@mat3ra/esse 2024.4.8-0 → 2024.4.8-2

package/dist/py/software_directory/ml/unit/processing/feature_selection/__init__.py

@@ -1,180 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  software_directory/ml/unit/processing/feature_selection.json
-#   version:   0.25.5
-
-from __future__ import annotations
-
-from enum import Enum
-from typing import Any, Dict, List, Optional, Union
-
-from pydantic import BaseModel, ConfigDict, Field, RootModel
-
-
-class Operation(Enum):
-    feature_selection = "feature_selection"
-
-
-class OperationType(Enum):
-    filter_based = "filter_based"
-
-
-class Algorithm(Enum):
-    f_regression = "f_regression"
-
-
-class InputData(BaseModel):
-    nFeatures: float
-    """
-    number of features to select for model training. If equal to 0, will use all available features
-    """
-    algorithm: Algorithm
-    """
-    feature selection algorithm following sklearn.feature_selection
-    """
-
-
-class Type(Enum):
-    processing = "processing"
-
-
-class Status(Enum):
-    idle = "idle"
-    active = "active"
-    warning = "warning"
-    error = "error"
-    finished = "finished"
-
-
-class Name(Enum):
-    default = "default"
-    atomsTooClose = "atomsTooClose"
-    atomsOverlap = "atomsOverlap"
-
-
-class Severity(Enum):
-    info = "info"
-    warning = "warning"
-    error = "error"
-
-
-class ConsistencyCheck(BaseModel):
-    key: str
-    """
-    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
-    """
-    name: Name
-    """
-    Name of the consistency check that is performed, which is listed in an enum.
-    """
-    severity: Severity
-    """
-    Severity level of the problem, which is used in UI to differentiate.
-    """
-    message: str
-    """
-    Message generated by the consistency check describing the problem.
-    """
-
-
-class NameResultSchema(BaseModel):
-    name: str
-    """
-    The name of this item. e.g. scf_accuracy
-    """
-
-
-class StatusTrackItem(BaseModel):
-    trackedAt: float
-    status: str
-    repetition: Optional[float] = None
-
-
-class FilterBasedFeatureSelectionUnitSchema(BaseModel):
-    model_config = ConfigDict(
-        extra="allow",
-    )
-    operation: Operation
-    """
-    Contains information about the operation used.
-    """
-    operationType: OperationType
-    """
-    Contains information about the specific type of the operation used.
-    """
-    inputData: InputData
-    """
-    unit input (type to be specified by the child units)
-    """
-    type: Type
-    """
-    type of the unit
-    """
-    field_id: Optional[str] = Field(None, alias="_id")
-    """
-    entity identity
-    """
-    isDraft: Optional[bool] = None
-    name: Optional[str] = None
-    """
-    name of the unit. e.g. pw_scf
-    """
-    status: Optional[Status] = None
-    """
-    Status of the unit.
-    """
-    head: Optional[bool] = None
-    """
-    Whether this unit is the first one to be executed.
-    """
-    flowchartId: str
-    """
-    Identity of the unit in the workflow. Used to trace the execution flow of the workflow.
-    """
-    next: Optional[str] = None
-    """
-    Next unit's flowchartId. If empty, the current unit is the last.
-    """
-    enableRender: Optional[bool] = None
-    """
-    Whether Rupy should attempt to use Jinja templating to add context variables into the unit
-    """
-    context: Optional[Dict[str, Any]] = None
-    slug: Optional[str] = None
-    """
-    entity slug
-    """
-    systemName: Optional[str] = None
-    consistencyChecks: Optional[List[ConsistencyCheck]] = None
-    schemaVersion: Optional[str] = "2022.8.16"
-    """
-    entity's schema version. Used to distinct between different schemas.
-    """
-    isDefault: Optional[bool] = False
-    """
-    Identifies that entity is defaultable
-    """
-    preProcessors: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the pre-processors for this calculation
-    """
-    postProcessors: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the post-processors for this calculation
-    """
-    monitors: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the monitors for this calculation
-    """
-    results: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the results for this calculation
-    """
-    tags: Optional[List[str]] = None
-    """
-    entity tags
-    """
-    statusTrack: Optional[List[StatusTrackItem]] = None
-
-
-class ESSE(RootModel[FilterBasedFeatureSelectionUnitSchema]):
-    root: FilterBasedFeatureSelectionUnitSchema

package/dist/py/software_directory/ml/unit/processing/feature_selection/filter_based.py

@@ -1,176 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  software_directory/ml/unit/processing/feature_selection/filter_based.json
-#   version:   0.25.5
-
-from __future__ import annotations
-
-from enum import Enum
-from typing import Any, Dict, List, Optional, Union
-
-from pydantic import BaseModel, ConfigDict, Field
-
-
-class Operation(Enum):
-    feature_selection = "feature_selection"
-
-
-class OperationType(Enum):
-    filter_based = "filter_based"
-
-
-class Algorithm(Enum):
-    f_regression = "f_regression"
-
-
-class InputData(BaseModel):
-    nFeatures: float
-    """
-    number of features to select for model training. If equal to 0, will use all available features
-    """
-    algorithm: Algorithm
-    """
-    feature selection algorithm following sklearn.feature_selection
-    """
-
-
-class Type(Enum):
-    processing = "processing"
-
-
-class Status(Enum):
-    idle = "idle"
-    active = "active"
-    warning = "warning"
-    error = "error"
-    finished = "finished"
-
-
-class Name(Enum):
-    default = "default"
-    atomsTooClose = "atomsTooClose"
-    atomsOverlap = "atomsOverlap"
-
-
-class Severity(Enum):
-    info = "info"
-    warning = "warning"
-    error = "error"
-
-
-class ConsistencyCheck(BaseModel):
-    key: str
-    """
-    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
-    """
-    name: Name
-    """
-    Name of the consistency check that is performed, which is listed in an enum.
-    """
-    severity: Severity
-    """
-    Severity level of the problem, which is used in UI to differentiate.
-    """
-    message: str
-    """
-    Message generated by the consistency check describing the problem.
-    """
-
-
-class NameResultSchema(BaseModel):
-    name: str
-    """
-    The name of this item. e.g. scf_accuracy
-    """
-
-
-class StatusTrackItem(BaseModel):
-    trackedAt: float
-    status: str
-    repetition: Optional[float] = None
-
-
-class FilterBasedFeatureSelectionUnitSchema(BaseModel):
-    model_config = ConfigDict(
-        extra="allow",
-    )
-    operation: Operation
-    """
-    Contains information about the operation used.
-    """
-    operationType: OperationType
-    """
-    Contains information about the specific type of the operation used.
-    """
-    inputData: InputData
-    """
-    unit input (type to be specified by the child units)
-    """
-    type: Type
-    """
-    type of the unit
-    """
-    field_id: Optional[str] = Field(None, alias="_id")
-    """
-    entity identity
-    """
-    isDraft: Optional[bool] = None
-    name: Optional[str] = None
-    """
-    name of the unit. e.g. pw_scf
-    """
-    status: Optional[Status] = None
-    """
-    Status of the unit.
-    """
-    head: Optional[bool] = None
-    """
-    Whether this unit is the first one to be executed.
-    """
-    flowchartId: str
-    """
-    Identity of the unit in the workflow. Used to trace the execution flow of the workflow.
-    """
-    next: Optional[str] = None
-    """
-    Next unit's flowchartId. If empty, the current unit is the last.
-    """
-    enableRender: Optional[bool] = None
-    """
-    Whether Rupy should attempt to use Jinja templating to add context variables into the unit
-    """
-    context: Optional[Dict[str, Any]] = None
-    slug: Optional[str] = None
-    """
-    entity slug
-    """
-    systemName: Optional[str] = None
-    consistencyChecks: Optional[List[ConsistencyCheck]] = None
-    schemaVersion: Optional[str] = "2022.8.16"
-    """
-    entity's schema version. Used to distinct between different schemas.
-    """
-    isDefault: Optional[bool] = False
-    """
-    Identifies that entity is defaultable
-    """
-    preProcessors: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the pre-processors for this calculation
-    """
-    postProcessors: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the post-processors for this calculation
-    """
-    monitors: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the monitors for this calculation
-    """
-    results: Optional[List[Union[NameResultSchema, str]]] = None
-    """
-    names of the results for this calculation
-    """
-    tags: Optional[List[str]] = None
-    """
-    entity tags
-    """
-    statusTrack: Optional[List[StatusTrackItem]] = None

package/dist/py/software_directory/modeling/__init__.py

@@ -1,3 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  schema
-#   version:   0.25.5

package/dist/py/software_directory/modeling/deepmd.py

@@ -1,112 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  software_directory/modeling/deepmd.json
-#   version:   0.25.5
-
-from __future__ import annotations
-
-from enum import Enum
-from typing import List, Optional
-
-from pydantic import BaseModel, ConfigDict, Field
-
-
-class Name(Enum):
-    deepmd = "deepmd"
-
-
-class Summary(Enum):
-    DeePMD_is_a_deep_learning_package_that_is_based_on_neural_network_fitted_first_principles_data_for_many_body_potential_energy_representation_and_molecular_dynamics = "DeePMD is a deep learning package that is based on neural network fitted first-principles data for many-body potential energy representation and molecular dynamics"
-
-
-class Version(Enum):
-    field_2_0_2 = "2.0.2"
-
-
-class Exec(Enum):
-    dp = "dp"
-    lmp = "lmp"
-    python = "python"
-
-
-class Name24(Enum):
-    default = "default"
-    atomsTooClose = "atomsTooClose"
-    atomsOverlap = "atomsOverlap"
-
-
-class Severity(Enum):
-    info = "info"
-    warning = "warning"
-    error = "error"
-
-
-class ConsistencyCheck(BaseModel):
-    key: str
-    """
-    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
-    """
-    name: Name24
-    """
-    Name of the consistency check that is performed, which is listed in an enum.
-    """
-    severity: Severity
-    """
-    Severity level of the problem, which is used in UI to differentiate.
-    """
-    message: str
-    """
-    Message generated by the consistency check describing the problem.
-    """
-
-
-class DeePMDAppSchema(BaseModel):
-    model_config = ConfigDict(
-        extra="allow",
-    )
-    name: Optional[Name] = None
-    """
-    entity name
-    """
-    summary: Optional[Summary] = None
-    """
-    Application's short description.
-    """
-    version: Optional[Version] = None
-    """
-    Application version. e.g. 5.3.5
-    """
-    exec: Optional[Exec] = None
-    shortName: Optional[str] = None
-    """
-    The short name of the application. e.g. qe
-    """
-    build: Optional[str] = None
-    """
-    Application build. e.g. VTST
-    """
-    hasAdvancedComputeOptions: Optional[bool] = None
-    """
-    Whether advanced compute options are present
-    """
-    isLicensed: Optional[bool] = None
-    """
-    Whether licensing is present
-    """
-    field_id: Optional[str] = Field(None, alias="_id")
-    """
-    entity identity
-    """
-    slug: Optional[str] = None
-    """
-    entity slug
-    """
-    systemName: Optional[str] = None
-    consistencyChecks: Optional[List[ConsistencyCheck]] = None
-    schemaVersion: Optional[str] = "2022.8.16"
-    """
-    entity's schema version. Used to distinct between different schemas.
-    """
-    isDefault: Optional[bool] = False
-    """
-    Identifies that entity is defaultable
-    """

package/dist/py/software_directory/modeling/espresso/__init__.py

@@ -1,39 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  software_directory/modeling/espresso.json
-#   version:   0.25.5
-
-from __future__ import annotations
-
-from enum import Enum
-from typing import Optional
-
-from pydantic import BaseModel
-
-
-class Name(Enum):
-    espresso = "espresso"
-
-
-class Summary(Enum):
-    Quantum_Espresso = "Quantum Espresso"
-
-
-class Version(Enum):
-    field_5_2_1 = "5.2.1"
-    field_5_4_0 = "5.4.0"
-    field_6_0_0 = "6.0.0"
-    field_6_3 = "6.3"
-    field_6_4_1 = "6.4.1"
-    field_6_5_0 = "6.5.0"
-    field_6_6_0 = "6.6.0"
-    field_6_7_0 = "6.7.0"
-    field_6_8_0 = "6.8.0"
-    field_7_0 = "7.0"
-    field_7_2 = "7.2"
-    field_7_3 = "7.3"
-
-
-class EspressoAppSchema(BaseModel):
-    name: Optional[Name] = None
-    summary: Optional[Summary] = None
-    version: Optional[Version] = None

package/dist/py/software_directory/modeling/espresso/arguments.py

@@ -1,35 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  software_directory/modeling/espresso/arguments.json
-#   version:   0.25.5
-
-from __future__ import annotations
-
-from typing import Optional
-
-from pydantic import BaseModel, ConfigDict, conint
-
-
-class QuantumEspressoArgumentsSchema(BaseModel):
-    model_config = ConfigDict(
-        extra="forbid",
-    )
-    nimage: Optional[conint(ge=1, le=100)] = 1
-    """
-    Processors can be divided into different `images`, each corresponding to a different self-consistent or linear-response calculation, loosely coupled to others.
-    """
-    npools: Optional[conint(ge=1, le=100)] = 1
-    """
-    Each image can be subpartitioned into `pools`, each taking care of a group of k-points.
-    """
-    nband: Optional[conint(ge=1, le=100)] = 1
-    """
-    Each pool is subpartitioned into `band groups`, each taking care of a group of Kohn-Sham orbitals (also called bands, or wavefunctions).
-    """
-    ntg: Optional[conint(ge=1, le=100)] = 1
-    """
-    In order to allow good parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes, FFTs on Kohn-Sham states are redistributed to `task` groups so that each group can process several wavefunctions at the same time.
-    """
-    ndiag: Optional[conint(ge=1, le=100)] = 1
-    """
-    A further level of parallelization, independent on PW or k-point parallelization, is the parallelization of subspace diagonalization / iterative orthonormalization. Both operations required the diagonalization of arrays whose dimension is the number of Kohn-Sham states (or a small multiple of it). All such arrays are distributed block-like across the `linear-algebra group`, a subgroup of the pool of processors, organized in a square 2D grid. As a consequence the number of processors in the linear-algebra group is given by n2, where n is an integer; n2 must be smaller than the number of processors in the PW group. The diagonalization is then performed in parallel using standard linear algebra operations.
-    """

package/dist/py/software_directory/modeling/nwchem.py

@@ -1,113 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  software_directory/modeling/nwchem.json
-#   version:   0.25.5
-
-from __future__ import annotations
-
-from enum import Enum
-from typing import List, Optional
-
-from pydantic import BaseModel, ConfigDict, Field
-
-
-class Name(Enum):
-    NWChem = "NWChem"
-
-
-class Summary(Enum):
-    NWChem__a_comprehensive_and_scalable_open_source_solution_for_large_scale_molecular_simulations = (
-        "NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations"
-    )
-
-
-class Version(Enum):
-    field_6_6 = "6.6"
-    field_7_0_2 = "7.0.2"
-
-
-class Exec(Enum):
-    nwchem = "nwchem"
-
-
-class Name146(Enum):
-    default = "default"
-    atomsTooClose = "atomsTooClose"
-    atomsOverlap = "atomsOverlap"
-
-
-class Severity(Enum):
-    info = "info"
-    warning = "warning"
-    error = "error"
-
-
-class ConsistencyCheck(BaseModel):
-    key: str
-    """
-    Key of the property of the entity on which the consistency check is performed in Mongo dot notation, e.g. 'basis.coordinates.1'
-    """
-    name: Name146
-    """
-    Name of the consistency check that is performed, which is listed in an enum.
-    """
-    severity: Severity
-    """
-    Severity level of the problem, which is used in UI to differentiate.
-    """
-    message: str
-    """
-    Message generated by the consistency check describing the problem.
-    """
-
-
-class NWChem(BaseModel):
-    model_config = ConfigDict(
-        extra="allow",
-    )
-    name: Optional[Name] = None
-    """
-    entity name
-    """
-    summary: Optional[Summary] = None
-    """
-    Application's short description.
-    """
-    version: Optional[Version] = None
-    """
-    Application version. e.g. 5.3.5
-    """
-    exec: Optional[Exec] = None
-    shortName: Optional[str] = None
-    """
-    The short name of the application. e.g. qe
-    """
-    build: Optional[str] = None
-    """
-    Application build. e.g. VTST
-    """
-    hasAdvancedComputeOptions: Optional[bool] = None
-    """
-    Whether advanced compute options are present
-    """
-    isLicensed: Optional[bool] = None
-    """
-    Whether licensing is present
-    """
-    field_id: Optional[str] = Field(None, alias="_id")
-    """
-    entity identity
-    """
-    slug: Optional[str] = None
-    """
-    entity slug
-    """
-    systemName: Optional[str] = None
-    consistencyChecks: Optional[List[ConsistencyCheck]] = None
-    schemaVersion: Optional[str] = "2022.8.16"
-    """
-    entity's schema version. Used to distinct between different schemas.
-    """
-    isDefault: Optional[bool] = False
-    """
-    Identifies that entity is defaultable
-    """

package/dist/py/software_directory/modeling/unit/__init__.py

@@ -1,3 +0,0 @@
-# generated by datamodel-codegen:
-#   filename:  schema
-#   version:   0.25.5