Many more type hint tweaks and ignores

optimade/adapters/__init__.py

@@ -3,4 +3,4 @@
 from .references import *  # noqa: F403
 from .structures import *  # noqa: F403
 
-__all__ = exceptions.__all__ + references.__all__ + structures.__all__  # noqa: F405
+__all__ = exceptions.__all__ + references.__all__ + structures.__all__  # type: ignore[name-defined]  # noqa: F405

optimade/adapters/base.py

@@ -19,12 +19,12 @@
 and [`StructureResource`][optimade.models.structures.StructureResource]s, respectively.
 """
 import re
-from typing import Any, Callable, Dict, List, Tuple, Type, Union
+from typing import Any, Callable, Dict, List, Optional, Tuple, Type, Union
 
 from pydantic import BaseModel  # pylint: disable=no-name-in-module
 
 from optimade.adapters.logger import LOGGER
-from optimade.models import EntryResource
+from optimade.models.entries import EntryResource
 
 
 class EntryAdapter:
@@ -48,15 +48,17 @@ def __init__(self, entry: dict) -> None:
         Parameters:
             entry (dict): A JSON OPTIMADE single resource entry.
         """
-        self._entry = None
-        self._converted = {}
+        self._entry: Optional[EntryResource] = None
+        self._converted: Dict[str, Any] = {}
 
-        self.entry = entry
+        self.entry: EntryResource = entry  # type: ignore[assignment]
 
         # Note that these return also the default values for otherwise non-provided properties.
         self._common_converters = {
-            "json": self.entry.json,  # Return JSON serialized string, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeljson
-            "dict": self.entry.dict,  # Return Python dict, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeldict
+            # Return JSON serialized string, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeljson
+            "json": self.entry.json,  # type: ignore[attr-defined]
+            # Return Python dict, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeldict
+            "dict": self.entry.dict,  # type: ignore[attr-defined]
         }
 
     @property
@@ -67,7 +69,7 @@ def entry(self) -> EntryResource:
             The entry resource.
 
         """
-        return self._entry
+        return self._entry  # type: ignore[return-value]
 
     @entry.setter
     def entry(self, value: dict) -> None:
@@ -171,12 +173,12 @@ def __getattr__(self, name: str) -> Any:
             return res
 
         # Non-valid attribute
-        entry_resource_name = re.match(
+        _entry_resource_name = re.match(
             r"(<class ')([a-zA-Z_]+\.)*([a-zA-Z_]+)('>)", str(self.ENTRY_RESOURCE)
         )
         entry_resource_name = (
-            entry_resource_name.group(3)
-            if entry_resource_name is not None
+            _entry_resource_name.group(3)
+            if _entry_resource_name is not None
             else "UNKNOWN RESOURCE"
         )
         raise AttributeError(

optimade/adapters/references/adapter.py

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

optimade/adapters/structures/aiida.py

@@ -44,13 +44,13 @@ def get_aiida_structure_data(optimade_structure: OptimadeStructure) -> Structure
     attributes = optimade_structure.attributes
 
     # Convert null/None values to float("nan")
-    lattice_vectors, adjust_cell = pad_cell(attributes.lattice_vectors)
+    lattice_vectors, adjust_cell = pad_cell(attributes.lattice_vectors)  # type: ignore[arg-type]
     structure = StructureData(cell=lattice_vectors)
 
     # If species not provided, infer data from species_at_sites
     species: Optional[List[OptimadeStructureSpecies]] = attributes.species
     if not species:
-        species = species_from_species_at_sites(attributes.species_at_sites)
+        species = species_from_species_at_sites(attributes.species_at_sites)  # type: ignore[arg-type]
 
     # Add Kinds
     for kind in species:
@@ -86,18 +86,18 @@ def get_aiida_structure_data(optimade_structure: OptimadeStructure) -> Structure
         )
 
     # Add Sites
-    for index in range(attributes.nsites):
+    for index in range(attributes.nsites):  # type: ignore[arg-type]
         # range() to ensure 1-to-1 between kind and site
         structure.append_site(
             Site(
-                kind_name=attributes.species_at_sites[index],
-                position=attributes.cartesian_site_positions[index],
+                kind_name=attributes.species_at_sites[index],  # type: ignore[index]
+                position=attributes.cartesian_site_positions[index],  # type: ignore[index]
             )
         )
 
     if adjust_cell:
         structure._adjust_default_cell(
-            pbc=[bool(dim.value) for dim in attributes.dimension_types]
+            pbc=[bool(dim.value) for dim in attributes.dimension_types]  # type: ignore[union-attr]
         )
 
     return structure

optimade/adapters/structures/ase.py

@@ -57,7 +57,7 @@ def get_ase_atoms(optimade_structure: OptimadeStructure) -> Atoms:
     species = attributes.species
     # If species is missing, infer data from species_at_sites
     if not species:
-        species = species_from_species_at_sites(attributes.species_at_sites)
+        species = species_from_species_at_sites(attributes.species_at_sites)  # type: ignore[arg-type]
 
     optimade_species: Dict[str, OptimadeStructureSpecies] = {_.name: _ for _ in species}
 
@@ -69,9 +69,9 @@ def get_ase_atoms(optimade_structure: OptimadeStructure) -> Atoms:
         )
 
     atoms = []
-    for site_number in range(attributes.nsites):
-        species_name = attributes.species_at_sites[site_number]
-        site = attributes.cartesian_site_positions[site_number]
+    for site_number in range(attributes.nsites):  # type: ignore[arg-type]
+        species_name = attributes.species_at_sites[site_number]  # type: ignore[index]
+        site = attributes.cartesian_site_positions[site_number]  # type: ignore[index]
 
         current_species = optimade_species[species_name]
 

optimade/adapters/structures/cif.py

@@ -33,7 +33,7 @@
 
     from optimade.adapters.warnings import AdapterPackageNotFound
 
-    np = None
+    np = None  # type: ignore[assignment]
     NUMPY_NOT_FOUND = "NumPy not found, cannot convert structure to CIF"
 
 
@@ -55,7 +55,7 @@ def get_cif(  # pylint: disable=too-many-locals,too-many-branches
     # NumPy is needed for calculations
     if globals().get("np", None) is None:
         warn(NUMPY_NOT_FOUND, AdapterPackageNotFound)
-        return None
+        return None  # type: ignore[return-value]
 
     cif = """#
 # Created from an OPTIMADE structure.
@@ -71,9 +71,9 @@ def get_cif(  # pylint: disable=too-many-locals,too-many-branches
 
     # Do this only if there's three non-zero lattice vectors
     # NOTE: This also negates handling of lattice_vectors with null/None values
-    if valid_lattice_vector(attributes.lattice_vectors):
+    if valid_lattice_vector(attributes.lattice_vectors):  # type:ignore[arg-type]
         a_vector, b_vector, c_vector, alpha, beta, gamma = cell_to_cellpar(
-            attributes.lattice_vectors
+            attributes.lattice_vectors  # type: ignore[arg-type]
         )
 
         cif += (
@@ -96,8 +96,8 @@ def get_cif(  # pylint: disable=too-many-locals,too-many-branches
         # we calculate the fractional coordinates if this is a 3D structure and we have all the necessary information.
         if not hasattr(attributes, "fractional_site_positions"):
             attributes.fractional_site_positions = fractional_coordinates(
-                cell=attributes.lattice_vectors,
-                cartesian_positions=attributes.cartesian_site_positions,
+                cell=attributes.lattice_vectors,  # type:ignore[arg-type]
+                cartesian_positions=attributes.cartesian_site_positions,  # type:ignore[arg-type]
             )
 
     # NOTE: This is otherwise a bit ahead of its time, since this OPTIMADE property is part of an open PR.
@@ -124,12 +124,12 @@ def get_cif(  # pylint: disable=too-many-locals,too-many-branches
         sites = attributes.cartesian_site_positions
 
     species: Dict[str, OptimadeStructureSpecies] = {
-        species.name: species for species in attributes.species
+        species.name: species for species in attributes.species  # type: ignore[union-attr]
     }
 
-    symbol_occurences = {}
-    for site_number in range(attributes.nsites):
-        species_name = attributes.species_at_sites[site_number]
+    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]
 
         current_species = species[species_name]

optimade/adapters/structures/jarvis.py

@@ -55,7 +55,7 @@ def get_jarvis_atoms(optimade_structure: OptimadeStructure) -> Atoms:
 
     return Atoms(
         lattice_mat=attributes.lattice_vectors,
-        elements=[specie.name for specie in attributes.species],
+        elements=[specie.name for specie in attributes.species],  # type: ignore[union-attr]
         coords=attributes.cartesian_site_positions,
         cartesian=True,
     )

optimade/adapters/structures/proteindatabank.py

@@ -30,7 +30,7 @@
 
     from optimade.adapters.warnings import AdapterPackageNotFound
 
-    np = None
+    np = None  # type: ignore[assignment]
     NUMPY_NOT_FOUND = "NumPy not found, cannot convert structure to your desired format"
 
 from optimade.adapters.structures.utils import (
@@ -63,7 +63,7 @@ def get_pdbx_mmcif(  # pylint: disable=too-many-locals
     """
     if globals().get("np", None) is None:
         warn(NUMPY_NOT_FOUND, AdapterPackageNotFound)
-        return None
+        return None  # type: ignore[return-value]
 
     cif = """#
 # Created from an OPTIMADE structure.
@@ -82,9 +82,9 @@ def get_pdbx_mmcif(  # pylint: disable=too-many-locals
     attributes = optimade_structure.attributes
 
     # Do this only if there's three non-zero lattice vectors
-    if valid_lattice_vector(attributes.lattice_vectors):
+    if valid_lattice_vector(attributes.lattice_vectors):  # type: ignore[arg-type]
         a_vector, b_vector, c_vector, alpha, beta, gamma = cell_to_cellpar(
-            attributes.lattice_vectors
+            attributes.lattice_vectors  # type: ignore[arg-type]
         )
 
         cif += (
@@ -107,8 +107,8 @@ def get_pdbx_mmcif(  # pylint: disable=too-many-locals
         # we calculate the fractional coordinates if this is a 3D structure and we have all the necessary information.
         if not hasattr(attributes, "fractional_site_positions"):
             attributes.fractional_site_positions = fractional_coordinates(
-                cell=attributes.lattice_vectors,
-                cartesian_positions=attributes.cartesian_site_positions,
+                cell=attributes.lattice_vectors,  # type: ignore[arg-type]
+                cartesian_positions=attributes.cartesian_site_positions,  # type: ignore[arg-type]
             )
 
     # NOTE: The following lines are perhaps needed to create a "valid" PDBx/mmCIF file.
@@ -165,11 +165,11 @@ def get_pdbx_mmcif(  # pylint: disable=too-many-locals
         sites = attributes.cartesian_site_positions
 
     species: Dict[str, OptimadeStructureSpecies] = {
-        species.name: species for species in attributes.species
+        species.name: species for species in attributes.species  # type: ignore[union-attr]
     }
 
-    for site_number in range(attributes.nsites):
-        species_name = attributes.species_at_sites[site_number]
+    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]
 
         current_species = species[species_name]
@@ -211,14 +211,14 @@ def get_pdb(  # pylint: disable=too-many-locals
     """
     if globals().get("np", None) is None:
         warn(NUMPY_NOT_FOUND, AdapterPackageNotFound)
-        return None
+        return None  # type: ignore[return-value]
 
     pdb = ""
 
     attributes = optimade_structure.attributes
 
     rotation = None
-    if valid_lattice_vector(attributes.lattice_vectors):
+    if valid_lattice_vector(attributes.lattice_vectors):  # type: ignore[arg-type]
         currentcell = np.asarray(attributes.lattice_vectors)
         cellpar = cell_to_cellpar(currentcell)
         exportedcell = cellpar_to_cell(cellpar)
@@ -241,15 +241,16 @@ def get_pdb(  # pylint: disable=too-many-locals
     pdb += "MODEL     1\n"
 
     species: Dict[str, OptimadeStructureSpecies] = {
-        species.name: species for species in attributes.species
+        species.name: species
+        for species in attributes.species  # type:ignore[union-attr]
     }
 
     sites = np.asarray(attributes.cartesian_site_positions)
     if rotation is not None:
         sites = sites.dot(rotation)
 
-    for site_number in range(attributes.nsites):
-        species_name = attributes.species_at_sites[site_number]
+    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]
 
         current_species = species[species_name]

optimade/adapters/structures/pymatgen.py

@@ -61,9 +61,9 @@ def get_pymatgen(optimade_structure: OptimadeStructure) -> Union[Structure, Mole
         warn(PYMATGEN_NOT_FOUND, AdapterPackageNotFound)
         return None
 
-    if valid_lattice_vector(optimade_structure.attributes.lattice_vectors) and (
-        optimade_structure.attributes.nperiodic_dimensions > 0
-        or any(optimade_structure.attributes.dimension_types)
+    if valid_lattice_vector(optimade_structure.attributes.lattice_vectors) and (  # type: ignore[arg-type]
+        optimade_structure.attributes.nperiodic_dimensions > 0  # type: ignore[operator]
+        or any(optimade_structure.attributes.dimension_types)  # type: ignore[arg-type]
     ):
         return _get_structure(optimade_structure)
 
@@ -78,9 +78,9 @@ def _get_structure(optimade_structure: OptimadeStructure) -> Structure:
     return Structure(
         lattice=Lattice(attributes.lattice_vectors, attributes.dimension_types),
         species=_pymatgen_species(
-            nsites=attributes.nsites,
+            nsites=attributes.nsites,  # type: ignore[arg-type]
             species=attributes.species,
-            species_at_sites=attributes.species_at_sites,
+            species_at_sites=attributes.species_at_sites,  # type: ignore[arg-type]
         ),
         coords=attributes.cartesian_site_positions,
         coords_are_cartesian=True,
@@ -94,9 +94,9 @@ def _get_molecule(optimade_structure: OptimadeStructure) -> Molecule:
 
     return Molecule(
         species=_pymatgen_species(
-            nsites=attributes.nsites,
-            species=attributes.species,
-            species_at_sites=attributes.species_at_sites,
+            nsites=attributes.nsites,  # type: ignore[arg-type]
+            species=attributes.species,  # type: ignore[arg-type]
+            species_at_sites=attributes.species_at_sites,  # type: ignore[arg-type]
         ),
         coords=attributes.cartesian_site_positions,
     )