Finish initial pass converting to v2 pydantic API. Have not done any …

…testing so very much a WIP still.

qcelemental/models/molecule.py

@@ -13,7 +13,6 @@
 import numpy as np
 
 from pydantic import Field, constr, field_validator
-from pydantic.v1 import Field as FE
 
 # molparse imports separated b/c https://github.com/python/mypy/issues/7203
 from ..molparse.from_arrays import from_arrays
@@ -401,34 +400,38 @@ def __init__(self, orient: bool = False, validate: Optional[bool] = None, **kwar
  elif validate or geometry_prep:
  values["geometry"] = float_prep(values["geometry"], geometry_noise)
 
- @validator("geometry")
- def _must_be_3n(cls, v, values, **kwargs):
- n = len(values["symbols"])
+ @field_validator("geometry")
+ @classmethod
+ def _must_be_3n(cls, v, info):
+ n = len(info.data["symbols"])
  try:
  v = v.reshape(n, 3)
  except (ValueError, AttributeError):
  raise ValueError("Geometry must be castable to shape (N,3)!")
  return v
 
- @validator("masses_", "real_")
- def _must_be_n(cls, v, values, **kwargs):
- n = len(values["symbols"])
+ @field_validator("masses_", "real_")
+ @classmethod
+ def _must_be_n(cls, v, info):
+ n = len(info.data["symbols"])
  if len(v) != n:
  raise ValueError("Masses and Real must be same number of entries as Symbols")
  return v
 
- @validator("real_")
- def _populate_real(cls, v, values, **kwargs):
+ @field_validator("real_")
+ @classmethod
+ def _populate_real(cls, v, info):
  # Can't use geometry here since its already been validated and not in values
- n = len(values["symbols"])
+ n = len(info.data["symbols"])
  if len(v) == 0:
  v = np.array([True for _ in range(n)])
  return v
 
- @validator("fragment_charges_", "fragment_multiplicities_")
- def _must_be_n_frag(cls, v, values, **kwargs):
- if "fragments_" in values and values["fragments_"] is not None:
- n = len(values["fragments_"])
+ @field_validator("fragment_charges_", "fragment_multiplicities_")
+ @classmethod
+ def _must_be_n_frag(cls, v, info):
+ if "fragments_" in info.data and info.data["fragments_"] is not None:
+ n = len(info.data["fragments_"])
  if len(v) != n:
  raise ValueError(
  "Fragment Charges and Fragment Multiplicities must be same number of entries as Fragments"
@@ -596,7 +599,7 @@ def __eq__(self, other):
  def dict(self, *args, **kwargs):
  kwargs["by_alias"] = True
  kwargs["exclude_unset"] = True
- return super().dict(*args, **kwargs)
+ return super().model_dump(*args, **kwargs)
 
  def pretty_print(self):
  r"""Print the molecule in Angstroms. Same as :py:func:`print_out` only always in Angstroms.

qcelemental/models/procedures.py

@@ -1,10 +1,7 @@
 from enum import Enum
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
 
-try:
- from pydantic.v1 import Field, conlist, constr, validator
-except ImportError: # Will also trap ModuleNotFoundError
- from pydantic import Field, conlist, constr, validator
+from pydantic import Field, conlist, constr, field_validator
 
 from ..util import provenance_stamp
 from .basemodels import ProtoModel
@@ -23,10 +20,7 @@
 from .results import AtomicResult
 
 if TYPE_CHECKING:
- try:
- from pydantic.v1.typing import ReprArgs
- except ImportError: # Will also trap ModuleNotFoundError
- from pydantic.typing import ReprArgs
+ from .common_models import ReprArgs
 
 
 class TrajectoryProtocolEnum(str, Enum):
@@ -58,7 +52,7 @@ class QCInputSpecification(ProtoModel):
  A compute description for energy, gradient, and Hessian computations used in a geometry optimization.
  """
 
- schema_name: constr(strip_whitespace=True, regex=qcschema_input_default) = qcschema_input_default # type: ignore
+ schema_name: constr(strip_whitespace=True, pattern=qcschema_input_default) = qcschema_input_default # type: ignore
  schema_version: int = 1
 
  driver: DriverEnum = Field(DriverEnum.gradient, description=str(DriverEnum.__doc__))
@@ -75,7 +69,7 @@ class OptimizationInput(ProtoModel):
  id: Optional[str] = None
  hash_index: Optional[str] = None
  schema_name: constr( # type: ignore
- strip_whitespace=True, regex=qcschema_optimization_input_default
+ strip_whitespace=True, pattern=qcschema_optimization_input_default
  ) = qcschema_optimization_input_default
  schema_version: int = 1
 
@@ -97,7 +91,7 @@ def __repr_args__(self) -> "ReprArgs":
 
 class OptimizationResult(OptimizationInput):
  schema_name: constr( # type: ignore
- strip_whitespace=True, regex=qcschema_optimization_output_default
+ strip_whitespace=True, pattern=qcschema_optimization_output_default
  ) = qcschema_optimization_output_default
 
  final_molecule: Optional[Molecule] = Field(..., description="The final molecule of the geometry optimization.")
@@ -115,13 +109,14 @@ class OptimizationResult(OptimizationInput):
  error: Optional[ComputeError] = Field(None, description=str(ComputeError.__doc__))
  provenance: Provenance = Field(..., description=str(Provenance.__doc__))
 
- @validator("trajectory", each_item=False)
- def _trajectory_protocol(cls, v, values):
+ @field_validator("trajectory")
+ @classmethod
+ def _trajectory_protocol(cls, v, info):
  # Do not propogate validation errors
- if "protocols" not in values:
+ if "protocols" not in info.data:
  raise ValueError("Protocols was not properly formed.")
 
- keep_enum = values["protocols"].trajectory
+ keep_enum = info.data["protocols"].trajectory
  if keep_enum == "all":
  pass
  elif keep_enum == "initial_and_final":
@@ -148,14 +143,17 @@ class OptimizationSpecification(ProtoModel):
  * This class is still provisional and may be subject to removal and re-design.
  """
 
- schema_name: constr(strip_whitespace=True, regex="qcschema_optimization_specification") = "qcschema_optimization_specification" # type: ignore
+ schema_name: constr(strip_whitespace=True,
+ pattern="qcschema_optimization_specification"
+ ) = "qcschema_optimization_specification" # type: ignore
  schema_version: int = 1
 
  procedure: str = Field(..., description="Optimization procedure to run the optimization with.")
  keywords: Dict[str, Any] = Field({}, description="The optimization specific keywords to be used.")
  protocols: OptimizationProtocols = Field(OptimizationProtocols(), description=str(OptimizationProtocols.__doc__))
 
- @validator("procedure")
+ @field_validator("procedure")
+ @classmethod
  def _check_procedure(cls, v):
  return v.lower()
 
@@ -205,14 +203,16 @@ class TorsionDriveInput(ProtoModel):
  * This class is still provisional and may be subject to removal and re-design.
  """
 
- schema_name: constr(strip_whitespace=True, regex=qcschema_torsion_drive_input_default) = qcschema_torsion_drive_input_default # type: ignore
+ schema_name: constr(strip_whitespace=True,
+ pattern=qcschema_torsion_drive_input_default
+ ) = qcschema_torsion_drive_input_default # type: ignore
  schema_version: int = 1
 
  keywords: TDKeywords = Field(..., description="The torsion drive specific keywords to be used.")
  extras: Dict[str, Any] = Field({}, description="Extra fields that are not part of the schema.")
 
  input_specification: QCInputSpecification = Field(..., description=str(QCInputSpecification.__doc__))
- initial_molecule: conlist(item_type=Molecule, min_items=1) = Field(
+ initial_molecule: conlist(item_type=Molecule, min_length=1) = Field(
  ..., description="The starting molecule(s) for the torsion drive."
  )
 
@@ -222,7 +222,8 @@ class TorsionDriveInput(ProtoModel):
 
  provenance: Provenance = Field(Provenance(**provenance_stamp(__name__)), description=str(Provenance.__doc__))
 
- @validator("input_specification")
+ @field_validator("input_specification")
+ @classmethod
  def _check_input_specification(cls, value):
  assert value.driver == DriverEnum.gradient, "driver must be set to gradient"
  return value
@@ -236,7 +237,9 @@ class TorsionDriveResult(TorsionDriveInput):
  * This class is still provisional and may be subject to removal and re-design.
  """
 
- schema_name: constr(strip_whitespace=True, regex=qcschema_torsion_drive_output_default) = qcschema_torsion_drive_output_default # type: ignore
+ schema_name: constr(strip_whitespace=True,
+ pattern=qcschema_torsion_drive_output_default
+ ) = qcschema_torsion_drive_output_default # type: ignore
  schema_version: int = 1
 
  final_energies: Dict[str, float] = Field(