Remove support for Python 3.9

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ on:
 
 env:
   PYTEST_ADDOPTS: "--color=yes"
-  LINTING_PY_VERSION: "3.9"  # The version of Python to use for linting (typically the minimum supported)
+  LINTING_PY_VERSION: "3.10"  # The version of Python to use for linting (typically the minimum supported)
 
 # Cancel running workflows when additional changes are pushed
 # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-using-a-fallback-value
@@ -126,7 +126,7 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
 
     services:
       mongo:
@@ -177,25 +177,25 @@ jobs:
         pip install -e .
 
     - name: Run non-server tests
-      run: pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml tests/ --ignore tests/server
+      run: pytest -rs -vvv --durations=10 --cov=./optimade/ --cov-report=xml tests/ --ignore tests/server
 
     - name: Install latest server dependencies
       run: pip install -r requirements-server.txt
 
     - name: Run server tests (using `mongomock`)
-      run: pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
+      run: pytest -rs -vvv --durations=10 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
 
     - name: Run server tests with no API validation (using `mongomock`)
       run:
-        pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
+        pytest -rs -vvv --durations=10 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
         OPTIMADE_VALIDATE_API_RESPONSE: false
 
     - name: Run server tests (using a real MongoDB)
-      run: pytest -rs -vvv --durations=0 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
+      run: pytest -rs -vvv --durations=10 --cov=./optimade/ --cov-report=xml --cov-append tests/server tests/filtertransformers
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongodb'
 

.github/workflows/ci_cd_updated_main.yml

@@ -42,11 +42,11 @@ jobs:
         fetch-depth: 0
         submodules: true
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       if: steps.release_check.outputs.release_run == 'false'
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.10'
 
     - name: Install dependencies
       if: steps.release_check.outputs.release_run == 'false'

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
     submodules: true
 
 default_language_version:
-  python: python3.9
+  python: python3.10
 
 # pre-commit hooks
 repos:
@@ -32,7 +32,7 @@ repos:
     rev: v3.17.0
     hooks:
     - id: pyupgrade
-      args: ["--py39-plus"]
+      args: [--py310-plus]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: 'v0.6.3'

optimade/adapters/base.py

@@ -20,8 +20,9 @@
 """
 
 import re
+from collections.abc import Callable
 from json import JSONDecodeError
-from typing import Any, Callable, Optional, Union
+from typing import Any
 
 from pydantic import BaseModel
 
@@ -106,7 +107,7 @@ def convert(self, format: str) -> Any:
         return self._converted[format]
 
     @classmethod
-    def ingest_from(cls, data: Any, format: Optional[str] = None) -> Any:
+    def ingest_from(cls, data: Any, format: str | None = None) -> Any:
         """Convert desired format to OPTIMADE format.
 
         Parameters:
@@ -182,7 +183,7 @@ def from_url(cls, url: str) -> Any:
 
     @staticmethod
     def _get_model_attributes(
-        starting_instances: Union[tuple[BaseModel, ...], list[BaseModel]], name: str
+        starting_instances: tuple[BaseModel, ...] | list[BaseModel], name: str
     ) -> Any:
         """Helper method for retrieving the OPTIMADE model's attribute, supporting "."-nested attributes"""
         for res in starting_instances:

optimade/adapters/structures/adapter.py

@@ -1,4 +1,4 @@
-from typing import Callable
+from collections.abc import Callable
 
 from optimade.adapters.base import EntryAdapter
 from optimade.models import StructureResource

optimade/adapters/structures/aiida.py

@@ -8,7 +8,6 @@
 This conversion function relies on the [`aiida-core`](https://github.com/aiidateam/aiida-core) package.
 """
 
-from typing import Optional
 from warnings import warn
 
 from optimade.adapters.structures.utils import pad_cell, species_from_species_at_sites
@@ -49,7 +48,7 @@ def get_aiida_structure_data(optimade_structure: OptimadeStructure) -> Structure
     structure = StructureData(cell=lattice_vectors)
 
     # If species not provided, infer data from species_at_sites
-    species: Optional[list[OptimadeStructureSpecies]] = attributes.species
+    species: list[OptimadeStructureSpecies] | None = attributes.species
     if not species:
         species = species_from_species_at_sites(attributes.species_at_sites)  # type: ignore[arg-type]
 

optimade/adapters/structures/pymatgen.py

@@ -8,7 +8,6 @@
 For more information on the pymatgen code see [their documentation](https://pymatgen.org).
 """
 
-from typing import Optional, Union
 from warnings import warn
 
 from optimade.adapters.structures.utils import (
@@ -39,7 +38,7 @@
 )
 
 
-def get_pymatgen(optimade_structure: OptimadeStructure) -> Union[Structure, Molecule]:
+def get_pymatgen(optimade_structure: OptimadeStructure) -> Structure | Molecule:
     """Get pymatgen `Structure` or `Molecule` from OPTIMADE structure.
 
     This function will return either a pymatgen `Structure` or `Molecule` based
@@ -109,7 +108,7 @@ def _get_molecule(optimade_structure: OptimadeStructure) -> Molecule:
 
 def _pymatgen_species(
     nsites: int,
-    species: Optional[list[OptimadeStructureSpecies]],
+    species: list[OptimadeStructureSpecies] | None,
     species_at_sites: list[str],
 ) -> list[dict[str, float]]:
     """

optimade/adapters/structures/utils.py

@@ -5,7 +5,6 @@
 """
 
 from collections.abc import Iterable
-from typing import Optional
 
 from optimade.models.structures import Species as OptimadeStructureSpecies
 from optimade.models.structures import Vector3D
@@ -165,7 +164,7 @@ def unit_vector(x: Vector3D) -> Vector3D:
 def cellpar_to_cell(
     cellpar: list[float],
     ab_normal: tuple[int, int, int] = (0, 0, 1),
-    a_direction: Optional[tuple[int, int, int]] = None,
+    a_direction: tuple[int, int, int] | None = None,
 ) -> list[Vector3D]:
     """Return a 3x3 cell matrix from `cellpar=[a,b,c,alpha,beta,gamma]`.
 
@@ -278,9 +277,9 @@ def cellpar_to_cell(
 
 def _pad_iter_of_iters(
     iterable: Iterable[Iterable],
-    padding: Optional[float] = None,
-    outer: Optional[type] = None,
-    inner: Optional[type] = None,
+    padding: float | None = None,
+    outer: type | None = None,
+    inner: type | None = None,
 ) -> tuple[Iterable[Iterable], bool]:
     """Turn any null/None values into a float in given iterable of iterables"""
     try:
@@ -309,7 +308,7 @@ def _pad_iter_of_iters(
 
 def pad_cell(
     lattice_vectors: tuple[Vector3D, Vector3D, Vector3D],
-    padding: Optional[float] = None,
+    padding: float | None = None,
 ) -> tuple:  # Setting this properly makes MkDocs fail.
     """Turn any `null`/`None` values into a `float` in given `tuple` of
     [`lattice_vectors`][optimade.models.structures.StructureResourceAttributes.lattice_vectors].