Release gemd 3.0.0; drop Python 3.9 support

.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

.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' }}

.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

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 <file>`). 
-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. 

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)

gemd/__version__.py

@@ -1 +1 @@
-__version__ = "2.4.0"
+__version__ = "3.0.0"

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

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

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)

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

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

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

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
@@ -26,15 +26,15 @@ 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
         self._conditions = None
         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