arctrl 3.0.0a3__tar.gz

arctrl-3.0.0a3/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 DataPLANT
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

arctrl-3.0.0a3/PKG-INFO

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+Metadata-Version: 2.3
+Name: arctrl
+Version: 3.0.0a3
+Summary: Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems.
+Keywords: arc,annotated research context,isa,research data,multi platform
+Author: Heinrich Lukas Weil
+Author-email: weil@rptu.de
+Maintainer: Florian Wetzels
+Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+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
+
+> **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
+
+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` ✨
+
+## 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 |  5 | 21 | 226 |
+| Table_AddRows | Add 10000 rows to a table with 4 columns. |  15 | 22 | 289 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 49 | 108 | 4813 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1099 | 481 | 6833 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  261 |  2266 | 717334 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  915 | 2459 | 28799 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  97 | 87 | 1249 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  621 | 379 | 9974 |
+

arctrl-3.0.0a3/README.md

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+
+![logo](logos/ARCtrl_horizontal.png)
+
+# ARCtrl
+
+> **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
+
+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` ✨
+
+## 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 |  5 | 21 | 226 |
+| Table_AddRows | Add 10000 rows to a table with 4 columns. |  15 | 22 | 289 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 49 | 108 | 4813 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1099 | 481 | 6833 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  261 |  2266 | 717334 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  915 | 2459 | 28799 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  97 | 87 | 1249 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  621 | 379 | 9974 |

arctrl-3.0.0a3/pyproject.toml

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+[project]
+name = "arctrl"
+version = "3.0.0a3"
+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 = ">=3.11"
+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",
+]
+
+[project.urls]
+Repository = "https://github.com/nfdi4plants/ARCtrl"
+
+[dependency-groups]
+dev = ["pytest>=8.1.1,<9"]
+
+[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-3.0.0a3/src/ARCtrl/__init__.py

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+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from .py.Contract.contract import Contract
+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
+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.json import JsonController
+from .py.xlsx import XlsxController
+from .py.arc import ARC

arctrl-3.0.0a3/src/ARCtrl/py/CWL/cwltypes.py

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+from __future__ import annotations
+from dataclasses import dataclass
+from typing import Any
+from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
+from ..fable_modules.dynamic_obj.dyn_obj import set_property
+from ..fable_modules.fable_library.reflection import (TypeInfo, class_type, string_type, option_type, bool_type, record_type, union_type, array_type)
+from ..fable_modules.fable_library.types import (Record, Array, Union, FSharpRef)
+
+def _expr2998() -> TypeInfo:
+    return class_type("ARCtrl.CWL.FileInstance", None, FileInstance, DynamicObj_reflection())
+
+
+class FileInstance(DynamicObj):
+    def __init__(self, __unit: None=None) -> None:
+        super().__init__()
+        pass
+
+
+FileInstance_reflection = _expr2998
+
+def FileInstance__ctor(__unit: None=None) -> FileInstance:
+    return FileInstance(__unit)
+
+
+def _expr2999() -> TypeInfo:
+    return class_type("ARCtrl.CWL.DirectoryInstance", None, DirectoryInstance, DynamicObj_reflection())
+
+
+class DirectoryInstance(DynamicObj):
+    def __init__(self, __unit: None=None) -> None:
+        super().__init__()
+        pass
+
+
+DirectoryInstance_reflection = _expr2999
+
+def DirectoryInstance__ctor(__unit: None=None) -> DirectoryInstance:
+    return DirectoryInstance(__unit)
+
+
+def _expr3000() -> TypeInfo:
+    return record_type("ARCtrl.CWL.DirentInstance", [], DirentInstance, lambda: [("Entry", string_type), ("Entryname", option_type(string_type)), ("Writable", option_type(bool_type))])
+
+
+@dataclass(eq = False, repr = False, slots = True)
+class DirentInstance(Record):
+    Entry: str
+    Entryname: str | None
+    Writable: bool | None
+
+DirentInstance_reflection = _expr3000
+
+def _expr3001() -> TypeInfo:
+    return union_type("ARCtrl.CWL.CWLType", [], CWLType, lambda: [[("Item", FileInstance_reflection())], [("Item", DirectoryInstance_reflection())], [("Item", DirentInstance_reflection())], [], [], [], [], [], [], [], [], [("Item", CWLType_reflection())]])
+
+
+class CWLType(Union):
+    def __init__(self, tag: int, *fields: Any) -> None:
+        super().__init__()
+        self.tag: int = tag or 0
+        self.fields: Array[Any] = list(fields)
+
+    @staticmethod
+    def cases() -> list[str]:
+        return ["File", "Directory", "Dirent", "String", "Int", "Long", "Float", "Double", "Boolean", "Stdout", "Null", "Array"]
+
+
+CWLType_reflection = _expr3001
+
+def _expr3002() -> TypeInfo:
+    return class_type("ARCtrl.CWL.InputRecordSchema", None, InputRecordSchema, DynamicObj_reflection())
+
+
+class InputRecordSchema(DynamicObj):
+    def __init__(self, __unit: None=None) -> None:
+        super().__init__()
+        pass
+
+
+InputRecordSchema_reflection = _expr3002
+
+def InputRecordSchema__ctor(__unit: None=None) -> InputRecordSchema:
+    return InputRecordSchema(__unit)
+
+
+def _expr3003() -> TypeInfo:
+    return class_type("ARCtrl.CWL.InputEnumSchema", None, InputEnumSchema, DynamicObj_reflection())
+
+
+class InputEnumSchema(DynamicObj):
+    def __init__(self, __unit: None=None) -> None:
+        super().__init__()
+        pass
+
+
+InputEnumSchema_reflection = _expr3003
+
+def InputEnumSchema__ctor(__unit: None=None) -> InputEnumSchema:
+    return InputEnumSchema(__unit)
+
+
+def _expr3004() -> TypeInfo:
+    return class_type("ARCtrl.CWL.InputArraySchema", None, InputArraySchema, DynamicObj_reflection())
+
+
+class InputArraySchema(DynamicObj):
+    def __init__(self, __unit: None=None) -> None:
+        super().__init__()
+        pass
+
+
+InputArraySchema_reflection = _expr3004
+
+def InputArraySchema__ctor(__unit: None=None) -> InputArraySchema:
+    return InputArraySchema(__unit)
+
+
+def _expr3005() -> TypeInfo:
+    return class_type("ARCtrl.CWL.SchemaDefRequirementType", None, SchemaDefRequirementType, DynamicObj_reflection())
+
+
+class SchemaDefRequirementType(DynamicObj):
+    def __init__(self, types: Any=None, definitions: Any=None) -> None:
+        super().__init__()
+        this: FSharpRef[SchemaDefRequirementType] = FSharpRef(None)
+        this.contents = self
+        self.init_004047: int = 1
+        set_property("types", definitions, this.contents)
+
+
+SchemaDefRequirementType_reflection = _expr3005
+
+def SchemaDefRequirementType__ctor_541DA560(types: Any=None, definitions: Any=None) -> SchemaDefRequirementType:
+    return SchemaDefRequirementType(types, definitions)
+
+
+def _expr3006() -> TypeInfo:
+    return record_type("ARCtrl.CWL.SoftwarePackage", [], SoftwarePackage, lambda: [("Package", string_type), ("Version", option_type(array_type(string_type))), ("Specs", option_type(array_type(string_type)))])
+
+
+@dataclass(eq = False, repr = False, slots = True)
+class SoftwarePackage(Record):
+    Package: str
+    Version: Array[str] | None
+    Specs: Array[str] | None
+
+SoftwarePackage_reflection = _expr3006
+
+__all__ = ["FileInstance_reflection", "DirectoryInstance_reflection", "DirentInstance_reflection", "CWLType_reflection", "InputRecordSchema_reflection", "InputEnumSchema_reflection", "InputArraySchema_reflection", "SchemaDefRequirementType_reflection", "SoftwarePackage_reflection"]
+