ARCtrl 3.2.1__tar.gz → 3.2.3__tar.gz

arctrl-3.2.3/PKG-INFO

@@ -0,0 +1,94 @@
+Metadata-Version: 2.4
+Name: arctrl
+Version: 3.2.3
+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/)
+
+## 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-3.2.3/README.md

@@ -0,0 +1,73 @@
+
+![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/)
+
+## 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-3.2.3/pyproject.toml

@@ -0,0 +1,44 @@
+[project]
+name = "arctrl"
+version = "3.2.3"
+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-3.2.3/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 ObjectExpr821:
+    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"]), ObjectExpr821())
+
+class ObjectExpr823:
+    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"]), ObjectExpr823())
+
+class ObjectExpr824:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+dirent_instance: FSharpSet[str] = of_seq(to_enumerable(["entry", "entryname", "writable"]), ObjectExpr824())
+
+class ObjectExpr825:
+    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"]), ObjectExpr825())
+
+class ObjectExpr826:
+    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"]), ObjectExpr826())
+
+class ObjectExpr827:
+    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"]), ObjectExpr827())
+
+class ObjectExpr828:
+    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"]), ObjectExpr828())
+
+class ObjectExpr829:
+    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"]), ObjectExpr829())
+
+class ObjectExpr830:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+software_package: FSharpSet[str] = of_seq(to_enumerable(["package", "version", "specs"]), ObjectExpr830())
+
+class ObjectExpr831:
+    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"]), ObjectExpr831())
+
+class ObjectExpr832:
+    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"]), ObjectExpr832())
+
+class ObjectExpr833:
+    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"]), ObjectExpr833())
+
+class ObjectExpr834:
+    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"]), ObjectExpr834())
+
+class ObjectExpr835:
+    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"]), ObjectExpr835())
+
+class ObjectExpr836:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+environment_def: FSharpSet[str] = of_seq(to_enumerable(["envName", "envValue"]), ObjectExpr836())
+
+class ObjectExpr837:
+    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"]), ObjectExpr837())
+
+class ObjectExpr838:
+    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"]), ObjectExpr838())
+
+class ObjectExpr839:
+    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"]), ObjectExpr839())
+
+class ObjectExpr840:
+    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"]), ObjectExpr840())
+
+class ObjectExpr841:
+    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"]), ObjectExpr841())
+
+class ObjectExpr842:
+    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"]), ObjectExpr842())
+
+class ObjectExpr844:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+hint_unknown_value: FSharpSet[str] = of_seq(to_enumerable(["class", "raw"]), ObjectExpr844())
+
+class ObjectExpr846:
+    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"]), ObjectExpr846())
+
+class ObjectExpr847:
+    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"]), ObjectExpr847())
+
+class ObjectExpr848:
+    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"]), ObjectExpr848())
+
+class ObjectExpr849:
+    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"]), ObjectExpr849())
+
+class ObjectExpr850:
+    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"]), ObjectExpr850())
+
+class ObjectExpr851:
+    def Compare(self, x: str, y: str) -> int:
+        return compare_primitives(x, y)
+
+
+step_output_parameter: FSharpSet[str] = of_seq(to_enumerable(["id"]), ObjectExpr851())
+
+class ObjectExpr852:
+    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"]), ObjectExpr852())
+
+class ObjectExpr853:
+    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"]), ObjectExpr853())
+
+__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"]
+