Mapping, Optional, Type, Union +from collections.abc import Iterable, Mapping from gemd.entity.attribute.condition import Condition from gemd.entity.attribute.parameter import Parameter @@ -71,15 +71,15 @@ def __init__( self, name: str, *, - spec: Union[MeasurementSpec, LinkByUID] = None, - material: Union[MaterialRun, LinkByUID] = None, - properties: Union[Property, Iterable[Property]] = None, - conditions: Union[Condition, Iterable[Condition]] = None, - parameters: Union[Parameter, Iterable[Parameter]] = None, + spec: MeasurementSpec | LinkByUID = None, + material: MaterialRun | LinkByUID = None, + properties: Property | Iterable[Property] = None, + conditions: Condition | Iterable[Condition] = None, + parameters: Parameter | Iterable[Parameter] = None, uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, source: PerformedSource = None, ): BaseObject.__init__( @@ -95,12 +95,12 @@ def __init__( self.material = material @property - def material(self) -> Union[MaterialRun, LinkByUID]: + def material(self) -> MaterialRun | LinkByUID: """Get the material.""" return self._material @material.setter - def material(self, value: Union[MaterialRun, LinkByUID]): + def material(self, value: MaterialRun | LinkByUID): if isinstance(self._material, MaterialRun): # This could throw an exception if it's not in the list, but then something else broke self._material.measurements.remove(self) @@ -113,6 +113,6 @@ def material(self, value: Union[MaterialRun, LinkByUID]): raise TypeError(f"material must be a MaterialRun or LinkByUID: {value}") @staticmethod - def _spec_type() -> Type: + def _spec_type() -> type: """Required method to satisfy HasTemplates mix-in.""" return MeasurementSpec diff --git a/gemd/entity/object/measurement_spec.py b/gemd/entity/object/measurement_spec.py index 65552d0..c20d869 100644 --- a/gemd/entity/object/measurement_spec.py +++ b/gemd/entity/object/measurement_spec.py @@ -1,4 +1,4 @@ -from typing import Iterable, Mapping, Optional, Type, Union +from collections.abc import Iterable, Mapping from gemd.entity.attribute.condition import Condition from gemd.entity.attribute.parameter import Parameter @@ -51,13 +51,13 @@ def __init__( self, name: str, *, - template: Optional[Union[MeasurementTemplate, LinkByUID]] = None, - conditions: Union[Condition, Iterable[Condition]] = None, - parameters: Union[Parameter, Iterable[Parameter]] = None, + template: MeasurementTemplate | LinkByUID | None = None, + conditions: Condition | Iterable[Condition] = None, + parameters: Parameter | Iterable[Parameter] = None, uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): BaseObject.__init__( self, name=name, uids=uids, tags=tags, notes=notes, file_links=file_links @@ -67,6 +67,6 @@ def __init__( HasConditions.__init__(self, conditions=conditions) @staticmethod - def _template_type() -> Type: + def _template_type() -> type: """Communicate expected template type to parent class.""" return MeasurementTemplate diff --git a/gemd/entity/object/process_run.py b/gemd/entity/object/process_run.py index 99a5985..25c244b 100644 --- a/gemd/entity/object/process_run.py +++ b/gemd/entity/object/process_run.py @@ -1,4 +1,5 @@ -from typing import Any, Dict, Iterable, List, Mapping, Optional, Type, TypeVar, Union +from collections.abc import Iterable, Mapping +from typing import Any, TypeVar from gemd.entity.attribute.condition import Condition from gemd.entity.attribute.parameter import Parameter @@ -64,13 +65,13 @@ def __init__( self, name: str, *, - spec: Union[ProcessSpec, LinkByUID] = None, - conditions: Union[Condition, Iterable[Condition]] = None, - parameters: Union[Parameter, Iterable[Parameter]] = None, + spec: ProcessSpec | LinkByUID = None, + conditions: Condition | Iterable[Condition] = None, + parameters: Parameter | Iterable[Parameter] = None, uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, source: PerformedSource = None, ): from gemd.entity.object.ingredient_run import IngredientRun @@ -87,7 +88,7 @@ def __init__( self._output_material = None @property - def output_material(self) -> Optional[MaterialRunType]: + def output_material(self) -> MaterialRunType | None: """The material run that this process run produces. The link is established by creating the material run and settings its @@ -97,7 +98,7 @@ def output_material(self) -> Optional[MaterialRunType]: return self._output_material @property - def ingredients(self) -> List[IngredientRunType]: + def ingredients(self) -> list[IngredientRunType]: """Ingredient runs that act as inputs to this process run. The link is established by creating each ingredient run and setting its @@ -107,11 +108,11 @@ def ingredients(self) -> List[IngredientRunType]: return self._ingredients @staticmethod - def _spec_type() -> Type: + def _spec_type() -> type: """Required method to satisfy HasTemplates mix-in.""" return ProcessSpec - def _dict_for_compare(self) -> Dict[str, Any]: + def _dict_for_compare(self) -> dict[str, Any]: """Support for recursive equals.""" base = super()._dict_for_compare() base["ingredients"] = self.ingredients diff --git a/gemd/entity/object/process_spec.py b/gemd/entity/object/process_spec.py index b07c117..0e0a920 100644 --- a/gemd/entity/object/process_spec.py +++ b/gemd/entity/object/process_spec.py @@ -1,4 +1,5 @@ -from typing import Any, Dict, Iterable, List, Mapping, Optional, Type, TypeVar, Union +from collections.abc import Iterable, Mapping +from typing import Any, TypeVar from gemd.entity.attribute.condition import Condition from gemd.entity.attribute.parameter import Parameter @@ -59,13 +60,13 @@ def __init__( self, name: str, *, - template: Optional[Union[ProcessTemplate, LinkByUID]] = None, - conditions: Union[Condition, Iterable[Condition]] = None, - parameters: Union[Parameter, Iterable[Parameter]] = None, + template: ProcessTemplate | LinkByUID | None = None, + conditions: Condition | Iterable[Condition] = None, + parameters: Parameter | Iterable[Parameter] = None, uids: Mapping[str, str] = None, tags: Iterable[str] = None, notes: str = None, - file_links: Optional[Union[Iterable[FileLink], FileLink]] = None, + file_links: Iterable[FileLink] | FileLink | None = None, ): from gemd.entity.link_by_uid import LinkByUID from gemd.entity.object.ingredient_spec import IngredientSpec @@ -84,12 +85,12 @@ def __init__( self._ingredients = validate_list(None, [IngredientSpec, LinkByUID]) @staticmethod - def _template_type() -> Type: + def _template_type() -> type: """Communicate expected template type to parent class.""" return ProcessTemplate @property - def ingredients(self) -> List[IngredientSpecType]: + def ingredients(self) -> list[IngredientSpecType]: """Ingredient specs that act as inputs to this process spec. The link is established by creating each ingredient spec and setting its @@ -99,7 +100,7 @@ def ingredients(self) -> List[IngredientSpecType]: return self._ingredients @property - def output_material(self) -> Optional[MaterialSpecType]: + def output_material(self) -> MaterialSpecType | None: """The material spec that this process spec produces. The link is established by creating the material spec and settings its @@ -108,7 +109,7 @@ def output_material(self) -> Optional[MaterialSpecType]: """ return self._output_material - def _dict_for_compare(self) -> Dict[str, Any]: + def _dict_for_compare(self) -> dict[str, Any]: """Support for recursive equals.""" base = super()._dict_for_compare() base["ingredients"] = self.ingredients diff --git a/gemd/entity/setters.py b/gemd/entity/setters.py index bac6515..f3a4624 100644 --- a/gemd/entity/setters.py +++ b/gemd/entity/setters.py @@ -1,6 +1,7 @@ """Methods for setting and validating.""" -from typing import Callable, Iterable, Optional, Type, TypeVar, Union +from collections.abc import Callable, Iterable +from typing import TypeVar from gemd.entity.valid_list import ValidList @@ -10,10 +11,10 @@ def validate_list( - obj: Optional[Union[Iterable[T], T]], - typ: Union[Iterable[Type], Type], + obj: Iterable[T] | T | None, + typ: Iterable[type] | type, *, - trigger: Callable[[T], Optional[T]] = None, + trigger: Callable[[T], T | None] = None, ) -> ValidList: """Attempts to return obj as a list, each element of which has type typ. diff --git a/gemd/entity/template/base_template.py b/gemd/entity/template/base_template.py index 0dbab71..5850919 100644 --- a/gemd/entity/template/base_template.py +++ b/gemd/entity/template/base_template.py @@ -1,6 +1,6 @@ """Base template.""" -from typing import Iterable, List, Mapping, Optional, Tuple, Union +from collections.abc import Iterable, Mapping from gemd.entity.base_entity import BaseEntity from gemd.entity.bounds.base_bounds import BaseBounds @@ -8,10 +8,10 @@ from gemd.entity.template.attribute_template import AttributeTemplate __all__ = ["BaseTemplate"] -_AttributeTemplateType = Union[AttributeTemplate, LinkByUID] -_AttributePairType = Tuple[_AttributeTemplateType, Optional[BaseBounds]] -_AttributeListPairType = List[Optional[Union[_AttributeTemplateType, BaseBounds]]] -_AttributeInputType = Union[_AttributeTemplateType, _AttributePairType, _AttributeListPairType] +_AttributeTemplateType = AttributeTemplate | LinkByUID +_AttributePairType = tuple[_AttributeTemplateType, BaseBounds | None] +_AttributeListPairType = list[_AttributeTemplateType | BaseBounds | None] +_AttributeInputType = _AttributeTemplateType | _AttributePairType | _AttributeListPairType class BaseTemplate(BaseEntity): diff --git a/gemd/entity/template/has_condition_templates.py b/gemd/entity/template/has_condition_templates.py index 337a1c4..89b026c 100644 --- a/gemd/entity/template/has_condition_templates.py +++ b/gemd/entity/template/has_condition_templates.py @@ -1,6 +1,7 @@ """For entities that have a condition template.""" -from typing import Iterable, List, Optional, Set, Tuple, TypeVar, Union +from collections.abc import Iterable +from typing import TypeVar from gemd.entity.bounds.base_bounds import BaseBounds from gemd.entity.has_dependencies import HasDependencies @@ -12,10 +13,10 @@ __all__ = ["HasConditionTemplates"] BaseEntityType = TypeVar("BaseEntityType", bound="BaseEntity") # noqa: F821 ConditionType = TypeVar("ConditionType", bound="Condition") # noqa: F821 -_ConditionTemplateType = Union[ConditionTemplate, LinkByUID] -_ConditionPairType = Tuple[_ConditionTemplateType, Optional[BaseBounds]] -_ConditionListPairType = List[Optional[Union[_ConditionTemplateType, BaseBounds]]] -_ConditionInputType = Union[_ConditionTemplateType, _ConditionPairType, _ConditionListPairType] +_ConditionTemplateType = ConditionTemplate | LinkByUID +_ConditionPairType = tuple[_ConditionTemplateType, BaseBounds | None] +_ConditionListPairType = list[_ConditionTemplateType | BaseBounds | None] +_ConditionInputType = _ConditionTemplateType | _ConditionPairType | _ConditionListPairType class HasConditionTemplates(HasDependencies): @@ -37,7 +38,7 @@ def __init__( self.conditions = conditions @property - def conditions(self) -> List[_ConditionPairType]: + def conditions(self) -> list[_ConditionPairType]: """Get the list of condition template/bounds tuples. Returns @@ -94,6 +95,6 @@ def validate_condition(self, condition: ConditionType) -> bool: else: return True # Nothing to check against - def _local_dependencies(self) -> Set[Union[BaseEntityType, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntityType | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {attr[0] for attr in self.conditions} diff --git a/gemd/entity/template/has_parameter_templates.py b/gemd/entity/template/has_parameter_templates.py index 1782468..3c35cb9 100644 --- a/gemd/entity/template/has_parameter_templates.py +++ b/gemd/entity/template/has_parameter_templates.py @@ -1,6 +1,7 @@ """For entities that have a parameter template.""" -from typing import Iterable, List, Optional, Set, Tuple, TypeVar, Union +from collections.abc import Iterable +from typing import TypeVar from gemd.entity.bounds.base_bounds import BaseBounds from gemd.entity.has_dependencies import HasDependencies @@ -12,10 +13,10 @@ __all__ = ["HasParameterTemplates"] ParameterType = TypeVar("ParameterType", bound="Parameter") # noqa: F821 BaseEntityType = TypeVar("BaseEntityType", bound="BaseEntity") # noqa: F821 -_ParameterTemplateType = Union[ParameterTemplate, LinkByUID] -_ParameterPairType = Tuple[_ParameterTemplateType, Optional[BaseBounds]] -_ParameterListPairType = List[Optional[Union[_ParameterTemplateType, BaseBounds]]] -_ParameterInputType = Union[_ParameterTemplateType, _ParameterPairType, _ParameterListPairType] +_ParameterTemplateType = ParameterTemplate | LinkByUID +_ParameterPairType = tuple[_ParameterTemplateType, BaseBounds | None] +_ParameterListPairType = list[_ParameterTemplateType | BaseBounds | None] +_ParameterInputType = _ParameterTemplateType | _ParameterPairType | _ParameterListPairType class HasParameterTemplates(HasDependencies): @@ -37,7 +38,7 @@ def __init__( self.parameters = parameters @property - def parameters(self) -> List[_ParameterPairType]: + def parameters(self) -> list[_ParameterPairType]: """Get the list of parameter template/bounds tuples. Returns @@ -94,6 +95,6 @@ def validate_parameter(self, parameter: ParameterType) -> bool: else: return True # Nothing to check against - def _local_dependencies(self) -> Set[Union[BaseEntityType, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntityType | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {attr[0] for attr in self.parameters} diff --git a/gemd/entity/template/has_property_templates.py b/gemd/entity/template/has_property_templates.py index a7224b5..429f5c9 100644 --- a/gemd/entity/template/has_property_templates.py +++ b/gemd/entity/template/has_property_templates.py @@ -1,6 +1,7 @@ """For entities that have a property template.""" -from typing import Iterable, List, Optional, Set, Tuple, TypeVar, Union +from collections.abc import Iterable +from typing import TypeVar from gemd.entity.bounds.base_bounds import BaseBounds from gemd.entity.has_dependencies import HasDependencies @@ -16,10 +17,10 @@ "PropertyAndConditionsType", bound="PropertyAndConditions", # noqa: F821 ) -_PropertyTemplateType = Union[PropertyTemplate, LinkByUID] -_PropertyPairType = Tuple[_PropertyTemplateType, Optional[BaseBounds]] -_PropertyListPairType = List[Optional[Union[_PropertyTemplateType, BaseBounds]]] -_PropertyInputType = Union[_PropertyTemplateType, _PropertyPairType, _PropertyListPairType] +_PropertyTemplateType = PropertyTemplate | LinkByUID +_PropertyPairType = tuple[_PropertyTemplateType, BaseBounds | None] +_PropertyListPairType = list[_PropertyTemplateType | BaseBounds | None] +_PropertyInputType = _PropertyTemplateType | _PropertyPairType | _PropertyListPairType class HasPropertyTemplates(HasDependencies): @@ -41,7 +42,7 @@ def __init__( self.properties = properties @property - def properties(self) -> List[_PropertyPairType]: + def properties(self) -> list[_PropertyPairType]: """Get the list of property template/bounds tuples. Returns @@ -75,7 +76,7 @@ def properties( trigger=BaseTemplate._homogenize_ranges, ) - def validate_property(self, prop: Union[PropertyType, PropertyAndConditionsType]) -> bool: + def validate_property(self, prop: PropertyType | PropertyAndConditionsType) -> bool: """Check if the property is consistent w/ this template.""" from gemd.entity.attribute import PropertyAndConditions @@ -94,6 +95,6 @@ def validate_property(self, prop: Union[PropertyType, PropertyAndConditionsType] else: return True # Nothing to check against - def _local_dependencies(self) -> Set[Union[BaseEntityType, LinkByUID]]: + def _local_dependencies(self) -> set[BaseEntityType | LinkByUID]: """Return a set of all immediate dependencies (no recursion).""" return {attr[0] for attr in self.properties} diff --git a/gemd/entity/util.py b/gemd/entity/util.py index a9ced92..e1fbe8d 100644 --- a/gemd/entity/util.py +++ b/gemd/entity/util.py @@ -1,6 +1,6 @@ """Utility methods.""" -from typing import Any, Dict, List +from typing import Any from gemd.util import recursive_foreach @@ -95,7 +95,7 @@ def array_like(): return _array_like -def complete_material_history(mat) -> List[Dict[str, Any]]: +def complete_material_history(mat) -> list[dict[str, Any]]: """Get a list of every single object in the material history, all as dictionaries. This is useful for testing, if we want the context list that can be used to rehydrate diff --git a/gemd/entity/valid_list.py b/gemd/entity/valid_list.py index cec3e8a..7b2cb16 100644 --- a/gemd/entity/valid_list.py +++ b/gemd/entity/valid_list.py @@ -1,6 +1,7 @@ """A list that can validate its contents.""" -from typing import Callable, Iterable, Optional, Type, TypeVar, Union +from collections.abc import Callable, Iterable +from typing import TypeVar __all__ = ["ValidList"] @@ -29,8 +30,8 @@ class ValidList(list): def __init__( self, _list: Iterable, - content_type: Optional[Union[Iterable[Type], Type]] = None, - trigger: Callable[[T], Optional[T]] = None, + content_type: Iterable[type] | type | None = None, + trigger: Callable[[T], T | None] = None, ): if content_type is None: content_type = tuple() diff --git a/gemd/entity/value/discrete_categorical.py b/gemd/entity/value/discrete_categorical.py index dce0a46..a223038 100644 --- a/gemd/entity/value/discrete_categorical.py +++ b/gemd/entity/value/discrete_categorical.py @@ -1,6 +1,6 @@ """Discrete distribution across several categories.""" -from typing import Mapping, Optional, Union +from collections.abc import Mapping from gemd.entity.bounds import CategoricalBounds from gemd.entity.setters import validate_str @@ -25,7 +25,7 @@ class DiscreteCategorical(CategoricalValue, typ="discrete_categorical"): """ - def __init__(self, probabilities: Union[str, Mapping[str, float]] = None): + def __init__(self, probabilities: str | Mapping[str, float] = None): self._probabilities = None self.probabilities = probabilities @@ -35,7 +35,7 @@ def probabilities(self) -> Mapping[str, float]: return self._probabilities @probabilities.setter - def probabilities(self, probabilities: Optional[Union[str, Mapping[str, float]]]): + def probabilities(self, probabilities: str | Mapping[str, float] | None): """Set the map from categories to probabilities.""" if probabilities is None: self._probabilities = None diff --git a/gemd/enumeration/base_enumeration.py b/gemd/enumeration/base_enumeration.py index 224bfd1..03282c6 100644 --- a/gemd/enumeration/base_enumeration.py +++ b/gemd/enumeration/base_enumeration.py @@ -1,7 +1,8 @@ """Base class for all enumerations.""" +from collections.abc import Callable from enum import Enum -from typing import Callable, Optional, Type +from typing import Optional from warnings import warn from deprecation import deprecated @@ -81,7 +82,7 @@ def _missing_(cls, value: object) -> Optional["BaseEnumeration"]: def migrated_enum( *, old_value: str, new_value: str, deprecated_in: str, removed_in: str -) -> Callable[[Type], Type]: +) -> Callable[[type], type]: """Decorator for registering an enumerated value as migrated to a new symbol. Parameters @@ -98,9 +99,7 @@ def migrated_enum( """ - def decorator(cls) -> Type: - print("Sear") - + def decorator(cls) -> type: class MixinMeta(type(cls)): """New derived metaclass for holding the deprecated symbol.""" diff --git a/gemd/json/gemd_json.py b/gemd/json/gemd_json.py index acbb01d..645e341 100644 --- a/gemd/json/gemd_json.py +++ b/gemd/json/gemd_json.py @@ -1,5 +1,5 @@ import json -from typing import Any, Dict, Type +from typing import Any from gemd.entity.base_entity import BaseEntity from gemd.entity.dict_serializable import DictSerializable @@ -10,7 +10,7 @@ __all__ = ["GEMDJson"] -class GEMDJson(object): +class GEMDJson: """Class that provides json load/dump functionality that is compatible with gemd objects. The serialization and deserialization strategy implemented by this class is described in @@ -205,9 +205,9 @@ def raw_loads(self, json_str, **kwargs): @staticmethod def _load_and_index( - d: Dict[str, Any], - object_index: Dict[str, DictSerializable], - clazz_index: Dict[str, Type], + d: dict[str, Any], + object_index: dict[str, DictSerializable], + clazz_index: dict[str, type], substitute: bool = False, ) -> DictSerializable: """Load the class based on the type string and index it, if a BaseEntity. diff --git a/gemd/units/impl.py b/gemd/units/impl.py index ce61de2..1054b8c 100644 --- a/gemd/units/impl.py +++ b/gemd/units/impl.py @@ -3,11 +3,12 @@ import functools import os import re +from collections.abc import Generator from importlib.resources import files from pathlib import Path from tempfile import TemporaryDirectory from tokenize import ERRORTOKEN, NAME, NUMBER, OP, TokenInfo -from typing import Any, Generator, List, Tuple, TypeAlias, Union +from typing import Any, TypeAlias from pint import UnitRegistry from pint.errors import DefinitionSyntaxError, UndefinedUnitError @@ -32,7 +33,7 @@ ] -def _deploy_default_files() -> Tuple[Path, Path]: +def _deploy_default_files() -> tuple[Path, Path]: """Copy the units & constants file into a temporary directory.""" resources = files("gemd.units") target_dir = Path(_TEMP_DIRECTORY.name) @@ -58,7 +59,7 @@ def _as_scientific(matchobj: re.Match) -> str: return re.sub(number, _as_scientific, input_string) -def _scaling_find_blocks(token_stream: Generator[TokenInfo, Any, None]) -> List[List[TokenInfo]]: +def _scaling_find_blocks(token_stream: Generator[TokenInfo, Any, None]) -> list[list[TokenInfo]]: """Supporting routine for _scaling_preprocessor; tokenizer stream -> blocks. Takes a stream of tokens, and breaks it into a lists of tokens that represent @@ -120,8 +121,8 @@ def _do_nothing(token_, exponent_context_, operator_stack_, result_): def _scaling_identify_factors( - input_string: str, blocks: List[List[TokenInfo]] -) -> List[Tuple[str, str, str]]: + input_string: str, blocks: list[list[TokenInfo]] +) -> list[tuple[str, str, str]]: """Supporting routine for _scaling_preprocessor; blocks -> scaling terms. Takes the input_string and the blocks output by _scaling_find_blocks and @@ -163,7 +164,7 @@ def _scaling_identify_factors( return todo -def _scaling_store_and_mangle(input_string: str, todo: List[Tuple[str, str, str]]) -> str: +def _scaling_store_and_mangle(input_string: str, todo: list[tuple[str, str, str]]) -> str: """Supporting routine for _scaling_preprocessor; scaling terms -> updated input_string. Takes the terms to be updated, and actually updates the input_string as well as @@ -290,8 +291,8 @@ def convert_units(value: float, starting_unit: str, final_unit: str) -> float: @functools.lru_cache(maxsize=1024) def parse_units( - units: Union[str, UnitRegistry.Unit, None], *, return_unit: bool = False -) -> Union[str, UnitRegistry.Unit, None]: + units: str | UnitRegistry.Unit | None, *, return_unit: bool = False +) -> str | UnitRegistry.Unit | None: """Parse a string or Unit into a standard string representation of the unit. Parameters @@ -326,7 +327,7 @@ def parse_units( @functools.lru_cache(maxsize=1024) -def get_base_units(units: Union[str, UnitRegistry.Unit]) -> Tuple[UnitRegistry.Unit, float, float]: +def get_base_units(units: str | UnitRegistry.Unit) -> tuple[UnitRegistry.Unit, float, float]: """Get the base units and conversion factors for the given unit. Parameters diff --git a/gemd/util/impl.py b/gemd/util/impl.py index 5f4a565..9fdffa2 100644 --- a/gemd/util/impl.py +++ b/gemd/util/impl.py @@ -2,18 +2,9 @@ import functools import uuid +from collections.abc import Callable, Iterable, Mapping, MutableSequence, Reversible from typing import ( Any, - Callable, - Iterable, - List, - Mapping, - MutableSequence, - Optional, - Reversible, - Tuple, - Type, - Union, ) from gemd.entity.base_entity import BaseEntity @@ -48,7 +39,7 @@ def func(base_obj): return -def cached_isinstance(obj: object, class_or_tuple: Union[Type, Tuple[Type]]) -> bool: +def cached_isinstance(obj: object, class_or_tuple: type | tuple[type]) -> bool: """Emulate isinstance builtin to take advantage of functools caching. Parameters @@ -69,7 +60,7 @@ def cached_isinstance(obj: object, class_or_tuple: Union[Type, Tuple[Type]]) -> @functools.lru_cache(maxsize=1024) -def _cached_issubclass(cls: Type, class_or_tuple: Union[Type, Tuple[Type]]) -> bool: +def _cached_issubclass(cls: type, class_or_tuple: type | tuple[type]) -> bool: """Emulate issubclass builtin to take advantage of functools caching. Parameters @@ -125,7 +116,7 @@ def _substitute( if cached_isinstance(replacement, MutableSequence): new = [_substitute(x, sub, applies, visited) for x in replacement] - elif cached_isinstance(replacement, Tuple): + elif cached_isinstance(replacement, tuple): new = tuple(_substitute(x, sub, applies, visited) for x in replacement) elif cached_isinstance(replacement, Mapping): new = { @@ -195,7 +186,7 @@ def _key(obj): if cached_isinstance(thing, MutableSequence): # Change list in place for i, x in enumerate(thing): thing[i] = _substitute_inplace(x, sub, applies, visited) - elif cached_isinstance(thing, Tuple): # Tuples are immutable; regenerate + elif cached_isinstance(thing, tuple): # Tuples are immutable; regenerate thing = tuple(_substitute_inplace(x, sub, applies, visited) for x in thing) visited[orig_key] = thing # We mutated it elif cached_isinstance(thing, Mapping): # Change dict in place, both keys & values @@ -257,7 +248,7 @@ def _emulator(inner_name: str) -> Callable: return setter -def make_index(obj: Union[Iterable, BaseEntity, DictSerializable]): +def make_index(obj: Iterable | BaseEntity | DictSerializable): """Generates an index that can be used for the substitute_objects method. This method builds a dictionary of GEMD objects found by recursively crawling the passed @@ -282,7 +273,7 @@ def _make_index(_obj: BaseEntity): def substitute_links( - obj: Any, scope: Optional[str] = None, *, allow_fallback: bool = True, inplace: bool = False + obj: Any, scope: str | None = None, *, allow_fallback: bool = True, inplace: bool = False ): """Recursively replace pointers to BaseEntity with LinkByUID objects. @@ -341,7 +332,7 @@ def substitute_objects(obj, index, *, inplace: bool = False): ) -def flatten(obj, scope=None) -> List[BaseEntity]: +def flatten(obj, scope=None) -> list[BaseEntity]: """Flatten a BaseEntity (or array of them) into objects connected by LinkByUID. This is a composite operation the amounts to: @@ -398,7 +389,7 @@ def _flatten(base_obj: BaseEntity): def recursive_foreach( - obj: Union[Iterable, DictSerializable], + obj: Iterable | DictSerializable, func: Callable[[BaseEntity], None], *, apply_first=False, @@ -456,11 +447,11 @@ def recursive_foreach( def recursive_flatmap( - obj: Union[Iterable, DictSerializable], + obj: Iterable | DictSerializable, func: Callable[[BaseEntity], Iterable], *, unidirectional=True, -) -> List: +) -> list: """Recursively apply and accumulate a list-valued function to BaseEntity members. Only :class:`BaseEntity` objects will have the function applied, but the recursion will walk @@ -516,7 +507,7 @@ def recursive_flatmap( return res -def writable_sort_order(key: Union[BaseEntity, str]) -> int: +def writable_sort_order(key: BaseEntity | str) -> int: """Sort order for flattening such that the objects can be read back and re-nested.""" from gemd.entity.object import ( IngredientRun, diff --git a/tests/builders/test_builders.py b/tests/builders/test_builders.py index 10a6b46..4fcdb9f 100644 --- a/tests/builders/test_builders.py +++ b/tests/builders/test_builders.py @@ -1,5 +1,3 @@ -from typing import Union - import pytest from gemd.builders import add_attribute, add_edge, add_measurement, make_attribute, make_node @@ -35,11 +33,11 @@ def contains(self, bounds): # pragma: no cover """Only here to satisfy abstract method.""" pass - def union(self, *others: Union["BaseBounds", "BaseValue"]) -> "BaseBounds": # pragma: no cover + def union(self, *others: BaseBounds | BaseValue) -> BaseBounds: # pragma: no cover """Only here to satisfy abstract method.""" pass - def update(self, *others: Union["BaseBounds", "BaseValue"]): # pragma: no cover + def update(self, *others: BaseBounds | BaseValue): # pragma: no cover """Only here to satisfy abstract method.""" pass diff --git a/tests/util/test_cached_isinstance.py b/tests/util/test_cached_isinstance.py index faaeeab..e384f24 100644 --- a/tests/util/test_cached_isinstance.py +++ b/tests/util/test_cached_isinstance.py @@ -1,4 +1,4 @@ -from typing import Iterable, List +from collections.abc import Iterable from gemd.util import cached_isinstance @@ -9,7 +9,7 @@ def test_cached_isinstance(): ("one", str), (1, int), ("one", (str, int)), - ([1, 2, 3], List), + ([1, 2, 3], list), ("one", Iterable), ] for obj, cls in passing_pairs: @@ -21,7 +21,7 @@ def test_cached_isinstance(): ("one", int), (1, str), ("one", (float, int)), - ("one", List), + ("one", list), (1, Iterable), ] for obj, cls in failing_pairs: From b7d92d10815e7b1583621cef05f2d53e25c57a7e Mon Sep 17 00:00:00 2001 From: Ken Kroenlein Date: Thu, 15 Oct 2026 08:23:58 -0600 Subject: [PATCH 3/7] Align CaseInsensitiveDict return types with dict Make CaseInsensitiveDict generic over its value type and add overloads to get and pop so each override returns the type dict declares. The key and default arguments of get and pop are now positional-only, as in dict. Ignore flake8 E704 because ruff format keeps overload stubs on one line. Co-Authored-By: Claude Opus 5.5 --- gemd/entity/case_insensitive_dict.py | 44 +++++++++++++++++++++------- tox.ini | 3 +- 2 files changed, 35 insertions(+), 12 deletions(-) diff --git a/gemd/entity/case_insensitive_dict.py b/gemd/entity/case_insensitive_dict.py index 5a919e7..e3e4f84 100644 --- a/gemd/entity/case_insensitive_dict.py +++ b/gemd/entity/case_insensitive_dict.py @@ -1,11 +1,15 @@ -from typing import Any, Mapping, Optional, Sequence, Tuple +from collections.abc import Mapping, Sequence +from typing import Any, TypeVar, overload __all__ = ["CaseInsensitiveDict"] -_RaiseKeyError = object() # singleton for no-default behavior +_VT = TypeVar("_VT") +_T = TypeVar("_T") +_RaiseKeyError: Any = object() # singleton for no-default behavior -class CaseInsensitiveDict(dict): + +class CaseInsensitiveDict(dict[str, _VT]): """A dictionary in which the keys are case-insensitive. It is initialized the same way as a typical dict, but the values can be accessed without @@ -29,10 +33,19 @@ def __init__(self, seq: Sequence = None, **kwargs) -> None: for key in self: self._register_key(key) - def __getitem__(self, key: str) -> Any: + def __getitem__(self, key: str) -> _VT: return super().__getitem__(self.lowercase_dict[key.lower()]) - def get(self, key: str, default: Any = None) -> Any: + @overload + def get(self, key: str, default: None = None, /) -> _VT | None: ... + + @overload + def get(self, key: str, default: _VT, /) -> _VT: ... + + @overload + def get(self, key: str, default: _T, /) -> _VT | _T: ... + + def get(self, key: str, default: Any = None, /) -> Any: """Get the value for a given case-insensitive key. Parameters @@ -55,7 +68,7 @@ def get(self, key: str, default: Any = None) -> Any: else: return default - def __setitem__(self, key: str, value: Any) -> None: + def __setitem__(self, key: str, value: _VT) -> None: self._register_key(key) super().__setitem__(key, value) @@ -72,7 +85,16 @@ def clear(self) -> None: super().clear() self.lowercase_dict.clear() - def pop(self, key: str, default=_RaiseKeyError) -> Any: + @overload + def pop(self, key: str, /) -> _VT: ... + + @overload + def pop(self, key: str, default: _VT, /) -> _VT: ... + + @overload + def pop(self, key: str, default: _T, /) -> _VT | _T: ... + + def pop(self, key: str, default: Any = _RaiseKeyError, /) -> Any: """Remove and return the value for a given key from the dictionary. If key is in the dictionary, remove it and return its value, else return default. @@ -103,7 +125,7 @@ def pop(self, key: str, default=_RaiseKeyError) -> Any: del self.lowercase_dict[key.lower()] return val - def popitem(self) -> Tuple: + def popitem(self) -> tuple[str, _VT]: """Remove and return a (key, value) pair from the dictionary. popitem() is useful to destructively iterate over a dictionary, as often used @@ -115,7 +137,7 @@ def popitem(self) -> Tuple: Returns ------- - Tuple(str, Any) + tuple[str, Any] The key-value pair """ @@ -123,7 +145,7 @@ def popitem(self) -> Tuple: del self.lowercase_dict[result[0].lower()] return result - def copy(self) -> "CaseInsensitiveDict": + def copy(self) -> "CaseInsensitiveDict[_VT]": """Return a shallow copy of the dictionary. Returns @@ -134,7 +156,7 @@ def copy(self) -> "CaseInsensitiveDict": """ return CaseInsensitiveDict(super().copy()) - def update(self, mapping: Optional[Mapping[str, Any]] = None, **kwargs) -> None: + def update(self, mapping: Mapping[str, Any] | None = None, **kwargs) -> None: """Update the dictionary with the key/value pairs from other, overwriting existing keys. update() accepts either another dictionary object or an iterable of diff --git a/tox.ini b/tox.ini index 881efa9..7e92e16 100644 --- a/tox.ini +++ b/tox.ini @@ -9,7 +9,8 @@ max-doc-length = 119 # D107: __init__ is self explanatory # D301: backslash is used in making docstrings for sphinx to parse # D401: Imperative mood requirement basically gets in the way -ignore = D100,D104,D105,D107,D301,D401 +# E704: ruff format keeps overload stubs on one line +ignore = D100,D104,D105,D107,D301,D401,E704 [run] omit = gemd/demo/* \ No newline at end of file From 94dfc41d14a87c661a2a5a0a4ede708bba829471 Mon Sep 17 00:00:00 2001 From: Ken Kroenlein Date: Thu, 15 Oct 2026 08:23:58 -0600 Subject: [PATCH 4/7] Use pathlib in file-based tests Read and write test files with Path.read_text and Path.write_text, and replace the legacy tmpdir fixture with tmp_path. Replace the demo test that wrote a temp file with a StringIO round trip in test_json, which covers gemd.json.dump and load directly. Co-Authored-By: Claude Opus 5.5 --- tests/demo/test_material_run_example.py | 28 +++------------------- tests/demo/test_measurement_run_example.py | 10 ++++---- tests/demo/test_table_example.py | 8 +++---- tests/json/test_json.py | 11 +++++++++ tests/units/test_parser.py | 6 ++--- 5 files changed, 24 insertions(+), 39 deletions(-) diff --git a/tests/demo/test_material_run_example.py b/tests/demo/test_material_run_example.py index 7d783d5..bc9ca68 100644 --- a/tests/demo/test_material_run_example.py +++ b/tests/demo/test_material_run_example.py @@ -1,9 +1,7 @@ """Test the ingestion of a material run.""" -import tempfile - from gemd.demo.material_run_example import ingest_material_run -from gemd.json import dump, load +from gemd.json import dumps, loads # Example data (that could have been loaded from a json file) example = { @@ -49,30 +47,10 @@ def test_example(tmp_path): assert len(result.measurements) == len(example["experiments"]) # write to a file (for human inspection) - with open(filename, "w") as f: - dump(result, f, indent=2) + filename.write_text(dumps(result, indent=2)) # read it back - with open(filename, "r") as f: - copy = load(f) + copy = loads(filename.read_text()) # very cursory check that we get out what we'd expect assert next(iter(copy.uids.values())) == example["sample_id"] - - -def test_example_with_temp(): - """Test the ingest of a material run via temp file and cleaning up.""" - # run the parsing to make sure no exceptions are thrown - result = ingest_material_run(example) - - # write/read with a temp file that is auto-deleted - with tempfile.TemporaryFile("w+") as fp: - # write to temp file - dump(result, fp, indent=2) - - # read it back - fp.seek(0) - copy = load(fp) - - # very cursory check that we get out what we'd expect - assert next(iter(copy.uids.values())) == example["sample_id"] diff --git a/tests/demo/test_measurement_run_example.py b/tests/demo/test_measurement_run_example.py index 70fba48..3c6bd8f 100644 --- a/tests/demo/test_measurement_run_example.py +++ b/tests/demo/test_measurement_run_example.py @@ -1,7 +1,7 @@ """Test measurement demo.""" from gemd.demo.measurement_example import make_demo_measurements -from gemd.json import dumps, load +from gemd.json import dumps, loads def test_measurement_example(tmp_path): @@ -9,11 +9,9 @@ def test_measurement_example(tmp_path): num_measurements = 4 results = make_demo_measurements(num_measurements, extra_tags={"demo"}) - with open(tmp_path / "flex_measurements.json", "w") as f: - f.write(dumps(results, indent=2)) - - with open(tmp_path / "flex_measurements.json", "r") as f: - copy = load(f) + filename = tmp_path / "flex_measurements.json" + filename.write_text(dumps(results, indent=2)) + copy = loads(filename.read_text()) assert len(copy) == len(results) assert all("demo" in x.tags for x in copy) diff --git a/tests/demo/test_table_example.py b/tests/demo/test_table_example.py index 67ec109..101db43 100644 --- a/tests/demo/test_table_example.py +++ b/tests/demo/test_table_example.py @@ -4,7 +4,7 @@ from gemd.demo.table_example import ingest_table from gemd.entity.object import MaterialRun -from gemd.json import dump, load +from gemd.json import dumps, loads data = [ {"vapor pressure": 2.0, "temperature": 300}, @@ -23,11 +23,9 @@ def test_table(tmp_path): filename = tmp_path / "table_example.json" # write to a file (for human inspection) - with open(filename, "w") as f: - dump(result, f, indent=2) + filename.write_text(dumps(result, indent=2)) # read it back - with open(filename, "r") as f: - copy = load(f) + copy = loads(filename.read_text()) assert isinstance(copy, MaterialRun) diff --git a/tests/json/test_json.py b/tests/json/test_json.py index 0a92199..92d088f 100644 --- a/tests/json/test_json.py +++ b/tests/json/test_json.py @@ -2,6 +2,7 @@ import json as json_builtin from copy import deepcopy +from io import StringIO from uuid import uuid4 import pytest @@ -77,6 +78,16 @@ def test_deserialize(): assert copy_meas.uids["auto"] == measurement.uids["auto"] +def test_file_round_trip(): + """Dumping to a file object and loading it back should leave the object unchanged.""" + condition = Condition(name="A condition", value=NominalReal(7, "")) + measurement = MeasurementRun("name", tags="A tag", conditions=condition) + buffer = StringIO() + gemd_json.dump(measurement, buffer, indent=2) + buffer.seek(0) + assert gemd_json.load(buffer) == measurement + + def test_uuid_serde(): """Any UUIDs in uids & LinkByUIDs shouldn't break stuff.""" process = ProcessSpec(name="A process", uids={"uuid": uuid4(), "word": "turnbuckle"}) diff --git a/tests/units/test_parser.py b/tests/units/test_parser.py index 2c0743b..aeaadfa 100644 --- a/tests/units/test_parser.py +++ b/tests/units/test_parser.py @@ -199,14 +199,14 @@ def _change_units(filename): change_definitions_file() -def test_file_change(tmpdir): +def test_file_change(tmp_path): """Test that swapping units files works.""" assert convert_units(1, "m", "cm") == 100 with pytest.raises(UndefinedUnitError): assert convert_units(1, "usd", "USD") == 1 - test_file = tmpdir / "test_units.txt" - test_file.write_binary(files("tests.units").joinpath("test_units.txt").read_bytes()) + test_file = tmp_path / "test_units.txt" + test_file.write_bytes(files("tests.units").joinpath("test_units.txt").read_bytes()) with _change_units(filename=test_file): with pytest.raises(UndefinedUnitError): assert convert_units(1, "m", "cm") == 100 From 98876b71c870cbd6cb0c7362502385183c1734de Mon Sep 17 00:00:00 2001 From: Ken Kroenlein Date: Thu, 15 Oct 2026 08:29:41 -0600 Subject: [PATCH 5/7] Manage the environment with uv and move CI to common-gh-actions v3 - Commit uv.lock and delete requirements.txt, test_requirements.txt, and doc_requirements.txt, which duplicated pyproject.toml - Move PR checks to repo-checks v3, which lints with ruff, verifies uv.lock, and checks the version bump only for PRs into main - Delete tox.ini and the flake8, flake8-docstrings, and derp dev dependencies, which the v3 checks replace - Delete scripts/run_tests.sh and scripts/validate_version_bump.py - Build docs for deployment with uv run, which puts sphinx-build on PATH; deploy-docs v3 runs make outside the uv environment - Update CONTRIBUTING.md for the uv workflow Co-Authored-By: Claude Opus 5.5 --- .github/workflows/deploy-docs.yml | 31 +- .github/workflows/pr-checks.yml | 3 +- CONTRIBUTING.md | 42 +- doc_requirements.txt | 3 - pyproject.toml | 6 +- requirements.txt | 2 - scripts/run_tests.sh | 44 - scripts/validate_version_bump.py | 62 -- test_requirements.txt | 7 - tox.ini | 16 - uv.lock | 1424 +++++++++++++++++++++++++++++ 11 files changed, 1473 insertions(+), 167 deletions(-) delete mode 100644 doc_requirements.txt delete mode 100644 requirements.txt delete mode 100755 scripts/run_tests.sh delete mode 100755 scripts/validate_version_bump.py delete mode 100644 test_requirements.txt delete mode 100644 tox.ini create mode 100644 uv.lock diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 9d167bd..517707b 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -10,6 +10,33 @@ permissions: pages: write id-token: write +# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. +# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete. +concurrency: + group: "pages" + cancel-in-progress: false + jobs: - deploy-docs: - uses: CitrineInformatics/common-gh-actions/.github/workflows/deploy-docs.yml@v1 + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Build Docs + # uv run puts the project environment, and so sphinx-build, on PATH for make + run: | + uv run --locked --group docs make -C docs/ html + touch docs/_build/html/.nojekyll + - name: Setup Pages + uses: actions/configure-pages@v5 + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + path: 'docs/_build/html' + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/pr-checks.yml b/.github/workflows/pr-checks.yml index 42dd901..6a2ec06 100644 --- a/.github/workflows/pr-checks.yml +++ b/.github/workflows/pr-checks.yml @@ -11,6 +11,7 @@ on: jobs: pr-checks: - uses: CitrineInformatics/common-gh-actions/.github/workflows/repo-checks.yml@v1 + uses: CitrineInformatics/common-gh-actions/.github/workflows/repo-checks.yml@v3 with: src: gemd + check_version_bump: ${{ github.base_ref == 'main' }} diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0d33f17..62e1582 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,10 +4,9 @@ Documentation is built using [Sphinx](https://www.sphinx-doc.org/en/master/) with the [autodoc](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#module-sphinx.ext.autodoc) -extension. In order to build the documentation, you can install the necessary packages and then use make: +extension. Build the documentation with [uv](https://docs.astral.sh/uv/): ```shell -pip install -r doc_requirements.txt -make make -C docs/ html +uv run --group docs make -C docs/ html ``` All documentation source files and configuration are in the `docs/source` directory. @@ -17,32 +16,25 @@ Additional reference material, such as tutorials, should be referenced in `index ## Testing Changes are gated on: - * Passing unit tests with minimum supported library versions + * Passing unit tests with the lowest supported versions of direct dependencies * 100% test coverage - * PEP8 style compliance, with some exceptions in the [tox file](tox.ini) - * Incrementing the package version number in [setup.py](setup.py) + * Passing `ruff check` and `ruff format --check`, configured in [pyproject.toml](pyproject.toml) + * Removing code whose deprecation has reached its `removed_in` version + * A [uv.lock](uv.lock) that matches [pyproject.toml](pyproject.toml) + * Incrementing the package version number in [gemd/\_\_version\_\_.py](gemd/__version__.py), for PRs into `main` -Additionally, PRs are checked against (but not blocked by): -* Passing unit tests with latest nominally supported versions of all dependencies -* Documentation builds without warnings +CI also runs the unit tests against the latest versions of all dependencies. Failures there do not block a PR. -In order to run tests locally, you'll need to install additional packages: +Run the same checks locally with uv: ```shell -pip install -r test_requirements.txt +uv run ruff check gemd tests +uv run ruff format --check gemd tests +uv run pytest --cov=gemd --cov-report term-missing:skip-covered --cov-fail-under=100 tests/ ``` -A test runner is available in `scripts/run_tests.sh`, which gives a convenient one-line invocation for testing. - -As it can be easy to forget to verify these prior to pushing, -it's possible to use [git hooks](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) -to enforce compliance during normal workflows. -Consider editing `.git/hooks/pre-commit` or `.git/hooks/pre-push` -(or adding them and marking them as executable: `chmod +x `). -For example, you could set your local `.git/hooks/pre-commit` to be -```shell -scripts/run_tests.sh --quiet --exitfirst -``` -to make sure you're not on the `main` branch, you've incremented the package version, you pass the linter and you have complete, passing tests. +To run these checks before every commit, add them to a +[git hook](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) such as `.git/hooks/pre-commit`, +and mark the hook executable with `chmod +x`. ## Coding Style This project follows [PEP8](https://www.python.org/dev/peps/pep-0008/), with the following exception: @@ -79,10 +71,10 @@ To create a release: * You can use `git diff` as well, if you prefer * In another tab, navigate to the [GitHub release creation page](https://github.com/CitrineInformatics/gemd-python/releases/new) * Set the `Target` to the commit you want to deploy, typically `main` - * Set the `Tag version` to `v{x.y.z}` where `x.y.z` is the version in [setup.py](setup.py), e.g. `v1.2.3` + * Set the `Tag version` to `v{x.y.z}` where `x.y.z` is the version in [gemd/\_\_version\_\_.py](gemd/__version__.py), e.g. `v1.2.3` * Set the `Release title` to "GEMD v{x.y.z} is released!" * Populate the release notes with a 1 or 2 sentence summary and `What's New`, `Improvements`, `Fixes`, and `Deprecated` sections, as appropriate -Travis will trigger the deploy due to the addition of the tag. +Publishing the release triggers GitHub Actions to deploy the package to PyPI and the documentation to GitHub Pages. Only commits on the **main** or backports branches can be released, but it need not be the most recent commit on the branch. The tests contained within this repository are sufficient to verify a release. diff --git a/doc_requirements.txt b/doc_requirements.txt deleted file mode 100644 index 0a0a47d..0000000 --- a/doc_requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -sphinx==5.0.0 -sphinx-rtd-theme==1.0.0 -sphinxcontrib-apidoc==0.3.0 diff --git a/pyproject.toml b/pyproject.toml index 99db244..3ca432c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,15 +44,12 @@ exclude = ["docs", "tests"] [dependency-groups] dev = [ "ruff==0.16.6", - "flake8==7.0.0", - "flake8-docstrings==1.7.0", "numpy>=2.0.2,<3; python_version<'3.14'", "numpy>=2.3.2,<3; python_version>='3.14'", # first release with 3.14 wheels "pandas>=2.3.0,<4; python_version<'3.14'", "pandas>=2.3.3,<4; python_version>='3.14'", # first release with 3.14 wheels "pytest==9.0.3", "pytest-cov==7.0.0", - "derp==0.1.1", "tomli>=2.2.1", ] docs = [ @@ -77,14 +74,13 @@ line-length = 99 target-version = "py310" [tool.ruff.lint] -# Mirror the flake8 configuration in tox.ini so both linters agree. preview = true explicit-preview-rules = true select = [ "E", # pycodestyle errors "W", # pycodestyle warnings "F", # pyflakes - "D", # pydocstyle (flake8-docstrings) + "D", # pydocstyle "I", # isort "E231", # missing whitespace after ',' (preview-only in ruff) "E275", # missing whitespace after keyword (preview-only in ruff) diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 23cfe0c..0000000 --- a/requirements.txt +++ /dev/null @@ -1,2 +0,0 @@ -pint==0.24.4 -deprecation==2.1.0 diff --git a/scripts/run_tests.sh b/scripts/run_tests.sh deleted file mode 100755 index b24d9ee..0000000 --- a/scripts/run_tests.sh +++ /dev/null @@ -1,44 +0,0 @@ -#!/usr/bin/env bash - -for i in "$@"; do - case $i in - -q|--quiet) - QUIET="--quiet --no-cov-on-fail " - shift # past argument=value - ;; - -x|--exitfirst) - EXITFIRST="--exitfirst " - shift # past argument=value - ;; - -*|--*) - echo "Unknown option $i" - exit 1 - ;; - *) - ;; - esac -done - -REPO_DIR=`git rev-parse --show-toplevel` - -# following https://docs.travis-ci.com/user/environment-variables/#convenience-variables -# the pull request isn't set to true if its a PR; its just set to false if its not. -if [ -z "$TRAVIS_PULL_REQUEST" ]; # Not Travis context -then - if [ "`git rev-parse --abbrev-ref HEAD`" == "main" ]; - then echo "On main branch"; exit 1; - else python $REPO_DIR/scripts/validate_version_bump.py || exit 1; - fi -# only run the validate-version_bump.py script on PR builds against main, -# since those have access to a "main" reference to git show the version -elif [ "$TRAVIS_PULL_REQUEST" != "false" ] && [ "$TRAVIS_BRANCH" == "main" ]; -then python $REPO_DIR/scripts/validate_version_bump.py || exit 1; -fi - -flake8 $REPO_DIR/gemd || exit 1; -derp $REPO_DIR/gemd $REPO_DIR/gemd/__version__.py || exit 1; -pytest $QUIET $EXITFIRST --cov=$REPO_DIR/gemd \ - --cov-report term-missing:skip-covered \ - --cov-config=$REPO_DIR/pyproject.toml \ - --no-cov-on-fail --cov-fail-under=100 \ - $REPO_DIR || exit 1; diff --git a/scripts/validate_version_bump.py b/scripts/validate_version_bump.py deleted file mode 100755 index d6ddc95..0000000 --- a/scripts/validate_version_bump.py +++ /dev/null @@ -1,62 +0,0 @@ -#!python -from os import getcwd, popen, system -from os.path import relpath -from packaging.version import Version -import re -import sys - - -def main(): - try: - repo_dir = popen("git rev-parse --show-toplevel", mode="r").read().rstrip() - version_path = relpath(f'{repo_dir}/gemd/__version__.py', getcwd()) - with open(version_path, "r") as fh: - new_version = extract_version(fh.read()) - except Exception as e: - raise ValueError(f"Couldn't extract version from working directory") from e - - try: - system("git fetch origin main") - with popen("git show origin/main:gemd/__version__.py", mode="r") as fh: - old_version = extract_version(fh.read()) - except Exception as e: - raise ValueError(f"Couldn't extract version from main branch") from e - - if new_version.major != old_version.major: - number = "major" - code = 1 - elif new_version.minor != old_version.minor: - number = "minor" - code = 2 - elif new_version.micro != old_version.micro: - number = "patch" - code = 3 - else: - number = "other component of" - code = 5 - - if new_version > old_version: - print(f"{number} version bump") - return 0 - elif new_version < old_version: - print(f"error - {number} version decreased! {new_version} < {old_version}") - return code - else: - print(f"error - version unchanged! {new_version} == {old_version}") - return 4 - - -def extract_version(text: str) -> Version: - version_re = r'''^\s*__version__\s*=\s*(['"])([\w\.]+)\1$''' - - if match := re.search(version_re, text, re.MULTILINE): - return Version(match.group(2)) - else: - raise ValueError(f"No version found\n{text}") - - -if __name__ == "__main__": - sys.tracebacklimit = 0 - result = main() - if result != 0: - sys.exit(result) diff --git a/test_requirements.txt 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Two of those builtin docstrings raise Sphinx warnings. Skip members implemented in C so the docs build cleanly with warnings as errors. Co-Authored-By: Claude Opus 5.5 --- docs/source/conf.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index 1a33d12..405db8a 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -11,6 +11,7 @@ # documentation root, use os.path.abspath to make it absolute, like shown here. # import gemd +import inspect import os import sys sys.path.insert(0, os.path.abspath('../../gemd')) @@ -89,3 +90,15 @@ 'sticky_navigation': False, 'logo_only': True } + + +def _skip_builtin_members(app, what, name, obj, skip, options): + """Skip members implemented in C, such as int.to_bytes inherited by IntEnum classes.""" + implemented_in_c = ( + inspect.isbuiltin(obj) or inspect.ismethoddescriptor(obj) or inspect.isgetsetdescriptor(obj) + ) + return True if implemented_in_c else None + + +def setup(app): + app.connect("autodoc-skip-member", _skip_builtin_members) From f8f740cbd1032db49ff685a67b80806d18213b51 Mon Sep 17 00:00:00 2001 From: Ken Kroenlein Date: Fri, 16 Oct 2026 09:26:37 -0600 Subject: [PATCH 7/7] Raise the numpy test floor to 2.1.0 below Python 3.14 numpy 2.0.2 publishes no Python 3.13 wheels. CI tests the lowest allowed versions, so the 3.13 lanes built numpy from source, and the build fails on the macOS runner. numpy 2.1.0 is the first release with 3.13 wheels. Co-Authored-By: Claude Opus 5.5 --- pyproject.toml | 2 +- uv.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 3ca432c..200e98e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,7 @@ exclude = ["docs", "tests"] [dependency-groups] dev = [ "ruff==0.16.6", - "numpy>=2.0.2,<3; python_version<'3.14'", + "numpy>=2.1.0,<3; python_version<'3.14'", # first release with 3.13 wheels "numpy>=2.3.2,<3; python_version>='3.14'", # first release with 3.14 wheels "pandas>=2.3.0,<4; python_version<'3.14'", "pandas>=2.3.3,<4; python_version>='3.14'", # first release with 3.14 wheels diff --git a/uv.lock b/uv.lock index f0b3ab2..1ea2d78 100644 --- a/uv.lock +++ b/uv.lock @@ -437,7 +437,7 @@ requires-dist = [ [package.metadata.requires-dev] dev = [ - { name = "numpy", marker = "python_full_version < '3.14'", specifier = ">=2.0.2,<3" }, + { name = "numpy", marker = "python_full_version < '3.14'", specifier = ">=2.1.0,<3" }, { name = "numpy", marker = "python_full_version >= '3.14'", specifier = ">=2.3.2,<3" }, { name = "pandas", marker = "python_full_version < '3.14'", specifier = ">=2.3.0,<4" }, { name = "pandas", marker = "python_full_version >= '3.14'", specifier = ">=2.3.3,<4" },