Dependencies: Update pydantic~=2.4

The requirement for `pydantic` was pinned to `v1` since `v2` has a lot
of backwards incompatible changes and it is difficult to provide a
version that is compatible with both versions.

As of `v2.5.0`, `aiida-core` also directly depends on `pydantic` and it
requires `~=2.4`, so here we apply the same requirement. The deprecated
code is replaced.

As a side effect, a test for `PwCalculation` started failing. It was
testing that no warnings were raised for specific inputs, but some
warnings _were_ being raised. These were not the warnings tested for in
the tests though, but raised by SQLAlchemy. AiiDA v2.5 upgraded to
SQLAlchemy v2 which as of v2.0.19 started emitting a warning. This is
ignored by a filter in `aiida-core`, but this is made undone by `pytest`.
The warning is filtered again in the `pyproject.toml` config for
`pytest` but this is not considered by `pytest.warns`. Therefore, the
warnings in `PwCalculation` are turned into the more specific
`UserWarning` such that the test can explicitly check for those.

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     'importlib_resources',
     'jsonschema',
     'numpy',
-    'pydantic~=1.10,>=1.10.8',
+    'pydantic~=2.0',
     'packaging',
     'qe-tools~=2.0',
     'xmlschema~=2.0'

src/aiida_quantumespresso/calculations/pw.py

@@ -210,15 +210,15 @@ def validate_inputs(cls, value, port_namespace):
                     'Please set one of the following in the input parameters:\n'
                     "    parameters['CONTROL']['restart_mode'] = 'restart'\n"
                     "    parameters['ELECTRONS']['startingpot'] = 'file'\n"
-                    "    parameters['ELECTRONS']['startingwfc'] = 'file'\n"
+                    "    parameters['ELECTRONS']['startingwfc'] = 'file'\n", UserWarning
                 )
 
         if calculation_type in ('nscf', 'bands'):
             if 'parent_folder' not in value:
                 warnings.warn(
                     f'`parent_folder` not provided for `{calculation_type}` calculation. For work chains wrapping this '
                     'calculation, you can disable this warning by excluding the `parent_folder` when exposing the '
-                    'inputs of the `PwCalculation`.'
+                    'inputs of the `PwCalculation`.', UserWarning
                 )
 
     @classproperty

src/aiida_quantumespresso/common/hubbard.py

@@ -3,7 +3,7 @@
 # pylint: disable=no-name-in-module, invalid-name
 from typing import List, Literal, Tuple
 
-from pydantic import BaseModel, conint, constr, validator
+from pydantic import BaseModel, conint, constr, field_validator
 
 __all__ = ('HubbardParameters', 'Hubbard')
 
@@ -39,7 +39,7 @@ class HubbardParameters(BaseModel):
     hubbard_type: Literal['Ueff', 'U', 'V', 'J', 'B', 'E2', 'E3']
     """Type of the Hubbard parameters used (`Ueff`, `U`, `V`, `J`, `B`, `E2`, `E3`)."""
 
-    @validator('atom_manifold', 'neighbour_manifold')  # cls is mandatory to use
+    @field_validator('atom_manifold', 'neighbour_manifold')  # cls is mandatory to use
     def check_manifolds(cls, value):  # pylint: disable=no-self-argument, no-self-use
         """Check the validity of the manifold input.
 

src/aiida_quantumespresso/data/hubbard_structure.py

@@ -59,15 +59,15 @@ def hubbard(self) -> Hubbard:
         :returns: a :class:`~aiida_quantumespresso.common.hubbard.Hubbard` instance.
         """
         with self.base.repository.open(self._hubbard_filename, mode='rb') as handle:
-            return Hubbard.parse_raw(json.load(handle))
+            return Hubbard.model_validate_json(json.load(handle))
 
     @hubbard.setter
     def hubbard(self, hubbard: Hubbard):
         """Set the full Hubbard information."""
         if not isinstance(hubbard, Hubbard):
             raise ValueError('the input is not of type `Hubbard`')
 
-        serialized = json.dumps(hubbard.json())
+        serialized = json.dumps(hubbard.model_dump_json())
         self.base.repository.put_object_from_bytes(serialized.encode('utf-8'), self._hubbard_filename)
 
     @staticmethod

src/aiida_quantumespresso/utils/hubbard.py

@@ -181,7 +181,7 @@ def reorder_atoms(self):
         reordered = structure.clone()  # to be set at the end
         reordered.clear_kinds()
 
-        hubbard = structure.hubbard.copy()
+        hubbard = structure.hubbard.model_copy()
         parameters = hubbard.to_list()
 
         sites = structure.sites

src/aiida_quantumespresso/workflows/xspectra/base.py

@@ -99,7 +99,7 @@ def get_builder_from_protocol(
         if isinstance(code, str):
             code = orm.load_code(code)
 
-        type_check(code, orm.Code)
+        type_check(code, orm.AbstractCode)
 
         inputs = cls.get_protocol_inputs(protocol, overrides)
 

tests/calculations/test_pw.py

@@ -288,24 +288,24 @@ def test_pw_validate_inputs_restart_base(
 
     # Add `parent_folder` but no restart tags -> warning
     inputs['parent_folder'] = remote_data
-    with pytest.warns(Warning, match='`parent_folder` input was provided for the'):
+    with pytest.warns(UserWarning, match='`parent_folder` input was provided for the'):
         generate_calc_job(fixture_sandbox, entry_point_name, inputs)
 
     # Set `restart_mode` to `'restart'` -> no warning
     parameters['CONTROL']['restart_mode'] = 'restart'
     inputs['parameters'] = orm.Dict(parameters)
-    with pytest.warns(None) as warnings:
+    with pytest.warns() as warnings:
         generate_calc_job(fixture_sandbox, entry_point_name, inputs)
-    assert len(warnings.list) == 0
+    assert len([w for w in warnings.list if w.category is UserWarning]) == 0, [w.message for w in warnings.list]
     parameters['CONTROL'].pop('restart_mode')
 
     # Set `startingwfc` or `startingpot` to `'file'` -> no warning
     for restart_setting in ('startingpot', 'startingwfc'):
         parameters['ELECTRONS'][restart_setting] = 'file'
         inputs['parameters'] = orm.Dict(parameters)
-        with pytest.warns(None) as warnings:
+        with pytest.warns() as warnings:
             generate_calc_job(fixture_sandbox, entry_point_name, inputs)
-        assert len(warnings.list) == 0
+        assert len([w for w in warnings.list if w.category is UserWarning]) == 0
         parameters['ELECTRONS'].pop(restart_setting)
 
 

tests/common/test_hubbard.py

@@ -50,7 +50,7 @@ def _get_hubbard():
 
 def test_safe_hubbard_parameters(get_hubbard_parameters):
     """Test valid inputs are stored correctly for py:meth:`HubbardParameters`."""
-    params = get_hubbard_parameters().dict()
+    params = get_hubbard_parameters().model_dump()
     assert params == VALID_PARAMETERS
 
 
@@ -60,7 +60,7 @@ def test_from_to_list_parameters(get_hubbard_parameters):
     hp_tuple = (0, '3d', 1, '2p', 5.0, (0, 0, 0), 'U')
     assert param.to_tuple() == hp_tuple
     param = HubbardParameters.from_tuple(hp_tuple)
-    assert param.dict() == VALID_PARAMETERS
+    assert param.model_dump() == VALID_PARAMETERS
 
 
 @pytest.mark.parametrize(
@@ -76,7 +76,7 @@ def test_from_to_list_parameters(get_hubbard_parameters):
 )
 def test_valid_hubbard_parameters(get_hubbard_parameters, overrides):
     """Test valid inputs for py:meth:`HubbardParameters`."""
-    hp_dict = get_hubbard_parameters(overrides=overrides).dict()
+    hp_dict = get_hubbard_parameters(overrides=overrides).model_dump()
     new_dict = deepcopy(VALID_PARAMETERS)
     new_dict.update(overrides)
     assert hp_dict == new_dict
@@ -85,12 +85,12 @@ def test_valid_hubbard_parameters(get_hubbard_parameters, overrides):
 @pytest.mark.parametrize(('overrides', 'match'), (
     ({
         'atom_index': -1
-    }, r'ensure this value is greater than or equal to 0'),
+    }, r'Input should be greater than or equal to 0'),
     (
         {
             'atom_index': 0.5
         },
-        r'value is not a valid integer',
+        r'Input should be a valid integer',
     ),
     (
         {
@@ -108,31 +108,31 @@ def test_valid_hubbard_parameters(get_hubbard_parameters, overrides):
         {
             'atom_manifold': '3d-3p-2s'
         },
-        r'ensure this value has at most 5 characters',
+        r'String should have at most 5 characters',
     ),
     (
         {
             'translation': (0, 0)
         },
-        r'wrong tuple length 2, expected 3',
+        r'translation\.2\n\s+Field required',
     ),
     (
         {
             'translation': (0, 0, 0, 0)
         },
-        r'wrong tuple length 4, expected 3',
+        r'Tuple should have at most 3 items after validation, not 4',
     ),
     (
         {
             'translation': (0, 0, -1.5)
         },
-        r'value is not a valid integer',
+        r'Input should be a valid integer',
     ),
     (
         {
             'hubbard_type': 'L'
         },
-        r"permitted: 'Ueff', 'U', 'V', 'J', 'B', 'E2', 'E3'",
+        r"Input should be 'Ueff', 'U', 'V', 'J', 'B', 'E2' or 'E3'",
     ),
 ))
 def test_invalid_hubbard_parameters(get_hubbard_parameters, overrides, match):
@@ -150,7 +150,7 @@ def test_from_to_list_hubbard(get_hubbard):
     assert hubbard.to_list() == hubbard_list
 
     hubbard = Hubbard.from_list(hubbard_list)
-    assert hubbard.dict() == {
+    assert hubbard.model_dump() == {
         'parameters': [VALID_PARAMETERS, VALID_PARAMETERS],
         'projectors': 'ortho-atomic',
         'formulation': 'dudarev',