arctrl 3.2.0__tar.gz → 3.2.1__tar.gz

{arctrl-3.2.0 → arctrl-3.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arctrl
-Version: 3.2.0
+Version: 3.2.1
 Summary: Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems.
 License-File: LICENSE
 Keywords: arc,annotated research context,isa,research data,multi platform

{arctrl-3.2.0 → arctrl-3.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "arctrl"
-version = "3.2.0"
+version = "3.2.1"
 description = "Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems."
 authors = [
     { name = "Heinrich Lukas Weil", email = "weil@rptu.de" },

{arctrl-3.2.0 → arctrl-3.2.1}/src/ARCtrl/__init__.py

@@ -1,22 +1,26 @@
 from __future__ import annotations
 from collections.abc import Callable
 from typing import Any
-from .py.Contract.contract import Contract
+from .py.Contract.contract import Contract, _DTO as DTO, _DTOType as DTOType, DTO_Spreadsheet, DTO_Text, DTO_CLITool
 from .py.Core.data_context import DataContext
 from .py.Core.datamap import Datamap
 from .py.Core.comment import Comment
 from .py.Core.ontology_annotation import OntologyAnnotation
 from .py.Core.person import Person
 from .py.Core.publication import Publication
-from .py.Core.Table.composite_header import IOType, CompositeHeader
-from .py.Core.Table.composite_cell import CompositeCell
+# Unions are transpiled into an implementation class holding the members and a
+# type alias over the case classes. Only the implementation class carries the
+# factories (`CompositeCell.free_text`, `IOType.source`, ...), so that is what
+# gets the public name here.
+from .py.Core.Table.composite_header import _IOType as IOType, _CompositeHeader as CompositeHeader
+from .py.Core.Table.composite_cell import _CompositeCell as CompositeCell
 from .py.Core.Table.composite_column import CompositeColumn
 from .py.Core.Table.arc_table import ArcTable
 from .py.Core.Table.arc_tables import ArcTables
 from .py.Core.arc_types import ArcAssay, ArcStudy, ArcRun, ArcWorkflow, ArcInvestigation
 from .py.Core.template import Template
 from .py.FileSystem.file_system import FileSystem
-from .py.FileSystem.file_system_tree import FileSystemTree
+from .py.FileSystem.file_system_tree import _FileSystemTree as FileSystemTree
 from .py.json import JsonController
 from .py.yaml import YamlController
 from .py.xlsx import XlsxController

arctrl-3.2.1/src/ARCtrl/cwl.py

@@ -0,0 +1,16 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+# Unions are transpiled into an implementation class holding the members and a
+# type alias over the case classes. The public name has to be the implementation
+# class, otherwise members and `isinstance` are unavailable. See ARCtrl/__init__.py.
+from .py.CWL.cwlprocessing_unit import _CWLProcessingUnit as CWLProcessingUnit
+from .py.CWL.cwltypes import _CWLType as CWLType, FileInstance, DirectoryInstance, DirentInstance, InputEnumSchema, InputRecordField, InputRecordSchema, InputArraySchema, SchemaDefRequirementType, SoftwarePackage
+from .py.CWL.parameter_value import _CWLParameterValue as CWLParameterValue, CWLParameterRecordField
+from .py.CWL.parameter_reference import CWLParameterReference
+from .py.CWL.inputs import CWLInput, InputBinding
+from .py.CWL.outputs import CWLOutput, OutputBinding
+from .py.CWL.tool_description import CWLToolDescription
+from .py.CWL.workflow_description import CWLWorkflowDescription
+from .py.CWL.workflow_steps import WorkflowStep, StepInput, _StepOutput as StepOutput
+from .py.CWL.requirements import _Requirement as Requirement, DockerRequirement, EnvironmentDef, ResourceRequirementInstance

{arctrl-3.2.0 → arctrl-3.2.1}/src/ARCtrl/py/CWL/cwlknown_field_names.py

@@ -9,215 +9,215 @@ from fable_library.core import int32
 from fable_library.set import of_seq
 from fable_library.util import (to_enumerable, compare_primitives, UNIT)
 
-class ObjectExpr796:
+class ObjectExpr883:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-file_instance: Any = of_seq(to_enumerable(["class", "type", "location", "path", "basename", "dirname", "nameroot", "nameext", "checksum", "size", "secondaryFiles", "format", "contents"]), ObjectExpr796())
+file_instance: Any = of_seq(to_enumerable(["class", "type", "location", "path", "basename", "dirname", "nameroot", "nameext", "checksum", "size", "secondaryFiles", "format", "contents"]), ObjectExpr883())
 
-class ObjectExpr797:
+class ObjectExpr884:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-directory_instance: Any = of_seq(to_enumerable(["class", "type", "location", "path", "basename", "listing"]), ObjectExpr797())
+directory_instance: Any = of_seq(to_enumerable(["class", "type", "location", "path", "basename", "listing"]), ObjectExpr884())
 
-class ObjectExpr798:
+class ObjectExpr885:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-dirent_instance: Any = of_seq(to_enumerable(["entry", "entryname", "writable"]), ObjectExpr798())
+dirent_instance: Any = of_seq(to_enumerable(["entry", "entryname", "writable"]), ObjectExpr885())
 
-class ObjectExpr799:
+class ObjectExpr886:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-input_enum_schema: Any = of_seq(to_enumerable(["type", "symbols", "label", "doc", "name"]), ObjectExpr799())
+input_enum_schema: Any = of_seq(to_enumerable(["type", "symbols", "label", "doc", "name"]), ObjectExpr886())
 
-class ObjectExpr800:
+class ObjectExpr887:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-input_record_field: Any = of_seq(to_enumerable(["name", "type", "doc", "label"]), ObjectExpr800())
+input_record_field: Any = of_seq(to_enumerable(["name", "type", "doc", "label"]), ObjectExpr887())
 
-class ObjectExpr801:
+class ObjectExpr889:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-input_record_schema: Any = of_seq(to_enumerable(["type", "fields", "label", "doc", "name"]), ObjectExpr801())
+input_record_schema: Any = of_seq(to_enumerable(["type", "fields", "label", "doc", "name"]), ObjectExpr889())
 
-class ObjectExpr802:
+class ObjectExpr890:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-input_array_schema: Any = of_seq(to_enumerable(["type", "items", "label", "doc", "name"]), ObjectExpr802())
+input_array_schema: Any = of_seq(to_enumerable(["type", "items", "label", "doc", "name"]), ObjectExpr890())
 
-class ObjectExpr803:
+class ObjectExpr892:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-schema_def_requirement_type: Any = of_seq(to_enumerable(["name", "type"]), ObjectExpr803())
+schema_def_requirement_type: Any = of_seq(to_enumerable(["name", "type"]), ObjectExpr892())
 
-class ObjectExpr804:
+class ObjectExpr893:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-software_package: Any = of_seq(to_enumerable(["package", "version", "specs"]), ObjectExpr804())
+software_package: Any = of_seq(to_enumerable(["package", "version", "specs"]), ObjectExpr893())
 
-class ObjectExpr805:
+class ObjectExpr894:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-input_binding: Any = of_seq(to_enumerable(["loadContents", "position", "prefix", "separate", "itemSeparator", "valueFrom", "shellQuote"]), ObjectExpr805())
+input_binding: Any = of_seq(to_enumerable(["loadContents", "position", "prefix", "separate", "itemSeparator", "valueFrom", "shellQuote"]), ObjectExpr894())
 
-class ObjectExpr806:
+class ObjectExpr895:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-cwl_input: Any = of_seq(to_enumerable(["id", "type", "label", "secondaryFiles", "streamable", "doc", "format", "loadContents", "loadListing", "default", "inputBinding"]), ObjectExpr806())
+cwl_input: Any = of_seq(to_enumerable(["id", "type", "label", "secondaryFiles", "streamable", "doc", "format", "loadContents", "loadListing", "default", "inputBinding"]), ObjectExpr895())
 
-class ObjectExpr807:
+class ObjectExpr896:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-output_binding: Any = of_seq(to_enumerable(["loadContents", "loadListing", "glob", "outputEval"]), ObjectExpr807())
+output_binding: Any = of_seq(to_enumerable(["loadContents", "loadListing", "glob", "outputEval"]), ObjectExpr896())
 
-class ObjectExpr808:
+class ObjectExpr897:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-cwl_output: Any = of_seq(to_enumerable(["id", "type", "label", "secondaryFiles", "streamable", "doc", "format", "outputBinding", "outputSource"]), ObjectExpr808())
+cwl_output: Any = of_seq(to_enumerable(["id", "type", "label", "secondaryFiles", "streamable", "doc", "format", "outputBinding", "outputSource"]), ObjectExpr897())
 
-class ObjectExpr809:
+class ObjectExpr898:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-docker_requirement: Any = of_seq(to_enumerable(["class", "dockerPull", "dockerFile", "dockerImageId", "dockerLoad", "dockerImport", "dockerOutputDirectory", "cwltool:dockerRunOptions"]), ObjectExpr809())
+docker_requirement: Any = of_seq(to_enumerable(["class", "dockerPull", "dockerFile", "dockerImageId", "dockerLoad", "dockerImport", "dockerOutputDirectory", "cwltool:dockerRunOptions"]), ObjectExpr898())
 
-class ObjectExpr810:
+class ObjectExpr899:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-environment_def: Any = of_seq(to_enumerable(["envName", "envValue"]), ObjectExpr810())
+environment_def: Any = of_seq(to_enumerable(["envName", "envValue"]), ObjectExpr899())
 
-class ObjectExpr811:
+class ObjectExpr900:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-load_listing_requirement_value: Any = of_seq(to_enumerable(["class", "loadListing"]), ObjectExpr811())
+load_listing_requirement_value: Any = of_seq(to_enumerable(["class", "loadListing"]), ObjectExpr900())
 
-class ObjectExpr812:
+class ObjectExpr902:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-work_reuse_requirement_value: Any = of_seq(to_enumerable(["class", "enableReuse"]), ObjectExpr812())
+work_reuse_requirement_value: Any = of_seq(to_enumerable(["class", "enableReuse"]), ObjectExpr902())
 
-class ObjectExpr813:
+class ObjectExpr904:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-network_access_requirement_value: Any = of_seq(to_enumerable(["class", "networkAccess"]), ObjectExpr813())
+network_access_requirement_value: Any = of_seq(to_enumerable(["class", "networkAccess"]), ObjectExpr904())
 
-class ObjectExpr814:
+class ObjectExpr905:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-inplace_update_requirement_value: Any = of_seq(to_enumerable(["class", "inplaceUpdate"]), ObjectExpr814())
+inplace_update_requirement_value: Any = of_seq(to_enumerable(["class", "inplaceUpdate"]), ObjectExpr905())
 
-class ObjectExpr815:
+class ObjectExpr906:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-resource_requirement_instance: Any = of_seq(to_enumerable(["class", "coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"]), ObjectExpr815())
+resource_requirement_instance: Any = of_seq(to_enumerable(["class", "coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"]), ObjectExpr906())
 
-class ObjectExpr816:
+class ObjectExpr907:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-inline_javascript_requirement_value: Any = of_seq(to_enumerable(["class", "expressionLib"]), ObjectExpr816())
+inline_javascript_requirement_value: Any = of_seq(to_enumerable(["class", "expressionLib"]), ObjectExpr907())
 
-class ObjectExpr817:
+class ObjectExpr908:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-hint_unknown_value: Any = of_seq(to_enumerable(["class", "raw"]), ObjectExpr817())
+hint_unknown_value: Any = of_seq(to_enumerable(["class", "raw"]), ObjectExpr908())
 
-class ObjectExpr818:
+class ObjectExpr909:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-tool_description: Any = of_seq(to_enumerable(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]), ObjectExpr818())
+tool_description: Any = of_seq(to_enumerable(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]), ObjectExpr909())
 
-class ObjectExpr819:
+class ObjectExpr910:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-expression_tool_description: Any = of_seq(to_enumerable(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "expression"]), ObjectExpr819())
+expression_tool_description: Any = of_seq(to_enumerable(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "expression"]), ObjectExpr910())
 
-class ObjectExpr820:
+class ObjectExpr911:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-operation_description: Any = of_seq(to_enumerable(["inputs", "outputs", "label", "doc", "intent", "class", "id", "requirements", "hints", "cwlVersion"]), ObjectExpr820())
+operation_description: Any = of_seq(to_enumerable(["inputs", "outputs", "label", "doc", "intent", "class", "id", "requirements", "hints", "cwlVersion"]), ObjectExpr911())
 
-class ObjectExpr821:
+class ObjectExpr912:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-workflow_description: Any = of_seq(to_enumerable(["inputs", "outputs", "label", "doc", "intent", "class", "steps", "id", "requirements", "hints", "cwlVersion"]), ObjectExpr821())
+workflow_description: Any = of_seq(to_enumerable(["inputs", "outputs", "label", "doc", "intent", "class", "steps", "id", "requirements", "hints", "cwlVersion"]), ObjectExpr912())
 
-class ObjectExpr822:
+class ObjectExpr913:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-step_input: Any = of_seq(to_enumerable(["id", "source", "default", "valueFrom", "linkMerge", "pickValue", "doc", "loadContents", "loadListing", "label"]), ObjectExpr822())
+step_input: Any = of_seq(to_enumerable(["id", "source", "default", "valueFrom", "linkMerge", "pickValue", "doc", "loadContents", "loadListing", "label"]), ObjectExpr913())
 
-class ObjectExpr823:
+class ObjectExpr914:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-step_output_parameter: Any = of_seq(to_enumerable(["id"]), ObjectExpr823())
+step_output_parameter: Any = of_seq(to_enumerable(["id"]), ObjectExpr914())
 
-class ObjectExpr824:
+class ObjectExpr915:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-workflow_step: Any = of_seq(to_enumerable(["id", "run", "in", "out", "requirements", "hints", "label", "doc", "scatter", "scatterMethod", "when"]), ObjectExpr824())
+workflow_step: Any = of_seq(to_enumerable(["id", "run", "in", "out", "requirements", "hints", "label", "doc", "scatter", "scatterMethod", "when"]), ObjectExpr915())
 
-class ObjectExpr825:
+class ObjectExpr916:
     def Compare(self, x: str, y: str) -> int32:
         return compare_primitives(x, y)
 
 
-parameter_reference: Any = of_seq(to_enumerable(["class", "path", "location", "type", "value"]), ObjectExpr825())
+parameter_reference: Any = of_seq(to_enumerable(["class", "path", "location", "type", "value"]), ObjectExpr916())
 
 __all__ = ["cwl_input", "cwl_output", "directory_instance", "dirent_instance", "docker_requirement", "environment_def", "expression_tool_description", "file_instance", "hint_unknown_value", "inline_javascript_requirement_value", "inplace_update_requirement_value", "input_array_schema", "input_binding", "input_enum_schema", "input_record_field", "input_record_schema", "load_listing_requirement_value", "network_access_requirement_value", "operation_description", "output_binding", "parameter_reference", "resource_requirement_instance", "schema_def_requirement_type", "software_package", "step_input", "step_output_parameter", "tool_description", "work_reuse_requirement_value", "workflow_description", "workflow_step"]