Merge branch 'master' into molextras

qcelemental/__init__.py

@@ -3,16 +3,23 @@
 """
 
 from . import models, molparse, molutil, util
-from .covalent_radii import CovalentRadii, covalentradii
 from .datum import Datum
 from .exceptions import ChoicesError, DataUnavailableError, MoleculeFormatError, NotAnElementError, ValidationError
 # Handle versioneer
 from .extras import get_information
 # Handle singletons, not their classes or modules
-from .periodic_table import periodictable
-from .physical_constants import PhysicalConstantsContext, constants
+from . import covalent_radii, periodic_table, physical_constants
+# from .physical_constants import PhysicalConstantsContext, constants
 from .testing import compare, compare_recursive, compare_values
 
+# Expose singletons from the modules
+periodictable = periodic_table.periodictable
+PhysicalConstantsContext = physical_constants.PhysicalConstantsContext
+constants = physical_constants.constants
+CovalentRadii = covalent_radii.CovalentRadii
+covalentradii = covalent_radii.covalentradii
+
+# Remove singleton-providing modules from known imported objects
 del periodic_table
 del physical_constants
 del covalent_radii

qcelemental/covalent_radii.py

@@ -4,7 +4,7 @@
 
 import collections
 from decimal import Decimal
-from typing import Union
+from typing import Union, Dict
 
 from .datum import Datum, print_variables
 from .exceptions import DataUnavailableError
@@ -38,21 +38,22 @@ class CovalentRadii:
 
  """
  def __init__(self, context: str = "ALVAREZ2008"):
- self.cr = collections.OrderedDict()
+ self.cr: Dict[str, Datum] = collections.OrderedDict()
 
  from .data import alvarez_2008_covalent_radii
 
  if context == "ALVAREZ2008":
  self.doi = alvarez_2008_covalent_radii["doi"]
  self.native_units = alvarez_2008_covalent_radii["units"]
 
- for cr in alvarez_2008_covalent_radii["covalent_radii"]:
+ # TypedDict wont be in until 3.8, have to ignore heterogeneous dicts for now
+ for cr in alvarez_2008_covalent_radii["covalent_radii"]: # type: ignore
  self.cr[cr[0]] = Datum(cr[0], self.native_units, Decimal(cr[1]), comment=cr[2], doi=self.doi)
  else:
  raise KeyError("Context set as '{}', only contexts {'ALVAREZ2008', } are currently supported")
 
  self.name = context
- self.year = int(alvarez_2008_covalent_radii["date"][:4])
+ self.year = int(alvarez_2008_covalent_radii["date"][:4]) # type: ignore
 
  # Extra relationships
  aliases = [
@@ -116,6 +117,7 @@ def get(self, atom: Union[int, str], *, return_tuple: bool = False, units: str =
  identifier = periodictable.to_E(atom)
 
  try:
+ assert isinstance(identifier, str) # Should be string by now
  qca = self.cr[identifier]
  except KeyError as e:
  if missing is not None and return_tuple is False:

qcelemental/models/align.py

@@ -17,9 +17,9 @@ class AlignmentMill(ProtoModel):
  then molecular system can be substantively changed by procedure.
 
  """
- shift: Array[float]
- rotation: Array[float]
- atommap: Array[int]
+ shift: Array[float] # type: ignore
+ rotation: Array[float] # type: ignore
+ atommap: Array[int] # type: ignore
  mirror: bool = False
 
  @validator('shift', whole=True)

qcelemental/models/basemodels.py

@@ -24,13 +24,13 @@ class Config:
  allow_mutation = False
  extra = "forbid"
  json_encoders = {np.ndarray: lambda v: v.flatten().tolist()}
- serialize_default_excludes = set()
+ serialize_default_excludes: Set = set()
  serialize_skip_defaults = False
  force_skip_defaults = False
  canonical_repr = False
 
  @classmethod
- def parse_raw(cls, data: Union[bytes, str], *, encoding: str = None) -> 'Model':
+ def parse_raw(cls, data: Union[bytes, str], *, encoding: str = None) -> 'ProtoModel': # type: ignore
  """
  Parses raw string or bytes into a Model object.
 
@@ -65,7 +65,7 @@ def parse_raw(cls, data: Union[bytes, str], *, encoding: str = None) -> 'Model':
  return cls.parse_obj(obj)
 
  @classmethod
- def parse_file(cls, path: Union[str, Path], *, encoding: str = None) -> 'Model':
+ def parse_file(cls, path: Union[str, Path], *, encoding: str = None) -> 'ProtoModel': # type: ignore
  """Parses a file into a Model object.
 
  Parameters
@@ -95,15 +95,16 @@ def parse_file(cls, path: Union[str, Path], *, encoding: str = None) -> 'Model':
 
  return cls.parse_raw(path.read_bytes(), encoding=encoding)
 
- def dict(self, *args, **kwargs) -> Dict[str, Any]:
+ def dict(self, **kwargs) -> Dict[str, Any]:
  encoding = kwargs.pop("encoding", None)
 
- kwargs["exclude"] = (kwargs.get("exclude", None) or set()) | self.__config__.serialize_default_excludes
- kwargs.setdefault("skip_defaults", self.__config__.serialize_skip_defaults)
- if self.__config__.force_skip_defaults:
+ kwargs["exclude"] = (
+ (kwargs.get("exclude", None) or set()) | self.__config__.serialize_default_excludes) # type: ignore
+ kwargs.setdefault("skip_defaults", self.__config__.serialize_skip_defaults) # type: ignore
+ if self.__config__.force_skip_defaults: # type: ignore
  kwargs["skip_defaults"] = True
 
- data = super().dict(*args, **kwargs)
+ data = super().dict(**kwargs)
 
  if encoding is None:
  return data
@@ -140,7 +141,7 @@ def serialize(self,
 
  return serialize(data, encoding=encoding)
 
- def compare(self, other: 'Model', **kwargs) -> bool:
+ def compare(self, other: Union['ProtoModel', BaseModel], **kwargs) -> bool:
  """Compares the current object to the provided object recursively.
 
  Parameters
@@ -158,7 +159,7 @@ def compare(self, other: 'Model', **kwargs) -> bool:
  return compare_recursive(self, other, **kwargs)
 
  def __str__(self) -> str: # lgtm: [py/inheritance/incorrect-overridden-signature]
- if self.__config__.canonical_repr:
+ if self.__config__.canonical_repr: # type: ignore
  return super().to_string()
  else:
  return f"{self.__class__.__name__}(ProtoModel)"

qcelemental/models/common_models.py

@@ -24,8 +24,9 @@ class Model(ProtoModel):
  """
  The quantum chemistry model specification for a given operation to compute against
  """
- method: str = Schema(..., description="The quantum chemistry method to evaluate (e.g., B3LYP, PBE, ...).")
- basis: Optional[str] = Schema(
+ method: str = Schema( # type: ignore
+ ..., description="The quantum chemistry method to evaluate (e.g., B3LYP, PBE, ...).")
+ basis: Optional[str] = Schema( # type: ignore
  None,
  description="The quantum chemistry basis set to evaluate (e.g., 6-31g, cc-pVDZ, ...). Can be ``None`` for "
  "methods without basis sets.")
@@ -53,15 +54,15 @@ def derivative_int(self):
 
 class ComputeError(ProtoModel):
  """The type of error message raised"""
- error_type: str = Schema( # Error enumeration not yet strict
- ...,
+ error_type: str = Schema( # type: ignore
+ ..., # Error enumeration not yet strict
  description="The type of error which was thrown. Restrict this field short classifiers e.g. 'input_error'.")
- error_message: str = Schema(
+ error_message: str = Schema( # type: ignore
  ...,
  description="Text associated with the thrown error, often the backtrace, but can contain additional "
  "information as well.")
- extras: Optional[Dict[str, Any]] = Schema(None,
-   description="Additional data to ship with the ComputeError object.")
+ extras: Optional[Dict[str, Any]] = Schema( # type: ignore
+ None, description="Additional data to ship with the ComputeError object.")
 
  def __str__(self) -> str:
  return f"{self.__class__.__name__}(error_type={self.error_type} error_message:\n{self.error_message}\n)"
@@ -73,25 +74,25 @@ class FailedOperation(ProtoModel):
  input data which generated the failure.
 
  """
- id: str = Schema(
+ id: str = Schema( # 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 = Schema(
+ input_data: Any = Schema( # 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 = Schema(
+ success: bool = Schema( # 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 = Schema(
+ error: ComputeError = Schema( # 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]] = Schema(
+ extras: Optional[Dict[str, Any]] = Schema( # type: ignore
  None,
  description="Additional information to bundle with this Failed Operation. Details which pertain specifically "
  "to a thrown error should be contained in the `error` field. See :class:`ComputeError` for details.")