Run pyupgrade --py39-plus to upgrade legacy annotations

optimade/adapters/base.py

@@ -19,7 +19,7 @@
 and [`StructureResource`][optimade.models.structures.StructureResource]s, respectively.
 """
 import re
-from typing import Any, Callable, Dict, List, Optional, Tuple, Type, Union
+from typing import Any, Callable, Optional, Union
 
 from pydantic import BaseModel  # pylint: disable=no-name-in-module
 
@@ -42,18 +42,18 @@ class EntryAdapter:
 
     """
 
-    ENTRY_RESOURCE: Type[EntryResource] = EntryResource
-    _type_converters: Dict[str, Callable] = {}
-    _type_ingesters: Dict[str, Callable] = {}
-    _type_ingesters_by_type: Dict[str, Type] = {}
+    ENTRY_RESOURCE: type[EntryResource] = EntryResource
+    _type_converters: dict[str, Callable] = {}
+    _type_ingesters: dict[str, Callable] = {}
+    _type_ingesters_by_type: dict[str, type] = {}
 
     def __init__(self, entry: dict) -> None:
         """
         Parameters:
             entry (dict): A JSON OPTIMADE single resource entry.
         """
         self._entry: Optional[EntryResource] = None
-        self._converted: Dict[str, Any] = {}
+        self._converted: dict[str, Any] = {}
 
         self.entry: EntryResource = entry  # type: ignore[assignment]
 
@@ -164,7 +164,7 @@ def ingest_from(cls, data: Any, format: Optional[str] = None) -> Any:
 
     @staticmethod
     def _get_model_attributes(
-        starting_instances: Union[Tuple[BaseModel, ...], List[BaseModel]], name: str
+        starting_instances: Union[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/references/adapter.py

@@ -1,5 +1,3 @@
-from typing import Type
-
 from optimade.adapters.base import EntryAdapter
 from optimade.models import ReferenceResource
 
@@ -21,4 +19,4 @@ class Reference(EntryAdapter):
 
     """
 
-    ENTRY_RESOURCE: Type[ReferenceResource] = ReferenceResource
+    ENTRY_RESOURCE: type[ReferenceResource] = ReferenceResource

optimade/adapters/structures/adapter.py

@@ -1,4 +1,4 @@
-from typing import Callable, Dict, Type
+from typing import Callable
 
 from optimade.adapters.base import EntryAdapter
 from optimade.models import StructureResource
@@ -44,8 +44,8 @@ class Structure(EntryAdapter):
 
     """
 
-    ENTRY_RESOURCE: Type[StructureResource] = StructureResource
-    _type_converters: Dict[str, Callable] = {
+    ENTRY_RESOURCE: type[StructureResource] = StructureResource
+    _type_converters: dict[str, Callable] = {
         "aiida_structuredata": get_aiida_structure_data,
         "ase": get_ase_atoms,
         "cif": get_cif,
@@ -55,12 +55,12 @@ class Structure(EntryAdapter):
         "jarvis": get_jarvis_atoms,
     }
 
-    _type_ingesters: Dict[str, Callable] = {
+    _type_ingesters: dict[str, Callable] = {
         "pymatgen": from_pymatgen,
         "ase": from_ase_atoms,
     }
 
-    _type_ingesters_by_type: Dict[str, Type] = {
+    _type_ingesters_by_type: dict[str, type] = {
         "pymatgen": PymatgenStructure,
         "ase": ASEAtoms,
     }

optimade/adapters/structures/aiida.py

@@ -7,7 +7,7 @@
 
 This conversion function relies on the [`aiida-core`](https://github.com/aiidateam/aiida-core) package.
 """
-from typing import List, Optional
+from typing import Optional
 from warnings import warn
 
 from optimade.adapters.structures.utils import pad_cell, species_from_species_at_sites
@@ -48,7 +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: Optional[list[OptimadeStructureSpecies]] = attributes.species
     if not species:
         species = species_from_species_at_sites(attributes.species_at_sites)  # type: ignore[arg-type]
 

optimade/adapters/structures/ase.py

@@ -7,7 +7,6 @@
 
 For more information on the ASE code see [their documentation](https://wiki.fysik.dtu.dk/ase/).
 """
-from typing import Dict
 
 from optimade.adapters.exceptions import ConversionError
 from optimade.adapters.structures.utils import (
@@ -66,7 +65,7 @@ def get_ase_atoms(optimade_structure: OptimadeStructure) -> Atoms:
     if not species:
         species = species_from_species_at_sites(attributes.species_at_sites)  # type: ignore[arg-type]
 
-    optimade_species: Dict[str, OptimadeStructureSpecies] = {_.name: _ for _ in species}
+    optimade_species: dict[str, OptimadeStructureSpecies] = {_.name: _ for _ in species}
 
     # Since we've made sure there are no species with more than 1 chemical symbol,
     # asking for index 0 will always work.

optimade/adapters/structures/cif.py

@@ -16,7 +16,6 @@
 
 This conversion function relies on the [NumPy](https://numpy.org/) library.
 """
-from typing import Dict
 
 from optimade.adapters.structures.utils import (
     cell_to_cellpar,
@@ -123,11 +122,11 @@ def get_cif(  # pylint: disable=too-many-locals,too-many-branches
     else:
         sites = attributes.cartesian_site_positions
 
-    species: Dict[str, OptimadeStructureSpecies] = {
+    species: dict[str, OptimadeStructureSpecies] = {
         species.name: species for species in attributes.species  # type: ignore[union-attr]
     }
 
-    symbol_occurences: Dict[str, int] = {}
+    symbol_occurences: dict[str, int] = {}
     for site_number in range(attributes.nsites):  # type: ignore[arg-type]
         species_name = attributes.species_at_sites[site_number]  # type: ignore[index]
         site = sites[site_number]

optimade/adapters/structures/proteindatabank.py

@@ -21,7 +21,6 @@
 Warning:
     Currently, the PDBx/mmCIF conversion function is not parsing as a complete PDBx/mmCIF file.
 """
-from typing import Dict
 
 try:
     import numpy as np
@@ -164,7 +163,7 @@ def get_pdbx_mmcif(  # pylint: disable=too-many-locals
     else:
         sites = attributes.cartesian_site_positions
 
-    species: Dict[str, OptimadeStructureSpecies] = {
+    species: dict[str, OptimadeStructureSpecies] = {
         species.name: species for species in attributes.species  # type: ignore[union-attr]
     }
 
@@ -240,7 +239,7 @@ def get_pdb(  # pylint: disable=too-many-locals
 
     pdb += "MODEL     1\n"
 
-    species: Dict[str, OptimadeStructureSpecies] = {
+    species: dict[str, OptimadeStructureSpecies] = {
         species.name: species
         for species in attributes.species  # type:ignore[union-attr]
     }

optimade/adapters/structures/pymatgen.py

@@ -7,7 +7,7 @@
 
 For more information on the pymatgen code see [their documentation](https://pymatgen.org).
 """
-from typing import Dict, List, Optional, Union
+from typing import Optional, Union
 
 from optimade.adapters.structures.utils import (
     species_from_species_at_sites,
@@ -105,9 +105,9 @@ def _get_molecule(optimade_structure: OptimadeStructure) -> Molecule:
 
 def _pymatgen_species(
     nsites: int,
-    species: Optional[List[OptimadeStructureSpecies]],
-    species_at_sites: List[str],
-) -> List[Dict[str, float]]:
+    species: Optional[list[OptimadeStructureSpecies]],
+    species_at_sites: list[str],
+) -> list[dict[str, float]]:
     """
     Create list of {"symbol": "concentration"} per site for values to pymatgen species parameters.
     Remove vacancies, if they are present.

optimade/adapters/structures/utils.py

@@ -3,7 +3,8 @@
 
 Most of these functions rely on the [NumPy](https://numpy.org/) library.
 """
-from typing import Iterable, List, Optional, Tuple, Type
+from collections.abc import Iterable
+from typing import Optional
 
 from optimade.models.structures import Species as OptimadeStructureSpecies
 from optimade.models.structures import Vector3D
@@ -19,7 +20,7 @@
     NUMPY_NOT_FOUND = "NumPy not found, cannot convert structure to your desired format"
 
 
-def valid_lattice_vector(lattice_vec: Tuple[Vector3D, Vector3D, Vector3D]):
+def valid_lattice_vector(lattice_vec: tuple[Vector3D, Vector3D, Vector3D]):
     if len(lattice_vec) != 3:
         return False
     for vector in lattice_vec:
@@ -31,8 +32,8 @@ def valid_lattice_vector(lattice_vec: Tuple[Vector3D, Vector3D, Vector3D]):
 
 
 def scaled_cell(
-    cell: Tuple[Vector3D, Vector3D, Vector3D]
-) -> Tuple[Vector3D, Vector3D, Vector3D]:
+    cell: tuple[Vector3D, Vector3D, Vector3D]
+) -> tuple[Vector3D, Vector3D, Vector3D]:
     """Return a scaled 3x3 cell from cartesian 3x3 cell (`lattice_vectors`).
     This 3x3 matrix can be used to calculate the fractional coordinates from the cartesian_site_positions.
 
@@ -62,8 +63,8 @@ def scaled_cell(
 
 
 def fractional_coordinates(
-    cell: Tuple[Vector3D, Vector3D, Vector3D], cartesian_positions: List[Vector3D]
-) -> List[Vector3D]:
+    cell: tuple[Vector3D, Vector3D, Vector3D], cartesian_positions: list[Vector3D]
+) -> list[Vector3D]:
     """Returns fractional coordinates and wraps coordinates to `[0,1[`.
 
     Note:
@@ -101,8 +102,8 @@ def fractional_coordinates(
 
 
 def cell_to_cellpar(
-    cell: Tuple[Vector3D, Vector3D, Vector3D], radians: bool = False
-) -> List[float]:
+    cell: tuple[Vector3D, Vector3D, Vector3D], radians: bool = False
+) -> list[float]:
     """Returns the cell parameters `[a, b, c, alpha, beta, gamma]`.
 
     Angles are in degrees unless `radian=True` is used.
@@ -161,10 +162,10 @@ 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,
-) -> List[Vector3D]:
+    cellpar: list[float],
+    ab_normal: tuple[int, int, int] = (0, 0, 1),
+    a_direction: Optional[tuple[int, int, int]] = None,
+) -> list[Vector3D]:
     """Return a 3x3 cell matrix from `cellpar=[a,b,c,alpha,beta,gamma]`.
 
     Angles must be in degrees.
@@ -277,9 +278,9 @@ def cellpar_to_cell(
 def _pad_iter_of_iters(
     iterable: Iterable[Iterable],
     padding: Optional[float] = None,
-    outer: Optional[Type] = None,
-    inner: Optional[Type] = None,
-) -> Tuple[Iterable[Iterable], bool]:
+    outer: Optional[type] = None,
+    inner: Optional[type] = None,
+) -> tuple[Iterable[Iterable], bool]:
     """Turn any null/None values into a float in given iterable of iterables"""
     try:
         padding = float(padding)  # type: ignore[arg-type]
@@ -306,7 +307,7 @@ def _pad_iter_of_iters(
 
 
 def pad_cell(
-    lattice_vectors: Tuple[Vector3D, Vector3D, Vector3D],
+    lattice_vectors: tuple[Vector3D, Vector3D, Vector3D],
     padding: Optional[float] = None,
 ) -> tuple:  # Setting this properly makes MkDocs fail.
     """Turn any `null`/`None` values into a `float` in given `tuple` of
@@ -333,8 +334,8 @@ def pad_cell(
 
 
 def species_from_species_at_sites(
-    species_at_sites: List[str],
-) -> List[OptimadeStructureSpecies]:
+    species_at_sites: list[str],
+) -> list[OptimadeStructureSpecies]:
     """When a list of species dictionaries is not provided, this function
     can be used to infer the species from the provided species_at_sites.
 
@@ -357,7 +358,7 @@ def species_from_species_at_sites(
     ]
 
 
-def elements_ratios_from_species_at_sites(species_at_sites: List[str]) -> List[float]:
+def elements_ratios_from_species_at_sites(species_at_sites: list[str]) -> list[float]:
     """Compute the OPTIMADE `elements_ratios` field from `species_at_sites` in the case where `species_at_sites` refers
     to sites wholly occupied by the given elements, e.g., not arbitrary species labels or with partial/mixed occupancy.
 

optimade/client/cli.py

@@ -166,13 +166,13 @@ def _get(
         base_urls=base_url,
         use_async=use_async,
         max_results_per_provider=max_results_per_provider,
-        include_providers=set(_.strip() for _ in include_providers.split(","))
+        include_providers={_.strip() for _ in include_providers.split(",")}
         if include_providers
         else None,
-        exclude_providers=set(_.strip() for _ in exclude_providers.split(","))
+        exclude_providers={_.strip() for _ in exclude_providers.split(",")}
         if exclude_providers
         else None,
-        exclude_databases=set(_.strip() for _ in exclude_databases.split(","))
+        exclude_databases={_.strip() for _ in exclude_databases.split(",")}
         if exclude_databases
         else None,
         silent=silent,
@@ -211,13 +211,15 @@ def _get(
 
     if not output_file:
         if pretty_print:
-            rich.print_json(data=results, indent=2, default=lambda _: _.dict())
+            rich.print_json(data=results, indent=2, default=lambda _: _.asdict())
         else:
-            sys.stdout.write(json.dumps(results, indent=2, default=lambda _: _.dict()))
+            sys.stdout.write(
+                json.dumps(results, indent=2, default=lambda _: _.asdict())
+            )
 
     if output_file:
         with open(output_file, "w") as f:
-            json.dump(results, f, indent=2, default=lambda _: _.dict())
+            json.dump(results, f, indent=2, default=lambda _: _.asdict())
 
 
 if __name__ == "__main__":