Source code for qcelemental.models.results

from enum import Enum
from functools import partial
from typing import TYPE_CHECKING, Any, Dict, Optional, Set, Union

import numpy as np
from pydantic import Field, constr, validator

from ..util import provenance_stamp
from .basemodels import ProtoModel, qcschema_draft
from .basis import BasisSet
from .common_models import ComputeError, DriverEnum, Model, Provenance, qcschema_input_default, qcschema_output_default
from .molecule import Molecule
from .types import Array

if TYPE_CHECKING:
    from pydantic.typing import ReprArgs


class AtomicResultProperties(ProtoModel):
    r"""Named properties of quantum chemistry computations following the MolSSI QCSchema.

    All arrays are stored flat but must be reshapable into the dimensions in attribute ``shape``, with abbreviations as follows:

      * nao: number of atomic orbitals = calcinfo_nbasis
      * nmo: number of molecular orbitals
    """

    # Calcinfo
    calcinfo_nbasis: Optional[int] = Field(None, description="The number of basis functions for the computation.")
    calcinfo_nmo: Optional[int] = Field(None, description="The number of molecular orbitals for the computation.")
    calcinfo_nalpha: Optional[int] = Field(None, description="The number of alpha electrons in the computation.")
    calcinfo_nbeta: Optional[int] = Field(None, description="The number of beta electrons in the computation.")
    calcinfo_natom: Optional[int] = Field(None, description="The number of atoms in the computation.")

    # Canonical
    nuclear_repulsion_energy: Optional[float] = Field(None, description="The nuclear repulsion energy.")
    return_energy: Optional[float] = Field(
        None,
        description="The energy of the requested method, identical to ``return_result`` for ``driver=energy`` computations.",
    )
    return_gradient: Optional[Array[float]] = Field(
        None,
        description="The gradient of the requested method, identical to ``return_result`` for ``driver=gradient`` computations.",
        units="E_h/a0",
    )
    return_hessian: Optional[Array[float]] = Field(
        None,
        description="The Hessian of the requested method, identical to ``return_result`` for ``driver=hessian`` computations.",
        units="E_h/a0^2",
    )

    # SCF Keywords
    scf_one_electron_energy: Optional[float] = Field(
        None,
        description="The one-electron (core Hamiltonian) energy contribution to the total SCF energy.",
        units="E_h",
    )
    scf_two_electron_energy: Optional[float] = Field(
        None,
        description="The two-electron energy contribution to the total SCF energy.",
        units="E_h",
    )
    scf_vv10_energy: Optional[float] = Field(
        None,
        description="The VV10 functional energy contribution to the total SCF energy.",
        units="E_h",
    )
    scf_xc_energy: Optional[float] = Field(
        None,
        description="The functional (XC) energy contribution to the total SCF energy.",
        units="E_h",
    )
    scf_dispersion_correction_energy: Optional[float] = Field(
        None,
        description="The dispersion correction appended to an underlying functional when a DFT-D method is requested.",
        units="E_h",
    )
    scf_dipole_moment: Optional[Array[float]] = Field(
        None,
        description="The SCF X, Y, and Z dipole components",
        units="e a0",
    )
    scf_quadrupole_moment: Optional[Array[float]] = Field(
        None,
        description="The quadrupole components (redundant; 6 unique).",
        shape=[3, 3],
        units="e a0^2",
    )
    scf_total_energy: Optional[float] = Field(
        None,
        description="The total electronic energy of the SCF stage of the calculation.",
        units="E_h",
    )
    scf_total_gradient: Optional[Array[float]] = Field(
        None,
        description="The total electronic gradient of the SCF stage of the calculation.",
        units="E_h/a0",
    )
    scf_total_hessian: Optional[Array[float]] = Field(
        None,
        description="The total electronic Hessian of the SCF stage of the calculation.",
        units="E_h/a0^2",
    )
    scf_iterations: Optional[int] = Field(None, description="The number of SCF iterations taken before convergence.")

    # MP2 Keywords
    mp2_same_spin_correlation_energy: Optional[float] = Field(
        None,
        description="The portion of MP2 doubles correlation energy from same-spin (i.e. triplet) correlations, without any user scaling.",
        units="E_h",
    )
    mp2_opposite_spin_correlation_energy: Optional[float] = Field(
        None,
        description="The portion of MP2 doubles correlation energy from opposite-spin (i.e. singlet) correlations, without any user scaling.",
        units="E_h",
    )
    mp2_singles_energy: Optional[float] = Field(
        None,
        description="The singles portion of the MP2 correlation energy. Zero except in ROHF.",
        units="E_h",
    )
    mp2_doubles_energy: Optional[float] = Field(
        None,
        description="The doubles portion of the MP2 correlation energy including same-spin and opposite-spin correlations.",
        units="E_h",
    )
    mp2_correlation_energy: Optional[float] = Field(
        None,
        description="The MP2 correlation energy.",
        units="E_h",
    )
    mp2_total_energy: Optional[float] = Field(
        None,
        description="The total MP2 energy (MP2 correlation energy + HF energy).",
        units="E_h",
    )
    mp2_dipole_moment: Optional[Array[float]] = Field(
        None,
        description="The MP2 X, Y, and Z dipole components.",
        shape=[3],
        units="e a0",
    )

    # CCSD Keywords
    ccsd_same_spin_correlation_energy: Optional[float] = Field(
        None,
        description="The portion of CCSD doubles correlation energy from same-spin (i.e. triplet) correlations, without any user scaling.",
        units="E_h",
    )
    ccsd_opposite_spin_correlation_energy: Optional[float] = Field(
        None,
        description="The portion of CCSD doubles correlation energy from opposite-spin (i.e. singlet) correlations, without any user scaling.",
        units="E_h",
    )
    ccsd_singles_energy: Optional[float] = Field(
        None,
        description="The singles portion of the CCSD correlation energy. Zero except in ROHF.",
        units="E_h",
    )
    ccsd_doubles_energy: Optional[float] = Field(
        None,
        description="The doubles portion of the CCSD correlation energy including same-spin and opposite-spin correlations.",
        units="E_h",
    )
    ccsd_correlation_energy: Optional[float] = Field(
        None,
        description="The CCSD correlation energy.",
        units="E_h",
    )
    ccsd_total_energy: Optional[float] = Field(
        None,
        description="The total CCSD energy (CCSD correlation energy + HF energy).",
        units="E_h",
    )
    ccsd_dipole_moment: Optional[Array[float]] = Field(
        None,
        description="The CCSD X, Y, and Z dipole components.",
        shape=[3],
        units="e a0",
    )
    ccsd_iterations: Optional[int] = Field(None, description="The number of CCSD iterations taken before convergence.")

    # CCSD(T) keywords
    ccsd_prt_pr_correlation_energy: Optional[float] = Field(
        None,
        description="The CCSD(T) correlation energy.",
        units="E_h",
    )
    ccsd_prt_pr_total_energy: Optional[float] = Field(
        None,
        description="The total CCSD(T) energy (CCSD(T) correlation energy + HF energy).",
        units="E_h",
    )
    ccsd_prt_pr_dipole_moment: Optional[Array[float]] = Field(
        None,
        description="The CCSD(T) X, Y, and Z dipole components.",
        shape=[3],
        units="e a0",
    )

    # CCSDT keywords
    ccsdt_correlation_energy: Optional[float] = Field(
        None,
        description="The CCSDT correlation energy.",
        units="E_h",
    )
    ccsdt_total_energy: Optional[float] = Field(
        None,
        description="The total CCSDT energy (CCSDT correlation energy + HF energy).",
        units="E_h",
    )
    ccsdt_dipole_moment: Optional[Array[float]] = Field(
        None,
        description="The CCSDT X, Y, and Z dipole components.",
        shape=[3],
        units="e a0",
    )
    ccsdt_iterations: Optional[int] = Field(
        None, description="The number of CCSDT iterations taken before convergence."
    )

    # CCSDTQ keywords
    ccsdtq_correlation_energy: Optional[float] = Field(
        None,
        description="The CCSDTQ correlation energy.",
        units="E_h",
    )
    ccsdtq_total_energy: Optional[float] = Field(
        None,
        description="The total CCSDTQ energy (CCSDTQ correlation energy + HF energy).",
        units="E_h",
    )
    ccsdtq_dipole_moment: Optional[Array[float]] = Field(
        None,
        description="The CCSDTQ X, Y, and Z dipole components.",
        shape=[3],
        units="e a0",
    )
    ccsdtq_iterations: Optional[int] = Field(
        None, description="The number of CCSDTQ iterations taken before convergence."
    )

    class Config(ProtoModel.Config):
        force_skip_defaults = True

    def __repr_args__(self) -> "ReprArgs":
        return [(k, v) for k, v in self.dict().items()]

    @validator(
        "scf_dipole_moment",
        "mp2_dipole_moment",
        "ccsd_dipole_moment",
        "ccsd_prt_pr_dipole_moment",
        "scf_quadrupole_moment",
    )
    def _validate_poles(cls, v, values, field):
        if v is None:
            return v

        if field.name.endswith("_dipole_moment"):
            order = 1
        elif field.name.endswith("_quadrupole_moment"):
            order = 2

        shape = tuple([3] * order)
        return np.asarray(v).reshape(shape)

    @validator(
        "return_gradient",
        "return_hessian",
        "scf_total_gradient",
        "scf_total_hessian",
    )
    def _validate_derivs(cls, v, values, field):
        if v is None:
            return v

        nat = values.get("calcinfo_natom", None)
        if nat is None:
            raise ValueError(f"Please also set ``calcinfo_natom``!")

        if field.name.endswith("_gradient"):
            shape = (nat, 3)
        elif field.name.endswith("_hessian"):
            shape = (3 * nat, 3 * nat)

        try:
            v = np.asarray(v).reshape(shape)
        except (ValueError, AttributeError):
            raise ValueError(f"Derivative must be castable to shape {shape}!")
        return v

    def dict(self, *args, **kwargs):
        # pure-json dict repr for QCFractal compliance, see https://github.com/MolSSI/QCFractal/issues/579
        # Sep 2021: commenting below for now to allow recomposing AtomicResult.properties for qcdb.
        #   This will break QCFractal tests for now, but future qcf will be ok with it.
        # kwargs["encoding"] = "json"
        return super().dict(*args, **kwargs)


class WavefunctionProperties(ProtoModel):
    r"""Wavefunction properties resulting from a computation. Matrix quantities are stored in column-major order. Presence and contents configurable by protocol."""

    # Class properties
    _return_results_names: Set[str] = {
        "orbitals_a",
        "orbitals_b",
        "density_a",
        "density_b",
        "fock_a",
        "fock_b",
        "eigenvalues_a",
        "eigenvalues_b",
        "occupations_a",
        "occupations_b",
    }

    # The full basis set description of the quantities
    basis: BasisSet = Field(..., description=str(BasisSet.__doc__))
    restricted: bool = Field(
        ...,
        description=str(
            "If the computation was restricted or not (alpha == beta). If True, all beta quantities are skipped."
        ),
    )

    # Core Hamiltonian
    h_core_a: Optional[Array[float]] = Field(
        None, description="Alpha-spin core (one-electron) Hamiltonian in the AO basis.", shape=["nao", "nao"]
    )
    h_core_b: Optional[Array[float]] = Field(
        None, description="Beta-spin core (one-electron) Hamiltonian in the AO basis.", shape=["nao", "nao"]
    )
    h_effective_a: Optional[Array[float]] = Field(
        None, description="Alpha-spin effective core (one-electron) Hamiltonian in the AO basis.", shape=["nao", "nao"]
    )
    h_effective_b: Optional[Array[float]] = Field(
        None, description="Beta-spin effective core (one-electron) Hamiltonian in the AO basis", shape=["nao", "nao"]
    )

    # SCF Results
    scf_orbitals_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin orbitals in the AO basis.", shape=["nao", "nmo"]
    )
    scf_orbitals_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin orbitals in the AO basis.", shape=["nao", "nmo"]
    )
    scf_density_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin density matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_density_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin density matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_fock_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin Fock matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_fock_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin Fock matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_eigenvalues_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin orbital eigenvalues.", shape=["nmo"]
    )
    scf_eigenvalues_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin orbital eigenvalues.", shape=["nmo"]
    )
    scf_occupations_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin orbital occupations.", shape=["nmo"]
    )
    scf_occupations_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin orbital occupations.", shape=["nmo"]
    )

    # BELOW from qcsk
    scf_coulomb_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin Coulomb matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_coulomb_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin Coulomb matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_exchange_a: Optional[Array[float]] = Field(
        None, description="SCF alpha-spin exchange matrix in the AO basis.", shape=["nao", "nao"]
    )
    scf_exchange_b: Optional[Array[float]] = Field(
        None, description="SCF beta-spin exchange matrix in the AO basis.", shape=["nao", "nao"]
    )

    # Localized-orbital SCF wavefunction quantities
    localized_orbitals_a: Optional[Array[float]] = Field(
        None,
        description="Localized alpha-spin orbitals in the AO basis. All nmo orbitals are included, even if only a subset were localized.",
        shape=["nao", "nmo"],
    )
    localized_orbitals_b: Optional[Array[float]] = Field(
        None,
        description="Localized beta-spin orbitals in the AO basis. All nmo orbitals are included, even if only a subset were localized.",
        shape=["nao", "nmo"],
    )
    localized_fock_a: Optional[Array[float]] = Field(
        None,
        description="Alpha-spin Fock matrix in the localized molecular orbital basis. All nmo orbitals are included, even if only a subset were localized.",
        shape=["nmo", "nmo"],
    )
    localized_fock_b: Optional[Array[float]] = Field(
        None,
        description="Beta-spin Fock matrix in the localized molecular orbital basis. All nmo orbitals are included, even if only a subset were localized.",
        shape=["nmo", "nmo"],
    )
    # ABOVE from qcsk

    # Return results, must be defined last
    orbitals_a: Optional[str] = Field(None, description="Index to the alpha-spin orbitals of the primary return.")
    orbitals_b: Optional[str] = Field(None, description="Index to the beta-spin orbitals of the primary return.")
    density_a: Optional[str] = Field(None, description="Index to the alpha-spin density of the primary return.")
    density_b: Optional[str] = Field(None, description="Index to the beta-spin density of the primary return.")
    fock_a: Optional[str] = Field(None, description="Index to the alpha-spin Fock matrix of the primary return.")
    fock_b: Optional[str] = Field(None, description="Index to the beta-spin Fock matrix of the primary return.")
    eigenvalues_a: Optional[str] = Field(
        None, description="Index to the alpha-spin orbital eigenvalues of the primary return."
    )
    eigenvalues_b: Optional[str] = Field(
        None, description="Index to the beta-spin orbital eigenvalues of the primary return."
    )
    occupations_a: Optional[str] = Field(
        None, description="Index to the alpha-spin orbital occupations of the primary return."
    )
    occupations_b: Optional[str] = Field(
        None, description="Index to the beta-spin orbital occupations of the primary return."
    )

    class Config(ProtoModel.Config):
        force_skip_defaults = True

    @validator("scf_eigenvalues_a", "scf_eigenvalues_b", "scf_occupations_a", "scf_occupations_b")
    def _assert1d(cls, v, values):

        try:
            v = v.reshape(-1)
        except (ValueError, AttributeError):
            raise ValueError("Vector must be castable to shape (-1, )!")
        return v

    @validator("scf_orbitals_a", "scf_orbitals_b")
    def _assert2d_nao_x(cls, v, values):
        bas = values.get("basis", None)

        # Do not raise multiple errors
        if bas is None:
            return v

        try:
            v = v.reshape(bas.nbf, -1)
        except (ValueError, AttributeError):
            raise ValueError("Matrix must be castable to shape (nbf, -1)!")
        return v

    @validator(
        "h_core_a",
        "h_core_b",
        "h_effective_a",
        "h_effective_b",
        # SCF
        "scf_density_a",
        "scf_density_b",
        "scf_fock_a",
        "scf_fock_b",
    )
    def _assert2d(cls, v, values):
        bas = values.get("basis", None)

        # Do not raise multiple errors
        if bas is None:
            return v

        try:
            v = v.reshape(bas.nbf, bas.nbf)
        except (ValueError, AttributeError):
            raise ValueError("Matrix must be castable to shape (nbf, nbf)!")
        return v

    @validator(
        "orbitals_a",
        "orbitals_b",
        "density_a",
        "density_b",
        "fock_a",
        "fock_b",
        "eigenvalues_a",
        "eigenvalues_b",
        "occupations_a",
        "occupations_b",
    )
    def _assert_exists(cls, v, values):

        if values.get(v, None) is None:
            raise ValueError(f"Return quantity {v} does not exist in the values.")
        return v


class WavefunctionProtocolEnum(str, Enum):
    r"""Wavefunction to keep from a computation."""

    all = "all"
    orbitals_and_eigenvalues = "orbitals_and_eigenvalues"
    return_results = "return_results"
    none = "none"


class ErrorCorrectionProtocol(ProtoModel):
    r"""Configuration for how QCEngine handles error correction

    WARNING: These protocols are currently experimental and only supported by NWChem tasks
    """

    default_policy: bool = Field(
        True, description="Whether to allow error corrections to be used " "if not directly specified in `policies`"
    )
    # TODO (wardlt): Consider support for common policies (e.g., 'only increase iterations') as strings (see #182)
    policies: Optional[Dict[str, bool]] = Field(
        None,
        description="Settings that define whether specific error corrections are allowed. "
        "Keys are the name of a known error and values are whether it is allowed to be used.",
    )

    def allows(self, policy: str):
        if self.policies is None:
            return self.default_policy
        return self.policies.get(policy, self.default_policy)


class NativeFilesProtocolEnum(str, Enum):
    r"""CMS program files to keep from a computation."""

    all = "all"
    input = "input"
    none = "none"


class AtomicResultProtocols(ProtoModel):
    r"""Protocols regarding the manipulation of computational result data."""

    wavefunction: WavefunctionProtocolEnum = Field(
        WavefunctionProtocolEnum.none, description=str(WavefunctionProtocolEnum.__doc__)
    )
    stdout: bool = Field(True, description="Primary output file to keep from the computation")
    error_correction: ErrorCorrectionProtocol = Field(
        default_factory=ErrorCorrectionProtocol, description="Policies for error correction"
    )
    native_files: NativeFilesProtocolEnum = Field(
        NativeFilesProtocolEnum.none,
        description="Policies for keeping processed files from the computation",
    )

    class Config:
        force_skip_defaults = True


### Primary models


[docs]class AtomicInput(ProtoModel): r"""The MolSSI Quantum Chemistry Schema""" id: Optional[str] = Field(None, description="The optional ID for the computation.") schema_name: constr(strip_whitespace=True, regex="^(qc_?schema_input)$") = Field( # type: ignore qcschema_input_default, description=( f"The QCSchema specification this model conforms to. Explicitly fixed as {qcschema_input_default}." ), ) schema_version: int = Field(1, description="The version number of ``schema_name`` to which this model conforms.") molecule: Molecule = Field(..., description="The molecule to use in the computation.") driver: DriverEnum = Field(..., description=str(DriverEnum.__doc__)) model: Model = Field(..., description=str(Model.__base_doc__)) keywords: Dict[str, Any] = Field({}, description="The program-specific keywords to be used.") protocols: AtomicResultProtocols = Field( AtomicResultProtocols(), description=str(AtomicResultProtocols.__base_doc__) ) extras: Dict[str, Any] = Field( {}, description="Additional information to bundle with the computation. Use for schema development and scratch space.", ) provenance: Provenance = Field( default_factory=partial(provenance_stamp, __name__), description=str(Provenance.__base_doc__) ) class Config(ProtoModel.Config): def schema_extra(schema, model): schema["$schema"] = qcschema_draft def __repr_args__(self) -> "ReprArgs": return [ ("driver", self.driver.value), ("model", self.model.dict()), ("molecule_hash", self.molecule.get_hash()[:7]), ]
[docs]class AtomicResult(AtomicInput): r"""Results from a CMS program execution.""" schema_name: constr(strip_whitespace=True, regex="^(qc_?schema_output)$") = Field( # type: ignore qcschema_output_default, description=( f"The QCSchema specification this model conforms to. Explicitly fixed as {qcschema_output_default}." ), ) 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( ..., description="The primary return specified by the ``driver`` field. Scalar if energy; array if gradient or hessian; dictionary with property keys if properties.", ) # type: ignore 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.") native_files: Optional[Dict[str, Any]] = Field(None, description="DSL files.") success: bool = Field(..., description="The success of program execution. If False, other fields may be blank.") error: Optional[ComputeError] = Field(None, description=str(ComputeError.__base_doc__)) provenance: Provenance = Field(..., description=str(Provenance.__base_doc__)) @validator("schema_name", pre=True) def _input_to_output(cls, v): r"""If qcschema_input is passed in, cast it to output, otherwise no""" if v.lower().strip() in [qcschema_input_default, qcschema_output_default]: return qcschema_output_default raise ValueError( "Only {0} or {1} is allowed for schema_name, " "which will be converted to {0}".format(qcschema_output_default, qcschema_input_default) ) @validator("return_result") def _validate_return_result(cls, v, values): if values["driver"] == "gradient": v = np.asarray(v).reshape(-1, 3) elif values["driver"] == "hessian": v = np.asarray(v) nsq = int(v.size ** 0.5) v.shape = (nsq, nsq) return v @validator("wavefunction", pre=True) def _wavefunction_protocol(cls, value, values): # We are pre, gotta do extra checks if value is None: return value elif isinstance(value, dict): wfn = value.copy() elif isinstance(value, WavefunctionProperties): wfn = value.dict() else: raise ValueError("wavefunction must be None, a dict, or a WavefunctionProperties object.") # Do not propagate validation errors if "protocols" not in values: raise ValueError("Protocols was not properly formed.") # Handle restricted restricted = wfn.get("restricted", None) if restricted is None: raise ValueError("`restricted` is required.") if restricted: for k in list(wfn.keys()): if k.endswith("_b"): wfn.pop(k) # Handle protocols wfnp = values["protocols"].wavefunction return_keep = None if wfnp == "all": pass elif wfnp == "none": wfn = None elif wfnp == "return_results": return_keep = [ "orbitals_a", "orbitals_b", "density_a", "density_b", "fock_a", "fock_b", "eigenvalues_a", "eigenvalues_b", "occupations_a", "occupations_b", ] elif wfnp == "orbitals_and_eigenvalues": return_keep = ["orbitals_a", "orbitals_b", "eigenvalues_a", "eigenvalues_b"] else: raise ValueError(f"Protocol `wavefunction:{wfnp}` is not understood.") if return_keep is not None: ret_wfn = {"restricted": restricted} if "basis" in wfn: ret_wfn["basis"] = wfn["basis"] for rk in return_keep: key = wfn.get(rk, None) if key is None: continue ret_wfn[rk] = key ret_wfn[key] = wfn[key] return ret_wfn else: return wfn @validator("stdout") def _stdout_protocol(cls, value, values): # Do not propagate validation errors if "protocols" not in values: raise ValueError("Protocols was not properly formed.") outp = values["protocols"].stdout if outp is True: return value elif outp is False: return None else: raise ValueError(f"Protocol `stdout:{outp}` is not understood") @validator("native_files") def _native_file_protocol(cls, value, values): ancp = values["protocols"].native_files if ancp == "all": return value elif ancp == "none": return None elif ancp == "input": return_keep = ["input"] if value is None: files = {} else: files = value.copy() else: raise ValueError(f"Protocol `native_files:{ancp}` is not understood") ret = {} for rk in return_keep: ret[rk] = files.get(rk, None) return ret
class ResultProperties(AtomicResultProperties): def __init__(self, *args, **kwargs): from warnings import warn warn( "ResultProperties has been renamed to AtomicResultProperties and will be removed in v0.13.0", DeprecationWarning, ) super().__init__(*args, **kwargs) class ResultProtocols(AtomicResultProtocols): def __init__(self, *args, **kwargs): from warnings import warn warn( "ResultProtocols has been renamed to AtomicResultProtocols and will be removed in v0.13.0", DeprecationWarning, ) super().__init__(*args, **kwargs) class ResultInput(AtomicInput): def __init__(self, *args, **kwargs): from warnings import warn warn("ResultInput has been renamed to AtomicInput and will be removed in v0.13.0", DeprecationWarning) super().__init__(*args, **kwargs) class Result(AtomicResult): def __init__(self, *args, **kwargs): from warnings import warn warn("Result has been renamed to AtomicResult and will be removed in v0.13.0", DeprecationWarning) super().__init__(*args, **kwargs)