Models: Consistent model nomenclature moving forward

docs/source/model_result.rst

@@ -1,27 +1,27 @@
-Result
+AtomicResult
 ======
 
 A Python implementation of the `MolSSI QCSchema
-<https://github.com/MolSSI/QCSchema>`_ ``Result`` object.
+<https://github.com/MolSSI/QCSchema>`_ ``AtomicResult`` object.
 
 
-ResultInput
+AtomicInput
 -----------
 
-.. autoclass:: qcelemental.models.ResultInput
+.. autoclass:: qcelemental.models.AtomicInput
 
-Result
+AtomicResult
 ------
 
-.. autoclass:: qcelemental.models.Result
+.. autoclass:: qcelemental.models.AtomicResult
 
 
 API
 ---
 
-.. autoclass:: qcelemental.models.results.ResultProtocols
+.. autoclass:: qcelemental.models.results.AtomicResultProtocols
 
-.. autoclass:: qcelemental.models.results.ResultProperties
+.. autoclass:: qcelemental.models.results.AtomicResultProperties
 
 .. autoclass:: qcelemental.models.results.WavefunctionProperties
 

qcelemental/datum.py

@@ -6,7 +6,6 @@
 from typing import Any, Dict, Optional
 
 import numpy as np
-
 from pydantic import BaseModel, validator
 
 

qcelemental/models/__init__.py

@@ -12,5 +12,5 @@
 from .basis import BasisSet
 from .common_models import ComputeError, DriverEnum, FailedOperation, Provenance
 from .molecule import Molecule
-from .procedures import Optimization, OptimizationInput
-from .results import Result, ResultInput, ResultProperties
+from .procedures import Optimization, OptimizationInput, OptimizationResult
+from .results import AtomicInput, AtomicResult, AtomicResultProperties, Result, ResultInput, ResultProperties

qcelemental/models/align.py

@@ -1,5 +1,4 @@
 import numpy as np
-
 from pydantic import validator
 
 from ..util import blockwise_contract, blockwise_expand

qcelemental/models/basemodels.py

@@ -3,8 +3,8 @@
 from typing import Any, Dict, Optional, Set, Union
 
 import numpy as np
-
 from pydantic import BaseModel, BaseSettings
+
 from qcelemental.testing import compare_recursive
 from qcelemental.util import deserialize, serialize
 from qcelemental.util.autodocs import AutoPydanticDocGenerator

qcelemental/models/common_models.py

@@ -2,7 +2,6 @@
 from typing import Any, Dict, Optional
 
 import numpy as np
-
 from pydantic import Field
 
 from .basemodels import ProtoModel

qcelemental/models/molecule.py

@@ -10,7 +10,6 @@
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import numpy as np
-
 from pydantic import Field, constr, validator
 
 from ..molparse import from_arrays, from_schema, from_string, to_schema, to_string

qcelemental/models/procedures.py

@@ -15,7 +15,7 @@
  qcschema_optimization_output_default,
 )
 from .molecule import Molecule
-from .results import Result
+from .results import AtomicResult
 
 
 class TrajectoryProtocolEnum(str, Enum):
@@ -81,13 +81,13 @@ def __repr_args__(self) -> "ReprArgs":
  ]
 
 
-class Optimization(OptimizationInput):
+class OptimizationResult(OptimizationInput):
  schema_name: constr( # type: ignore
  strip_whitespace=True, regex=qcschema_optimization_output_default
  ) = qcschema_optimization_output_default
 
  final_molecule: Optional[Molecule] = Field(..., description="The final molecule of the geometry optimization.")
- trajectory: List[Result] = Field(
+ trajectory: List[AtomicResult] = Field(
  ..., description="A list of ordered Result objects for each step in the optimization."
  )
  energies: List[float] = Field(..., description="A list of ordered energies for each step in the optimization.")
@@ -123,3 +123,10 @@ def _trajectory_protocol(cls, v, values):
  raise ValueError(f"Protocol `trajectory:{keep_enum}` is not understood.")
 
  return v
+
+
+def Optimization(*args, **kwargs):
+ from warnings import warn
+
+ warn("Optimization has been renamed to OptimizationResult and will be removed in v0.13.0", DeprecationWarning)
+ return OptimizationResult(*args, **kwargs)

qcelemental/models/results.py

@@ -2,7 +2,6 @@
 from typing import Any, Dict, List, Optional, Set, Union
 
 import numpy as np
-
 from pydantic import Field, constr, validator
 
 from ..util import provenance_stamp
@@ -13,7 +12,7 @@
 from .types import Array
 
 
-class ResultProperties(ProtoModel):
+class AtomicResultProperties(ProtoModel):
  """
  Named properties of quantum chemistry computations following the MolSSI QCSchema.
  """
@@ -259,7 +258,7 @@ class WavefunctionProtocolEnum(str, Enum):
  none = "none"
 
 
-class ResultProtocols(ProtoModel):
+class AtomicResultProtocols(ProtoModel):
  """
  Protocols regarding the manipulation of a Result output data.
  """
@@ -276,7 +275,7 @@ class Config:
 ### Primary models
 
 
-class ResultInput(ProtoModel):
+class AtomicInput(ProtoModel):
  """The MolSSI Quantum Chemistry Schema"""
 
  id: Optional[str] = Field(None, description="An optional ID of the ResultInput object.")
@@ -287,7 +286,9 @@ class ResultInput(ProtoModel):
  driver: DriverEnum = Field(..., description=str(DriverEnum.__doc__))
  model: Model = Field(..., description=str(Model.__base_doc__))
  keywords: Dict[str, Any] = Field({}, description="The program specific keywords to be used.")
- protocols: ResultProtocols = Field(ResultProtocols(), description=str(ResultProtocols.__base_doc__))
+ protocols: AtomicResultProtocols = Field(
+ AtomicResultProtocols(), description=str(AtomicResultProtocols.__base_doc__)
+ )
 
  extras: Dict[str, Any] = Field({}, description="Extra fields that are not part of the schema.")
 
@@ -301,10 +302,10 @@ def __repr_args__(self) -> "ReprArgs":
  ]
 
 
-class Result(ResultInput):
+class AtomicResult(AtomicInput):
  schema_name: constr(strip_whitespace=True, regex=qcschema_output_default) = qcschema_output_default # type: ignore
 
- properties: ResultProperties = Field(..., description=str(ResultProperties.__base_doc__))
+ properties: AtomicResultProperties = Field(..., description=str(AtomicResultProperties.__base_doc__))
  wavefunction: Optional[WavefunctionProperties] = Field(None, description=str(WavefunctionProperties.__base_doc__))
 
  return_result: Union[float, Array[float], Dict[str, Any]] = Field(
@@ -424,3 +425,33 @@ def _stdout_protocol(cls, value, values):
  return None
  else:
  raise ValueError(f"Protocol `stdout:{outp}` is not understood")
+
+
+def ResultProtocols(*args, **kwargs):
+ from warnings import warn
+
+ warn("ResultProtocols has been renamed to AtomicResultProtocols and will be removed in v0.13.0", DeprecationWarning)
+ return AtomicResultProtocols(*args, **kwargs)
+
+
+def ResultProperties(*args, **kwargs):
+ from warnings import warn
+
+ warn(
+ "ResultProperties has been renamed to AtomicResultProperties and will be removed in v0.13.0", DeprecationWarning
+ )
+ return AtomicResultProperties(*args, **kwargs)
+
+
+def ResultInput(*args, **kwargs):
+ from warnings import warn
+
+ warn("ResultInput has been renamed to AtomicInput and will be removed in v0.13.0", DeprecationWarning)
+ return AtomicInput(*args, **kwargs)
+
+
+def Result(*args, **kwargs):
+ from warnings import warn
+
+ warn("Result has been renamed to AtomicResult and will be removed in v0.13.0", DeprecationWarning)
+ return AtomicResult(*args, **kwargs)

qcelemental/molutil/test_molutil.py

@@ -2,9 +2,9 @@
 import pprint
 
 import numpy as np
+import pydantic
 import pytest
 
-import pydantic
 import qcelemental as qcel
 from qcelemental.testing import compare, compare_molrecs, compare_recursive, compare_values
 

qcelemental/testing.py

@@ -5,7 +5,6 @@
 from typing import Callable, Dict, List, Union
 
 import numpy as np
-
 from pydantic import BaseModel
 
 pp = pprint.PrettyPrinter(width=120)

qcelemental/tests/test_datum.py

@@ -1,9 +1,9 @@
 from decimal import Decimal
 
 import numpy as np
+import pydantic
 import pytest
 
-import pydantic
 import qcelemental as qcel
 from qcelemental.testing import compare_recursive, compare_values
 

qcelemental/tests/test_model_general.py

@@ -1,30 +1,30 @@
 import pytest
 
 from qcelemental.models import (
+ AtomicInput,
+ AtomicResult,
+ AtomicResultProperties,
  ComputeError,
  FailedOperation,
  Molecule,
  Optimization,
  OptimizationInput,
  ProtoModel,
  Provenance,
- Result,
- ResultInput,
- ResultProperties,
 )
 
 
 def test_result_properties_default_skip():
 
- obj = ResultProperties(scf_one_electron_energy="-5.0")
+ obj = AtomicResultProperties(scf_one_electron_energy="-5.0")
 
  assert pytest.approx(obj.scf_one_electron_energy) == -5.0
 
  assert obj.dict().keys() == {"scf_one_electron_energy"}
 
 
 def test_result_properties_default_repr():
- obj = ResultProperties(scf_one_electron_energy="-5.0")
+ obj = AtomicResultProperties(scf_one_electron_energy="-5.0")
  assert "none" not in str(obj).lower()
  assert "scf_one_electron_energy" in str(obj)
  assert len(str(obj)) < 100
@@ -56,7 +56,7 @@ def test_repr_failed_op():
 
 def test_repr_result():
 
- result = ResultInput(
+ result = AtomicInput(
  **{"driver": "gradient", "model": {"method": "UFF"}, "molecule": {"symbols": ["He"], "geometry": [0, 0, 0]}}
  )
  assert "molecule_hash" in str(result)

qcelemental/tests/test_model_results.py

@@ -214,25 +214,25 @@ def test_basis_map_raises():
 
 
 def test_result_build(result_data_fixture):
- ret = qcel.models.Result(**result_data_fixture)
+ ret = qcel.models.AtomicResult(**result_data_fixture)
  assert ret.wavefunction is None
 
 
 def test_result_build_wavefunction_delete(wavefunction_data_fixture):
  del wavefunction_data_fixture["protocols"]
- ret = qcel.models.Result(**wavefunction_data_fixture)
+ ret = qcel.models.AtomicResult(**wavefunction_data_fixture)
  assert ret.wavefunction is None
 
 
 def test_wavefunction_build(wavefunction_data_fixture):
- assert qcel.models.Result(**wavefunction_data_fixture)
+ assert qcel.models.AtomicResult(**wavefunction_data_fixture)
 
 
 def test_wavefunction_matrix_size_error(wavefunction_data_fixture):
 
  wavefunction_data_fixture["wavefunction"]["scf_orbitals_a"] = np.random.rand(2, 2)
  with pytest.raises(ValueError) as e:
- qcel.models.Result(**wavefunction_data_fixture)
+ qcel.models.AtomicResult(**wavefunction_data_fixture)
 
  assert "castable to shape" in str(e.value)
 
@@ -241,7 +241,7 @@ def test_wavefunction_return_result_pointer(wavefunction_data_fixture):
 
  del wavefunction_data_fixture["wavefunction"]["scf_orbitals_a"]
  with pytest.raises(ValueError) as e:
- qcel.models.Result(**wavefunction_data_fixture)
+ qcel.models.AtomicResult(**wavefunction_data_fixture)
 
  assert "does not exist" in str(e.value)
 
@@ -288,7 +288,7 @@ def test_wavefunction_protocols(protocol, restricted, provided, expected, wavefu
  else:
  wfn_data[scf_name] = np.random.rand(bas.nbf, bas.nbf)
 
- wfn = qcel.models.Result(**wavefunction_data_fixture)
+ wfn = qcel.models.AtomicResult(**wavefunction_data_fixture)
 
  if len(expected) == 0:
  assert wfn.wavefunction is None
@@ -305,7 +305,7 @@ def test_optimization_trajectory_protocol(keep, indices, optimization_data_fixtu
 
  if keep is not None:
  optimization_data_fixture["protocols"] = {"trajectory": keep}
- opt = qcel.models.Optimization(**optimization_data_fixture)
+ opt = qcel.models.OptimizationResult(**optimization_data_fixture)
 
  assert len(opt.trajectory) == len(indices)
  for result, index in zip(opt.trajectory, indices):
@@ -314,12 +314,12 @@ def test_optimization_trajectory_protocol(keep, indices, optimization_data_fixtu
 
 def test_result_build_stdout_delete(result_data_fixture):
  result_data_fixture["protocols"] = {"stdout": False}
- ret = qcel.models.Result(**result_data_fixture)
+ ret = qcel.models.AtomicResult(**result_data_fixture)
  assert ret.stdout is None
 
 
 def test_result_build_stdout(result_data_fixture):
- ret = qcel.models.Result(**result_data_fixture)
+ ret = qcel.models.AtomicResult(**result_data_fixture)
  assert ret.stdout == "I ran."
 
 
@@ -342,3 +342,18 @@ def test_failed_operation(result_data_fixture):
  failed_json = failed.json()
  assert isinstance(failed_json, str)
  assert "its all good" in failed_json
+
+
+def test_result_model_deprecations(result_data_fixture, optimization_data_fixture):
+
+ with pytest.warns(DeprecationWarning):
+ qcel.models.ResultProperties(scf_one_electron_energy="-5.0")
+
+ with pytest.warns(DeprecationWarning):
+ qcel.models.ResultInput(**{k: result_data_fixture[k] for k in ["molecule", "model", "driver"]})
+
+ with pytest.warns(DeprecationWarning):
+ qcel.models.Result(**result_data_fixture)
+
+ with pytest.warns(DeprecationWarning):
+ qcel.models.Optimization(**optimization_data_fixture)

qcelemental/tests/test_utils.py

@@ -2,9 +2,9 @@
 
 import numpy as np
 import pytest
+from pydantic import BaseModel, Field
 
 import qcelemental as qcel
-from pydantic import BaseModel, Field
 from qcelemental.testing import compare_recursive, compare_values
 
 from .addons import serialize_extensions

qcelemental/util/serialization.py

@@ -2,7 +2,6 @@
 from typing import Any, Union
 
 import numpy as np
-
 from pydantic.json import pydantic_encoder
 
 from .importing import which_import