arctrl 3.2.0__tar.gz → 3.2.2__tar.gz

arctrl-3.2.2/PKG-INFO

@@ -0,0 +1,158 @@
+Metadata-Version: 2.4
+Name: arctrl
+Version: 3.2.2
+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
+Author: Heinrich Lukas Weil
+Author-email: weil@rptu.de
+Maintainer: Florian Wetzels
+Requires-Python: >=3.12
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3.15
+Requires-Dist: fable-library (==5.18.0)
+Requires-Dist: openpyxl (>=3.1.5,<4)
+Requires-Dist: requests (>=2.28.1,<3.0.0)
+Project-URL: Repository, https://github.com/nfdi4plants/ARCtrl
+Description-Content-Type: text/markdown
+
+
+![logo](logos/ARCtrl_horizontal.png)
+
+# ARCtrl
+
+[![DOI](https://img.shields.io/badge/Cite%20Us-10.5281%2Fzenodo.15194394-008273?logo=zenodo&logoColor=C70039)](https://doi.org/10.5281/zenodo.15194394)
+
+> **ARCtrl** the easy way to read, manipulate and write ARCs in __.NET__, __JavaScript__ and __Python__! ❤️
+
+| Version | Downloads |
+| :--------|-----------:|
+|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/v/ARCtrl?logo=nuget&color=%234fb3d9"></a>|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9"></a>|
+|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/v/%40nfdi4plants/arctrl?logo=npm&color=%234fb3d9"></a>|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9"></a>|
+|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pypi/v/arctrl?logo=pypi&color=%234fb3d9"></a>|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pepy/dt/arctrl?color=%234fb3d9"></a>|
+
+## Install
+
+#### .NET
+
+```fsharp
+#r "nuget: ARCtrl"
+```
+
+```bash
+<PackageReference Include="ARCtrl" Version="1.1.0" />
+```
+
+#### JavaScript
+
+```bash
+npm i @nfdi4plants/arctrl
+```
+
+#### Python
+
+```bash
+pip install arctrl
+```
+
+## Docs
+
+Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arctrl/)
+
+## Development
+
+#### Requirements
+
+- [nodejs and npm](https://nodejs.org/en/download)
+    - verify with `node --version` (Tested with v18.16.1)
+    - verify with `npm --version` (Tested with v9.2.0)
+- [.NET SDK](https://dotnet.microsoft.com/en-us/download)
+    - verify with `dotnet --version` (Tested with 7.0.306)
+- [Python](https://www.python.org/downloads/)
+    - verify with `py --version` (Tested with 3.12.2, known to work only for >=3.11)
+
+#### Local Setup
+
+##### Windows
+
+On windows you can use the `setup.cmd` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+
+    `npm install`
+
+3. Setup python environment
+
+    `py -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
+   2. `.\.venv\Scripts\python.exe -m pip install uv`
+   3. `.\.venv\Scripts\python.exe -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `./build.cmd runtests` ✨
+
+##### Linux / macOS
+
+On unix you can use the `setup.sh` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+
+    `npm install`
+
+3. Setup python environment
+
+    `python -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.venv/bin/python -m pip install -U pip setuptools`
+   2. `.venv/bin/python -m pip install uv`
+   3. `.venv/bin/python -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `bash build.sh runtests` ✨
+
+## Branding
+
+Feel free to reference `ARCtrl` on slides or elsewhere using our logos:
+
+|Square | Horizontal | Vertical |
+| - | - | - |
+| ![square](logos/ARCtrl_square.png) | ![horizontal](logos/ARCtrl_horizontal.png) |  ![vertical](logos/ARCtrl_vertical.png) |
+
+## Performance
+
+Measured on 13th Gen Intel(R) Core(TM) i7-13800H
+
+| Name | Description | FSharp Time (ms) | JavaScript Time (ms) | Python Time (ms) |
+| --- | --- | --- | --- | --- |
+| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code | 0 ± 0 | 0 ± 1 | 91 ± 12 |
+| Table_AddDistinctRows | Add 10000 distinct rows to a table with 4 columns. | 13 ± 2 | 14 ± 4 | 119 ± 12 |
+| Table_AddIdenticalRows | Add 10000 identical rows to a table with 4 columns. | 6 ± 2 | 6 ± 1 | 104 ± 6 |
+| Table_AddColumnsWithDistinctValues | Add 4 columns with 10000 distinct values each. | 8 ± 3 | 10 ± 1 | 53 ± 1 |
+| Table_AddColumnsWithIdenticalValues | Add 4 columns with 10000 identical values each. | 5 ± 1 | 4 ± 0 | 47 ± 1 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 0 ± 0 |  2 ± 1 | 6 ± 4 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json, with 3 fixed and 2 variable columns. | 227 ± 64 | 68 ± 18 | 7851 ± 1411 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json, with 3 fixed and 2 variable columns. | 147 ± 15 | 2878 ± 135 | 6303 ± 1798 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json, with 3 fixed and 3 variable columns. | 330 ± 36 | 88 ± 9 | 12644 ± 550 |
+| Assay_fromJson | Parse an assay with one table with 10000 rows and 6 columns from json, with 3 fixed and 3 variable columns. | 355 ± 66 | 61 ± 6 | 6499 ± 1068 |
+| Assay_toISAJson | Parse an assay with one table with 10000 rows and 6 columns to json, with 3 fixed and 3 variable columns | 487 ± 36 | 959 ± 36 | 15618 ± 482 |
+| Assay_fromISAJson | Parse an assay with one table with 10000 rows and 6 columns from json, with 3 fixed and 3 variable columns | 359 ± 29 | 706 ± 46 | 9587 ± 621 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy | 29 ± 14 | 62 ± 5 | 818 ± 36 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook | 240 ± 31 | 284 ± 24 | 3657 ± 199 |
+| Investigation_FromWorkbook_ManyStudies | Parse a workbook with 1500 studies to an ArcInvestigation | 127 ± 20 | 498 ± 21 | 9469 ± 412 |
+| ARC_ToROCrate | Parse an ARC with one assay with 10000 rows and 6 columns to a RO-Crate metadata file. | 1431 ± 99 | 3526 ± 264 | 61224 ± 728 |

arctrl-3.2.2/pyproject.toml

@@ -0,0 +1,44 @@
+[project]
+name = "arctrl"
+version = "3.2.2"
+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" },
+    { name = "Kevin Frey", email = "freymaurer@gmx.de" },
+]
+requires-python = ">=3.12"
+readme = "README.md"
+maintainers = [{ name = "Florian Wetzels" }]
+keywords = [
+    "arc",
+    "annotated research context",
+    "isa",
+    "research data",
+    "multi platform",
+]
+dependencies = [
+    "requests>= 2.28.1, <3.0.0",
+    "openpyxl>=3.1.5,<4",
+    "fable-library==5.18.0"
+]
+
+[project.urls]
+Repository = "https://github.com/nfdi4plants/ARCtrl"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.1.1,<9",
+    "twine>=4.0.2"
+]
+
+[tool.poetry]
+include = [
+    "src/ARCtrl/py/**/*.py"
+]
+packages = [
+    { include = "**/*.py", from = "src/ARCtrl/", to = "arctrl" }
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

arctrl-3.2.2/src/ARCtrl/__init__.py

@@ -0,0 +1,28 @@
+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+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
+# 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 as FileSystemTree
+from .py.json import JsonController
+from .py.yaml import YamlController
+from .py.xlsx import XlsxController
+from .py.arc import ARC
+from fable_library.async_ import start_as_task

arctrl-3.2.2/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-3.2.2/src/ARCtrl/py/CWL/cwlknown_field_names.py

@@ -0,0 +1,221 @@
+"""Backing values for KnownFieldNames static properties.
+
+Fable's Python backend cannot initialize non-trivial static property getters
+on AttachMembers types and otherwise emits None. Plain references to these
+module-level values compile consistently across .NET, JavaScript, and Python.
+"""
+from fable_library.set import (of_seq, FSharpSet)
+from fable_library.util import (to_enumerable, compare_primitives, UNIT)
+
+class ObjectExpr852:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+file_instance: FSharpSet[str] = of_seq(to_enumerable(["class", "type", "location", "path", "basename", "dirname", "nameroot", "nameext", "checksum", "size", "secondaryFiles", "format", "contents"]), ObjectExpr852())
+
+class ObjectExpr853:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+directory_instance: FSharpSet[str] = of_seq(to_enumerable(["class", "type", "location", "path", "basename", "listing"]), ObjectExpr853())
+
+class ObjectExpr854:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+dirent_instance: FSharpSet[str] = of_seq(to_enumerable(["entry", "entryname", "writable"]), ObjectExpr854())
+
+class ObjectExpr855:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+input_enum_schema: FSharpSet[str] = of_seq(to_enumerable(["type", "symbols", "label", "doc", "name"]), ObjectExpr855())
+
+class ObjectExpr856:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+input_record_field: FSharpSet[str] = of_seq(to_enumerable(["name", "type", "doc", "label"]), ObjectExpr856())
+
+class ObjectExpr857:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+input_record_schema: FSharpSet[str] = of_seq(to_enumerable(["type", "fields", "label", "doc", "name"]), ObjectExpr857())
+
+class ObjectExpr858:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+input_array_schema: FSharpSet[str] = of_seq(to_enumerable(["type", "items", "label", "doc", "name"]), ObjectExpr858())
+
+class ObjectExpr859:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+schema_def_requirement_type: FSharpSet[str] = of_seq(to_enumerable(["name", "type"]), ObjectExpr859())
+
+class ObjectExpr860:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+software_package: FSharpSet[str] = of_seq(to_enumerable(["package", "version", "specs"]), ObjectExpr860())
+
+class ObjectExpr862:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+input_binding: FSharpSet[str] = of_seq(to_enumerable(["loadContents", "position", "prefix", "separate", "itemSeparator", "valueFrom", "shellQuote"]), ObjectExpr862())
+
+class ObjectExpr864:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+cwl_input: FSharpSet[str] = of_seq(to_enumerable(["id", "type", "label", "secondaryFiles", "streamable", "doc", "format", "loadContents", "loadListing", "default", "inputBinding"]), ObjectExpr864())
+
+class ObjectExpr865:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+output_binding: FSharpSet[str] = of_seq(to_enumerable(["loadContents", "loadListing", "glob", "outputEval"]), ObjectExpr865())
+
+class ObjectExpr866:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+cwl_output: FSharpSet[str] = of_seq(to_enumerable(["id", "type", "label", "secondaryFiles", "streamable", "doc", "format", "outputBinding", "outputSource"]), ObjectExpr866())
+
+class ObjectExpr867:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+docker_requirement: FSharpSet[str] = of_seq(to_enumerable(["class", "dockerPull", "dockerFile", "dockerImageId", "dockerLoad", "dockerImport", "dockerOutputDirectory", "cwltool:dockerRunOptions"]), ObjectExpr867())
+
+class ObjectExpr868:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+environment_def: FSharpSet[str] = of_seq(to_enumerable(["envName", "envValue"]), ObjectExpr868())
+
+class ObjectExpr869:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+load_listing_requirement_value: FSharpSet[str] = of_seq(to_enumerable(["class", "loadListing"]), ObjectExpr869())
+
+class ObjectExpr871:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+work_reuse_requirement_value: FSharpSet[str] = of_seq(to_enumerable(["class", "enableReuse"]), ObjectExpr871())
+
+class ObjectExpr872:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+network_access_requirement_value: FSharpSet[str] = of_seq(to_enumerable(["class", "networkAccess"]), ObjectExpr872())
+
+class ObjectExpr873:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+inplace_update_requirement_value: FSharpSet[str] = of_seq(to_enumerable(["class", "inplaceUpdate"]), ObjectExpr873())
+
+class ObjectExpr875:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+resource_requirement_instance: FSharpSet[str] = of_seq(to_enumerable(["class", "coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"]), ObjectExpr875())
+
+class ObjectExpr876:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+inline_javascript_requirement_value: FSharpSet[str] = of_seq(to_enumerable(["class", "expressionLib"]), ObjectExpr876())
+
+class ObjectExpr877:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+hint_unknown_value: FSharpSet[str] = of_seq(to_enumerable(["class", "raw"]), ObjectExpr877())
+
+class ObjectExpr879:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+tool_description: FSharpSet[str] = of_seq(to_enumerable(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]), ObjectExpr879())
+
+class ObjectExpr881:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+expression_tool_description: FSharpSet[str] = of_seq(to_enumerable(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "expression"]), ObjectExpr881())
+
+class ObjectExpr882:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+operation_description: FSharpSet[str] = of_seq(to_enumerable(["inputs", "outputs", "label", "doc", "intent", "class", "id", "requirements", "hints", "cwlVersion"]), ObjectExpr882())
+
+class ObjectExpr883:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+workflow_description: FSharpSet[str] = of_seq(to_enumerable(["inputs", "outputs", "label", "doc", "intent", "class", "steps", "id", "requirements", "hints", "cwlVersion"]), ObjectExpr883())
+
+class ObjectExpr884:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+step_input: FSharpSet[str] = of_seq(to_enumerable(["id", "source", "default", "valueFrom", "linkMerge", "pickValue", "doc", "loadContents", "loadListing", "label"]), ObjectExpr884())
+
+class ObjectExpr885:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+step_output_parameter: FSharpSet[str] = of_seq(to_enumerable(["id"]), ObjectExpr885())
+
+class ObjectExpr886:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+workflow_step: FSharpSet[str] = of_seq(to_enumerable(["id", "run", "in", "out", "requirements", "hints", "label", "doc", "scatter", "scatterMethod", "when"]), ObjectExpr886())
+
+class ObjectExpr887:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+parameter_reference: FSharpSet[str] = of_seq(to_enumerable(["class", "path", "location", "type", "value"]), ObjectExpr887())
+
+__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"]
+