update to Pydantic 2+ and fix other outdated things

cp2k_input_tools/basissets/cp2k.py

@@ -6,22 +6,22 @@
 from decimal import Decimal
 from typing import Iterator, List, Optional, Sequence, Tuple
 
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel
 
 from ..utils import SYM2NUM, DatafileIterMixin, FromDictMixin, dformat
 
 N_VAL_EL_MATCH = re.compile(r"q(?P<nvalel>\d+)$")
 
 
-class BasisSetCoefficients(BaseModel, extra=Extra.forbid):
+class BasisSetCoefficients(BaseModel, extra="forbid"):
     """A 'shell' in one single basis set"""
 
     n: int
     l: List[Tuple[int, int]]  # noqa: E741
     coefficients: List[List[Decimal]]
 
 
-class BasisSetData(BaseModel, DatafileIterMixin, FromDictMixin, extra=Extra.forbid):
+class BasisSetData(BaseModel, DatafileIterMixin, FromDictMixin, extra="forbid"):
     """Basis set data for a single element"""
 
     element: str

cp2k_input_tools/basissets/crystal.py

@@ -6,15 +6,15 @@
 from decimal import Decimal
 from typing import Iterator, List, Optional, Sequence, Tuple
 
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel
 
 from ..pseudopotentials.ecp import ECP
 from ..utils import NUM2SYM, DatafileIterMixin, FromDictMixin
 
 BLOCK_MATCH = re.compile(r"^\s*\d+\s+\d+\s*$")
 
 
-class BasisSetCoefficients(BaseModel, extra=Extra.forbid):
+class BasisSetCoefficients(BaseModel, extra="forbid"):
     """A 'shell' in one single basis set"""
 
     shell: int  # 0: s, 1: s and p, 2: p, 3: d, 4:f
@@ -23,7 +23,7 @@ class BasisSetCoefficients(BaseModel, extra=Extra.forbid):
     coefficients: List[Tuple[Decimal, Decimal]]
 
 
-class BasisSetData(BaseModel, DatafileIterMixin, FromDictMixin, extra=Extra.forbid):
+class BasisSetData(BaseModel, DatafileIterMixin, FromDictMixin, extra="forbid"):
     """Basis set data for a single element"""
 
     Z: int

cp2k_input_tools/pseudopotentials/cp2k.py

@@ -5,7 +5,7 @@
 from decimal import Decimal, InvalidOperation
 from typing import Iterator, List, Sequence
 
-from pydantic import BaseModel, Extra, Field, root_validator
+from pydantic import BaseModel, Field, model_validator
 
 from ..utils import DatafileIterMixin, FromDictMixin, dformat
 
@@ -14,37 +14,37 @@ class PseudopotentialDataLocal(BaseModel):
     r: Decimal
     coefficients: List[Decimal] = Field(..., alias="coeffs")
 
-    class Config:
-        extra = "forbid"
-        allow_population_by_field_name = True
+    model_config = {
+        "extra": "forbid",
+        "populate_by_name": True,
+    }
 
 
 class PseudopotentialDataNonLocal(BaseModel):
     r: Decimal
     nproj: int
     coefficients: List[Decimal] = Field(..., alias="coeffs")
 
-    @root_validator
-    def check_coefficients(cls, values):
-        assert (
-            len(values["coefficients"]) == values["nproj"] * (values["nproj"] + 1) // 2
-        ), "invalid number of coefficients for non-local projection"
-        return values
+    @model_validator(mode="after")
+    def check_coefficients(cls, obj):
+        assert len(obj.coefficients) == obj.nproj * (obj.nproj + 1) // 2, "invalid number of coefficients for non-local projection"
+        return obj
 
-    class Config:
-        extra = "forbid"
-        allow_population_by_field_name = True
+    model_config = {
+        "extra": "forbid",
+        "populate_by_name": True,
+    }
 
 
-class PseudopotentialDataNLCC(BaseModel, extra=Extra.forbid):
+class PseudopotentialDataNLCC(BaseModel, extra="forbid"):
     """Nonlinear Core Correction data"""
 
     r: Decimal
     n: int
     c: Decimal
 
 
-class PseudopotentialData(BaseModel, DatafileIterMixin, FromDictMixin, extra=Extra.forbid):
+class PseudopotentialData(BaseModel, DatafileIterMixin, FromDictMixin, extra="forbid"):
     element: str
     identifiers: List[str]
     n_el: List[int]

cp2k_input_tools/pseudopotentials/ecp.py

@@ -1,12 +1,12 @@
 from decimal import Decimal
 from typing import Iterator, List, Tuple
 
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel
 
 from ..utils import NUM2SYM, dformat
 
 
-class ECP(BaseModel, extra=Extra.forbid):
+class ECP(BaseModel, extra="forbid"):
     """ECP for a single element"""
 
     Z: int

pyproject.toml

@@ -22,7 +22,7 @@ Pint = ">=0.15,<0.23"
 "ruamel.yaml" = {version = ">=0.16.5,<0.18.0", optional = true}
 pygls = {version = "^1.0.0", optional = true}
 Jinja2 = ">=2.11.3,<4.0.0"
-pydantic = "^1.8"
+pydantic = ">=2,<3.0"
 click = ">=7.1.2,<9"
 
 [tool.poetry.extras]
@@ -32,7 +32,7 @@ lsp = ["pygls"]
 [tool.poetry.dev-dependencies]
 pytest = "^7.1"
 pytest-cov = "^4.0"
-pytest-console-scripts = "^1.2"
+pytest-console-scripts = "^1.4"
 sphinx = "^6.1.3"
 sphinx-rtd-theme = "^1.0.0"
 taskipy = "^1.4"

tests/test_basisset.py

@@ -47,7 +47,7 @@ def test_check_formatting():
 def test_datafile_lint(script_runner):
     """check that reformatting a formatted file leaves it as is"""
     bsetfile = INPUTS_DIR / "BASIS_SET.formatted"
-    ret = script_runner.run("cp2k-datafile-lint", "basisset", str(bsetfile))
+    ret = script_runner.run(["cp2k-datafile-lint", "basisset", str(bsetfile)])
 
     assert ret.stderr == ""
     assert ret.success
@@ -58,7 +58,7 @@ def test_datafile_lint_crystal(script_runner):
     """check that reformatting a formatted file leaves it as is"""
     bsetfile = INPUTS_DIR / "29_Cu.pob-DZVP-rev2"
     ret = script_runner.run(
-        "cp2k-datafile-lint", "basisset", "--input-basis-format", "crystal", "--output-basis-format", "crystal", str(bsetfile)
+        ["cp2k-datafile-lint", "basisset", "--input-basis-format", "crystal", "--output-basis-format", "crystal", str(bsetfile)]
     )
 
     assert ret.stderr == ""
@@ -240,8 +240,8 @@ def test_bset_from_dicts():
     }
 
     # NOTE: they are not identical since the first one goes via the internal bit-representation of the float
-    BasisSetData.parse_obj(floated_dict)
-    BasisSetData.parse_obj(stringified_dict)
+    BasisSetData.model_validate(floated_dict)
+    BasisSetData.model_validate(stringified_dict)
 
 
 def test_new_style_ae_basisset_import():