Refactored models. Moved common fields to parent classes. Created sta…

…ndardized input and result interface.

qcelemental/models/__init__.py

@@ -8,14 +8,12 @@
 
 from . import types
 from .align import AlignmentMill
-from .basemodels import AutodocBaseSettings, ProtoModel
+from .basemodels import AutodocBaseSettings, ProtoModel, Provenance
 from .basis import BasisSet
-from .common_models import ComputeError, DriverEnum, FailedOperation, Provenance
+from .common_models import ComputeError, DriverEnum
 from .molecule import Molecule
-from .procedures import OptimizationInput, OptimizationResult
-from .procedures import Optimization  # scheduled for removal
+from .procedures import OptimizationInput, OptimizationResult, FailedOperation, TorsionDriveInput, TorsionDriveResult
 from .results import AtomicInput, AtomicResult, AtomicResultProperties
-from .results import Result, ResultInput, ResultProperties  # scheduled for removal
 
 
 def qcschema_models():

qcelemental/models/abcmodels.py

@@ -0,0 +1,91 @@
+import abc
+import json
+from pathlib import Path
+from typing import Any, Dict, Optional, Set, Union
+
+import numpy as np
+from pydantic import BaseModel, BaseSettings, Field
+from typing_extensions import Literal
+
+from qcelemental.testing import compare_recursive
+from qcelemental.util import deserialize, serialize
+from qcelemental.util.autodocs import AutoPydanticDocGenerator
+
+from ..util import provenance_stamp
+from .basemodels import ProtoModel, Provenance
+from .molecule import Molecule
+
+
+class InputResultBase(ProtoModel, abc.ABC):
+    """Base class from which input and result models are derived
+
+
+    NOTE: Abstract implementation coming from Samuel Colvin's suggestion:
+        https://github.com/samuelcolvin/pydantic/discussions/2410#discussioncomment-408613
+    """
+
+    @property
+    @abc.abstractmethod
+    def schema_name(self) -> str:
+        """The QCSchema specification this model conforms to"""
+
+    schema_version: Literal[2] = Field(
+        2, description="The version number of ``schema_name`` to which this model conforms."
+    )
+    id: Optional[str] = Field(None, description="The optional ID for the computation.")
+    extras: Dict[str, Any] = Field(
+        {},
+        description="Additional information to bundle with the computation. Use for schema development and scratch space.",
+    )
+
+    provenance: Provenance = Field(..., description=str(Provenance.__doc__))
+
+
+class InputBase(InputResultBase):
+    """Base Class for all input objects"""
+
+    provenance: Provenance = Field(Provenance(**provenance_stamp(__name__)), description=str(Provenance.__doc__))
+
+
+class ResultBase(InputResultBase):
+    """Base class for all result classes"""
+
+    input_data: Any = Field(..., description="The input data supplied to generate the computation")
+    success: bool = Field(..., description="The success of program execution")
+
+    stdout: Optional[str] = Field(
+        None,
+        description="The primary logging output of the program, whether natively standard output or a file. Presence vs. absence (or null-ness?) configurable by protocol.",
+    )
+    stderr: Optional[str] = Field(None, description="The standard error of the program execution.")
+
+
+class SuccessfulResultBase(ResultBase):
+    """Base object for any successfully returned result"""
+
+    success: Literal[True] = Field(
+        True,
+        description="A boolean indicator that the operation succeeded consistent with the model of successful operations. "
+        "Should always be True. Allows programmatic assessment of all operations regardless of if they failed or "
+        "succeeded",
+    )
+
+
+class InputSpecificationBase(InputBase):
+    """Input specification base"""
+
+    keywords: Dict[str, Any] = Field({}, description="The program specific keywords to be used.")
+    protocols: Any = Field(..., description="Protocols associated with the input")
+
+
+class InputComputationBase(InputBase):
+    """Base input directed at any computational chemistry program"""
+
+    input_spec: InputSpecificationBase = Field(..., description="The input specification for the computation")
+    molecule: Molecule = Field(..., description="The molecule to use in the computation.")
+
+    @property
+    def initial_molecule(self) -> Molecule:
+        """To maintain backwards compatibility to access the 'initial_molecule' attribute"""
+        # NOTE: Useful? Still have to use 'molecule' for instantiating the object...
+        return self.molecule

qcelemental/models/basemodels.py

@@ -1,14 +1,17 @@
+import abc
 import json
 from pathlib import Path
 from typing import Any, Dict, Optional, Set, Union
 
 import numpy as np
-from pydantic import BaseModel, BaseSettings
+from pydantic import BaseModel, BaseSettings, Field
 
 from qcelemental.testing import compare_recursive
 from qcelemental.util import deserialize, serialize
 from qcelemental.util.autodocs import AutoPydanticDocGenerator
 
+from ..util import provenance_stamp
+
 
 def _repr(self) -> str:
     return f'{self.__repr_name__()}({self.__repr_str__(", ")})'
@@ -189,6 +192,24 @@ def compare(self, other: Union["ProtoModel", BaseModel], **kwargs) -> bool:
         return compare_recursive(self, other, **kwargs)
 
 
+class Provenance(ProtoModel):
+    """Provenance information."""
+
+    creator: str = Field(..., description="The name of the program, library, or person who created the object.")
+    version: str = Field(
+        "",
+        description="The version of the creator, blank otherwise. This should be sortable by the very broad [PEP 440](https://www.python.org/dev/peps/pep-0440/).",
+    )
+    routine: str = Field("", description="The name of the routine or function within the creator, blank otherwise.")
+
+    class Config(ProtoModel.Config):
+        canonical_repr = True
+        extra: str = "allow"
+
+        def schema_extra(schema, model):
+            schema["$schema"] = qcschema_draft
+
+
 class AutodocBaseSettings(BaseSettings):
     def __init_subclass__(cls) -> None:
         cls.__doc__ = AutoPydanticDocGenerator(cls, always_apply=True)

qcelemental/models/common_models.py

@@ -15,24 +15,6 @@
 ndarray_encoder = {np.ndarray: lambda v: v.flatten().tolist()}
 
 
-class Provenance(ProtoModel):
-    """Provenance information."""
-
-    creator: str = Field(..., description="The name of the program, library, or person who created the object.")
-    version: str = Field(
-        "",
-        description="The version of the creator, blank otherwise. This should be sortable by the very broad [PEP 440](https://www.python.org/dev/peps/pep-0440/).",
-    )
-    routine: str = Field("", description="The name of the routine or function within the creator, blank otherwise.")
-
-    class Config(ProtoModel.Config):
-        canonical_repr = True
-        extra: str = "allow"
-
-        def schema_extra(schema, model):
-            schema["$schema"] = qcschema_draft
-
-
 class Model(ProtoModel):
     """The computational molecular sciences model to run."""
 
@@ -94,45 +76,13 @@ def __repr_args__(self) -> "ReprArgs":
         return [("error_type", self.error_type), ("error_message", self.error_message)]
 
 
-class FailedOperation(ProtoModel):
-    """Record indicating that a given operation (program, procedure, etc.) has failed and containing the reason and input data which generated the failure."""
-
-    id: str = Field(  # type: ignore
-        None,
-        description="A unique identifier which links this FailedOperation, often of the same Id of the operation "
-        "should it have been successful. This will often be set programmatically by a database such as "
-        "Fractal.",
-    )
-    input_data: Any = Field(  # type: ignore
-        None,
-        description="The input data which was passed in that generated this failure. This should be the complete "
-        "input which when attempted to be run, caused the operation to fail.",
-    )
-    success: bool = Field(  # type: ignore
-        False,
-        description="A boolean indicator that the operation failed consistent with the model of successful operations. "
-        "Should always be False. Allows programmatic assessment of all operations regardless of if they failed or "
-        "succeeded",
-    )
-    error: ComputeError = Field(  # type: ignore
-        ...,
-        description="A container which has details of the error that failed this operation. See the "
-        ":class:`ComputeError` for more details.",
-    )
-    extras: Optional[Dict[str, Any]] = Field(  # type: ignore
-        None,
-        description="Additional information to bundle with the failed operation. Details which pertain specifically "
-        "to a thrown error should be contained in the `error` field. See :class:`ComputeError` for details.",
-    )
-
-    def __repr_args__(self) -> "ReprArgs":
-        return [("error", self.error)]
-
-
 qcschema_input_default = "qcschema_input"
 qcschema_output_default = "qcschema_output"
+qcschema_input_specification_default = "qcschema_input_specification"
+qcschema_optimization_specification_default = "qcschema_optimization_specification"
 qcschema_optimization_input_default = "qcschema_optimization_input"
 qcschema_optimization_output_default = "qcschema_optimization_output"
 qcschema_torsion_drive_input_default = "qcschema_torsion_drive_input"
 qcschema_torsion_drive_output_default = "qcschema_torsion_drive_output"
-qcschema_molecule_default = "qcschema_molecule"
+qcschema_torsion_drive_specification_default = "qcschema_torsion_drive_specification"
+qcschema_molecule_default = "qcschema_molecule"

qcelemental/models/molecule.py

@@ -22,8 +22,8 @@
 from ..physical_constants import constants
 from ..testing import compare, compare_values
 from ..util import deserialize, measure_coordinates, msgpackext_loads, provenance_stamp, which_import
-from .basemodels import ProtoModel, qcschema_draft
-from .common_models import Provenance, qcschema_molecule_default
+from .basemodels import ProtoModel, Provenance, qcschema_draft
+from .common_models import qcschema_molecule_default
 from .types import Array
 
 if TYPE_CHECKING:
@@ -113,12 +113,7 @@ class Molecule(ProtoModel):
 
     """
 
-    schema_name: constr(strip_whitespace=True, regex="^(qcschema_molecule)$") = Field(  # type: ignore
-        qcschema_molecule_default,
-        description=(
-            f"The QCSchema specification to which this model conforms. Explicitly fixed as {qcschema_molecule_default}."
-        ),
-    )
+    schema_name: constr(strip_whitespace=True, regex=qcschema_molecule_default) = qcschema_molecule_default  # type: ignore
     schema_version: int = Field(  # type: ignore
         2, description="The version number of ``schema_name`` to which this model conforms."
     )