Modernize all Python 3.8 annotations (#1815)

* Use Python 3.9 as the 'base' CI version for linting

* Update pre-commit hooks

* Run `pyupgrade --py39-plus` to upgrade legacy annotations

* Add `--exit-non-zero-on-fix` for ruff

Co-authored-by: Casper Welzel Andersen <43357585+CasperWA@users.noreply.github.com>

* Use f-string over format

Co-authored-by: Casper Welzel Andersen <43357585+CasperWA@users.noreply.github.com>

---------

Co-authored-by: Casper Welzel Andersen <43357585+CasperWA@users.noreply.github.com>

.github/workflows/ci.yml

@@ -26,10 +26,10 @@ jobs:
       with:
         submodules: true
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.9'
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt
@@ -56,10 +56,10 @@ jobs:
       with:
         submodules: true
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.9'
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt
@@ -227,27 +227,27 @@ jobs:
       run: pytest -rs -vvv --cov=./optimade/ --cov-report=xml --cov-append tests/adapters/
 
     - name: Run tests for validator only to assess coverage (mongomock)
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.9
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongomock'
 
     - name: Run tests for validator only to assess coverage (Elasticsearch)
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.9
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'elastic'
         OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data
 
     - name: Run tests for validator only to assess coverage (MongoDB)
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.9
       run: pytest -rs --cov=./optimade/ --cov-report=xml:validator_cov.xml --cov-append tests/server/test_server_validation.py
       env:
         OPTIMADE_DATABASE_BACKEND: 'mongodb'
         OPTIMADE_INSERT_TEST_DATA: false # Must be specified as previous steps will have already inserted the test data
 
     - name: Run the OPTIMADE Client CLI
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.9
       run: |
         coverage run --append --source optimade optimade/client/cli.py \
            --filter 'nsites = 1' \
@@ -275,15 +275,15 @@ jobs:
         coverage xml
 
     - name: Upload coverage to Codecov
-      if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
+      if: matrix.python-version == '3.9' && github.repository == 'Materials-Consortia/optimade-python-tools'
       uses: codecov/codecov-action@v3
       with:
         name: project
         file: ./coverage.xml
         flags: project
 
     - name: Upload validator coverage to Codecov
-      if: matrix.python-version == '3.10' && github.repository == 'Materials-Consortia/optimade-python-tools'
+      if: matrix.python-version == '3.9' && github.repository == 'Materials-Consortia/optimade-python-tools'
       uses: codecov/codecov-action@v3
       with:
         name: validator
@@ -300,7 +300,7 @@ jobs:
 
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.9'
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt
@@ -330,10 +330,10 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v4
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.9'
         cache: 'pip'
         cache-dependency-path: |
           requirements*.txt

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3.10
+  python: python3.9
 
 repos:
   - repo: https://github.com/ambv/black
@@ -9,7 +9,7 @@ repos:
       name: Blacken
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-symlinks
     - id: check-yaml
@@ -23,11 +23,17 @@ repos:
     - id: trailing-whitespace
       args: [--markdown-linebreak-ext=md]
 
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    - id: pyupgrade
+      args: ["--py39-plus"]
+
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.291'
+    rev: 'v0.0.292'
     hooks:
     - id: ruff
-      args: [--fix]
+      args: [--fix, --exit-non-zero-on-fix]
 
   - repo: local
     hooks:
@@ -46,7 +52,7 @@ repos:
       description: Update the API Reference documentation whenever a Python file is touched in the code base.
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.6.0
     hooks:
       - id: mypy
         name: "MyPy"

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.