From 062ee63222572685edcc21f5f9532bfd4c9fb3cd Mon Sep 17 00:00:00 2001 From: Kevin Schneider Date: Wed, 3 Jan 2024 14:03:31 +0100 Subject: [PATCH] update docs to latest fsdocs with ipynb input --- .config/dotnet-tools.json | 8 +- .github/workflows/publish-docs.yml | 8 +- .gitignore | 1 + ARCTokenization.sln | 33 +--- build/DocumentationTasks.fs | 64 ++++--- docs/ARCTokenization/Introduction.ipynb | 59 ++++++ docs/ControlledVocabulary/CvParam.ipynb | 172 ++++++++++++++++++ .../Introduction.ipynb} | 94 +++++++--- docs/convert-notebook.ps1 | 6 - docs/convert-notebooks.ps1 | 14 -- docs/docfx_project/.gitignore | 9 - docs/docfx_project/ARCTokenization/intro.md | 2 - .../ControlledVocabulary/CvParam.ipynb | 117 ------------ .../ControlledVocabulary/CvParam.md | 44 ----- .../ControlledVocabulary/index.md | 95 ---------- .../ControlledVocabulary/intro.md | 64 ------- docs/docfx_project/api/.gitignore | 5 - docs/docfx_project/api/index.md | 2 - docs/docfx_project/docfx.json | 69 ------- docs/docfx_project/index.md | 4 - docs/docfx_project/toc.yml | 15 -- docs/index.ipynb | 51 ++++++ src/ARCTokenization/RELEASE_NOTES.md | 3 +- .../arc_file_structure_ontology.obo | 2 +- .../assay_metadata_structural_ontology.obo | 2 +- ...stigation_metadata_structural_ontology.obo | 2 +- .../study_metadata_structural_ontology.obo | 2 +- 27 files changed, 414 insertions(+), 533 deletions(-) create mode 100644 docs/ARCTokenization/Introduction.ipynb create mode 100644 docs/ControlledVocabulary/CvParam.ipynb rename docs/{docfx_project/ControlledVocabulary/intro.ipynb => ControlledVocabulary/Introduction.ipynb} (54%) delete mode 100644 docs/convert-notebook.ps1 delete mode 100644 docs/convert-notebooks.ps1 delete mode 100644 docs/docfx_project/.gitignore delete mode 100644 docs/docfx_project/ARCTokenization/intro.md delete mode 100644 docs/docfx_project/ControlledVocabulary/CvParam.ipynb delete mode 100644 docs/docfx_project/ControlledVocabulary/CvParam.md delete mode 100644 docs/docfx_project/ControlledVocabulary/index.md delete mode 100644 docs/docfx_project/ControlledVocabulary/intro.md delete mode 100644 docs/docfx_project/api/.gitignore delete mode 100644 docs/docfx_project/api/index.md delete mode 100644 docs/docfx_project/docfx.json delete mode 100644 docs/docfx_project/index.md delete mode 100644 docs/docfx_project/toc.yml create mode 100644 docs/index.ipynb diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json index 1238f3c..e67b77a 100644 --- a/.config/dotnet-tools.json +++ b/.config/dotnet-tools.json @@ -3,15 +3,15 @@ "isRoot": true, "tools": { "fsdocs-tool": { - "version": "18.1.1", + "version": "20.0.0-alpha-016", "commands": [ "fsdocs" ] }, - "docfx": { - "version": "2.70.1", + "dotnet-repl": { + "version": "0.1.208", "commands": [ - "docfx" + "dotnet-repl" ] } } diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml index 7020190..d2c77da 100644 --- a/.github/workflows/publish-docs.yml +++ b/.github/workflows/publish-docs.yml @@ -13,16 +13,12 @@ jobs: steps: - name: Checkout uses: actions/checkout@v3 - - name: Setup .NET 6.0 + - name: Setup .NET 8.0 uses: actions/setup-dotnet@v3 with: - dotnet-version: '6.0.x' + dotnet-version: '8.0.x' - name: Restore tools run: dotnet tool restore - - name: setup-conda - uses: s-weigand/setup-conda@v1.1.1 - - name: install nbconvert - run: conda install nbconvert -y - name: make script executable run: chmod u+x build.sh - name: Build docs diff --git a/.gitignore b/.gitignore index 1d20b13..aca1760 100644 --- a/.gitignore +++ b/.gitignore @@ -352,3 +352,4 @@ MigrationBackup/ /tests/ArcGraphModel.JsNativeTests/fable/**/*.js.map /.fsdocs /tmp/watch +/output diff --git a/ARCTokenization.sln b/ARCTokenization.sln index 6c2a36e..935834b 100644 --- a/ARCTokenization.sln +++ b/ARCTokenization.sln @@ -40,35 +40,21 @@ EndProject Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCTokenization.Tests", "tests\ARCTokenization.Tests\ARCTokenization.Tests.fsproj", "{30177EF1-3980-4FFE-9B49-90B75DCEBDA3}" EndProject Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{551D4715-5ECD-4CAB-8A4A-41E246F4A7B5}" -EndProject -Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docfx_project", "docfx_project", "{86CD7F81-ADB4-4991-A960-063FE02D907D}" ProjectSection(SolutionItems) = preProject - docs\docfx_project\.gitignore = docs\docfx_project\.gitignore - docs\convert-notebook.ps1 = docs\convert-notebook.ps1 - docs\convert-notebooks.ps1 = docs\convert-notebooks.ps1 - docs\docfx_project\docfx.json = docs\docfx_project\docfx.json - docs\docfx_project\index.md = docs\docfx_project\index.md - docs\docfx_project\toc.yml = docs\docfx_project\toc.yml + docs\index.ipynb = docs\index.ipynb EndProjectSection EndProject -Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ARCTokenization", "ARCTokenization", "{E669BA6D-4327-40AE-8CE1-E6FEA8F89A15}" +Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ARCTokenization", "ARCTokenization", "{699C5B9A-EA4B-4D25-B05D-16CA14320CFB}" ProjectSection(SolutionItems) = preProject - docs\docfx_project\ARCTokenization\intro.md = docs\docfx_project\ARCTokenization\intro.md + docs\ARCTokenization\Introduction.ipynb = docs\ARCTokenization\Introduction.ipynb EndProjectSection EndProject -Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ControlledVocabulary", "ControlledVocabulary", "{F6471491-8FE4-48A7-BA9E-1113DE63B5F5}" +Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "ControlledVocabulary", "ControlledVocabulary", "{524F5156-C079-4AEF-822E-F01DAE6874AA}" ProjectSection(SolutionItems) = preProject - docs\docfx_project\ControlledVocabulary\CvParam.ipynb = docs\docfx_project\ControlledVocabulary\CvParam.ipynb - docs\docfx_project\ControlledVocabulary\intro.ipynb = docs\docfx_project\ControlledVocabulary\intro.ipynb + docs\ControlledVocabulary\CvParam.ipynb = docs\ControlledVocabulary\CvParam.ipynb + docs\ControlledVocabulary\Introduction.ipynb = docs\ControlledVocabulary\Introduction.ipynb EndProjectSection EndProject -Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "api", "api", "{9031C346-A994-4943-AB58-1095882E725C}" - ProjectSection(SolutionItems) = preProject - docs\docfx_project\api\index.md = docs\docfx_project\api\index.md - EndProjectSection -EndProject -Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "images", "images", "{31DCBC4B-41D9-4CE1-9E5D-3F5A3F5E01CA}" -EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Any CPU = Debug|Any CPU @@ -105,11 +91,8 @@ Global {ED24D0E3-BA79-4F6D-9A30-D05FF4EBAFDB} = {3DB2A5F4-23F6-4A06-9AE5-CEAC0707735B} {24D99DC2-DF18-45A3-B444-B60351F131DB} = {67DA0DCC-75F4-4F30-91C3-309A48B13D49} {30177EF1-3980-4FFE-9B49-90B75DCEBDA3} = {2EB71559-9BE4-4E02-9763-9092876D1E4A} - {86CD7F81-ADB4-4991-A960-063FE02D907D} = {551D4715-5ECD-4CAB-8A4A-41E246F4A7B5} - {E669BA6D-4327-40AE-8CE1-E6FEA8F89A15} = {86CD7F81-ADB4-4991-A960-063FE02D907D} - {F6471491-8FE4-48A7-BA9E-1113DE63B5F5} = {86CD7F81-ADB4-4991-A960-063FE02D907D} - {9031C346-A994-4943-AB58-1095882E725C} = {86CD7F81-ADB4-4991-A960-063FE02D907D} - {31DCBC4B-41D9-4CE1-9E5D-3F5A3F5E01CA} = {86CD7F81-ADB4-4991-A960-063FE02D907D} + {699C5B9A-EA4B-4D25-B05D-16CA14320CFB} = {551D4715-5ECD-4CAB-8A4A-41E246F4A7B5} + {524F5156-C079-4AEF-822E-F01DAE6874AA} = {551D4715-5ECD-4CAB-8A4A-41E246F4A7B5} EndGlobalSection GlobalSection(ExtensibilityGlobals) = postSolution SolutionGuid = {933E3470-7D09-4F22-A056-2407458B9600} diff --git a/build/DocumentationTasks.fs b/build/DocumentationTasks.fs index 0a41173..b3ba7af 100644 --- a/build/DocumentationTasks.fs +++ b/build/DocumentationTasks.fs @@ -5,33 +5,47 @@ open ProjectInfo open BasicTasks open BlackFox.Fake -open System.IO -open Fake.Core -open Fake.IO - -let notebooks = Directory.EnumerateFiles("docs", "*.ipynb", SearchOption.AllDirectories) - -let preprocessNotebooks = - BuildTask.create "PreprocessNotebooks" [ ] { - notebooks - |> Seq.iter (fun nb -> - let dir = Path.GetDirectoryName nb - let file = Path.GetFileName nb - CreateProcess.fromRawCommandLine "jupyter" $"nbconvert {nb} --to markdown --output-dir={dir}" - |> Proc.run // start with the above configuration - |> ignore // ignore exit code - File.ReadAllText(nb.Replace(".ipynb", ".md")) - |> String.replace "polyglot-notebook" "fsharp" - |> fun p -> File.WriteAllText(nb.Replace(".ipynb", ".md"), p) - ) - } let buildDocs = - BuildTask.create "BuildDocs" [ build; preprocessNotebooks ] { - runDotNet "docfx docs/docfx_project/docfx.json" "./" + BuildTask.create "BuildDocs" [ build ] { + printfn "building docs with stable version %s" stableDocsVersionTag + + runDotNet + (sprintf + "fsdocs build --eval --clean --properties Configuration=Release --parameters fsdocs-package-version %s" + stableDocsVersionTag) + "./" + } + +let buildDocsPrerelease = + BuildTask.create "BuildDocsPrerelease" [ setPrereleaseTag; build ] { + printfn "building docs with prerelease version %s" prereleaseTag + + runDotNet + (sprintf + "fsdocs build --eval --clean --properties Configuration=Release --parameters fsdocs-package-version %s" + prereleaseTag) + "./" } let watchDocs = - BuildTask.create "WatchDocs" [ build; preprocessNotebooks ] { - runDotNet "docfx docs/docfx_project/docfx.json --serve" "./" - } \ No newline at end of file + BuildTask.create "WatchDocs" [ build ] { + printfn "watching docs with stable version %s" stableDocsVersionTag + + runDotNet + (sprintf + "fsdocs watch --eval --clean --properties Configuration=Release --parameters fsdocs-package-version %s" + stableDocsVersionTag) + "./" + } + +let watchDocsPrerelease = + BuildTask.create "WatchDocsPrerelease" [ setPrereleaseTag; build ] { + printfn "watching docs with prerelease version %s" prereleaseTag + + runDotNet + (sprintf + "fsdocs watch --eval --clean --properties Configuration=Release --parameters fsdocs-package-version %s" + prereleaseTag) + "./" + } diff --git a/docs/ARCTokenization/Introduction.ipynb b/docs/ARCTokenization/Introduction.ipynb new file mode 100644 index 0000000..96df80d --- /dev/null +++ b/docs/ARCTokenization/Introduction.ipynb @@ -0,0 +1,59 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:31.5046702+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:31.5267655+01:00" + }, + "source": [ + "---\n", + "\n", + "title: Introduction\n", + "\n", + "category: ARCTokenization\n", + "\n", + "categoryindex: 2\n", + "\n", + "index: 1\n", + "\n", + "---\n", + "\n", + "# ARCTokenization\n", + "\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".NET (F#)", + "language": "F#", + "name": ".net-fsharp" + }, + "language_info": { + "file_extension": ".fs", + "mimetype": "text/x-fsharp", + "name": "F#", + "pygments_lexer": "fsharp", + "version": "6.0" + }, + "polyglot_notebook": { + "defaultKernelName": "fsharp", + "items": [ + { + "name": "fsharp" + } + ] + }, + "dotnet_interactive": { + "defaultKernelName": "fsharp", + "items": [ + { + "name": "fsharp" + } + ] + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} \ No newline at end of file diff --git a/docs/ControlledVocabulary/CvParam.ipynb b/docs/ControlledVocabulary/CvParam.ipynb new file mode 100644 index 0000000..c275349 --- /dev/null +++ b/docs/ControlledVocabulary/CvParam.ipynb @@ -0,0 +1,172 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:32.9473996+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:32.9691789+01:00" + }, + "source": [ + "---\n", + "\n", + "category: ControlledVocabulary\n", + "\n", + "categoryindex: 1\n", + "\n", + "index: 2\n", + "\n", + "---\n", + "\n", + "# CvParam" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:32.9703093+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:36.4319344+01:00", + "dotnet_interactive": { + "language": "fsharp" + }, + "polyglot_notebook": { + "kernelName": "fsharp" + } + }, + "outputs": [ + { + "data": { + "text/html": [ + "
Installing Packages
  • ControlledVocabulary
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
Installing Packages
  • ControlledVocabulary.
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
Installing Packages
  • ControlledVocabulary..
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
Installed Packages
  • ControlledVocabulary, 1.0.1
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "#r \"nuget: ControlledVocabulary\"" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:36.4320438+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:36.4322926+01:00" + }, + "source": [ + "`CvParam` is a value that is annotated with a controlled vocabulary term.\n", + "\n", + "Suppose we have the name of a person (`\"Kevin Schneider\"`).\n", + "\n", + "We can annotate this value with a term to indicate that it is a name:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:36.4323025+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:36.5805982+01:00", + "dotnet_interactive": { + "language": "fsharp" + }, + "polyglot_notebook": { + "kernelName": "fsharp" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "\"CvParam: Full Name\n", + "\tID: TO:00042069\n", + "\tRefUri: https://link/to/reference/vocabulary/named/TO\n", + "\tValue: Value \"Kevin Schneider\"\n", + "\tAttributes: []\"\r\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "open ControlledVocabulary\n", + "\n", + "let human =\n", + " CvTerm.create(\n", + " accession = \"TO:00042069\", // the term's unique accession number\n", + " name = \"Full Name\", // the term name\n", + " ref = \"https://link/to/reference/vocabulary/named/TO\" // the reference vocabulary\n", + " )\n", + "\n", + "let cvp = \n", + " CvParam(\n", + " cvTerm = human,\n", + " pv = ParamValue.Value \"Kevin Schneider\"\n", + " )\n", + "\n", + "cvp.ToString()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".NET (F#)", + "language": "F#", + "name": ".net-fsharp" + }, + "language_info": { + "file_extension": ".fs", + "mimetype": "text/x-fsharp", + "name": "F#", + "pygments_lexer": "fsharp", + "version": "6.0" + }, + "polyglot_notebook": { + "defaultKernelName": "fsharp", + "items": [ + { + "name": "fsharp" + } + ] + }, + "dotnet_interactive": { + "defaultKernelName": "fsharp", + "items": [ + { + "name": "fsharp" + } + ] + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} \ No newline at end of file diff --git a/docs/docfx_project/ControlledVocabulary/intro.ipynb b/docs/ControlledVocabulary/Introduction.ipynb similarity index 54% rename from docs/docfx_project/ControlledVocabulary/intro.ipynb rename to docs/ControlledVocabulary/Introduction.ipynb index 51d3c17..ce7f9a0 100644 --- a/docs/docfx_project/ControlledVocabulary/intro.ipynb +++ b/docs/ControlledVocabulary/Introduction.ipynb @@ -2,8 +2,22 @@ "cells": [ { "cell_type": "markdown", - "metadata": {}, + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:39.5727874+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:39.5950134+01:00" + }, "source": [ + "---\n", + "\n", + "category: ControlledVocabulary\n", + "\n", + "categoryindex: 1\n", + "\n", + "title: Introduction\n", + "\n", + "index: 1\n", + "\n", + "---\n", "# ControlledVocabulary\n", "\n", "ControlledVocabulary is a .NET library for modelling and working with controlled vocabularies." @@ -11,8 +25,10 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:39.5961426+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:43.0014709+01:00", "dotnet_interactive": { "language": "fsharp" }, @@ -24,7 +40,7 @@ { "data": { "text/html": [ - "
Installed Packages
  • ControlledVocabulary, 1.0.0
  • Plotly.NET, 4.2.0
  • Plotly.NET.Interactive, 4.2.1
" + "
Installing Packages
  • ControlledVocabulary
" ] }, "metadata": {}, @@ -32,8 +48,26 @@ }, { "data": { - "text/plain": [ - "Loading extensions from `C:\\Users\\schne\\.nuget\\packages\\plotly.net.interactive\\4.2.1\\interactive-extensions\\dotnet\\Plotly.NET.Interactive.dll`" + "text/html": [ + "
Installing Packages
  • ControlledVocabulary.
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
Installing Packages
  • ControlledVocabulary..
" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
Installed Packages
  • ControlledVocabulary, 1.0.1
" ] }, "metadata": {}, @@ -41,20 +75,25 @@ } ], "source": [ - "#r \"nuget: ControlledVocabulary, 1.0.0\"" + "#r \"nuget: ControlledVocabulary\"" ] }, { "cell_type": "markdown", - "metadata": {}, + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:43.0015818+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:43.0018194+01:00" + }, "source": [ "In its barest form, a term from a controlled vocabulary consists of the term name itself, a URI for the term, and a reference to the controlled vocabulary that contains the term:" ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:43.0018298+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:43.1276945+01:00", "dotnet_interactive": { "language": "fsharp" }, @@ -66,7 +105,10 @@ { "data": { "text/html": [ - "
{ Accession = "TO:00042069"\\n Name = "yup"\\n RefUri = "https://link/to/reference/vocabulary/named/TO" }
Accession
TO:00042069
Name
yup
RefUri
https://link/to/reference/vocabulary/named/TO
- diff --git a/docs/docfx_project/ControlledVocabulary/intro.md b/docs/docfx_project/ControlledVocabulary/intro.md deleted file mode 100644 index ac53c91..0000000 --- a/docs/docfx_project/ControlledVocabulary/intro.md +++ /dev/null @@ -1,64 +0,0 @@ -# ControlledVocabulary - -ControlledVocabulary is a .NET library for modelling and working with controlled vocabularies. - - -```fsharp -#r "nuget: ControlledVocabulary, 1.0.0" -``` - - -
Installed Packages
  • ControlledVocabulary, 1.0.0
  • Plotly.NET, 4.2.0
  • Plotly.NET.Interactive, 4.2.1
- - - - Loading extensions from `C:\Users\schne\.nuget\packages\plotly.net.interactive\4.2.1\interactive-extensions\dotnet\Plotly.NET.Interactive.dll` - - -In its barest form, a term from a controlled vocabulary consists of the term name itself, a URI for the term, and a reference to the controlled vocabulary that contains the term: - - -```fsharp -open ControlledVocabulary - -CvTerm.create( - accession = "TO:00042069", // the term's unique accession number - name = "yup", // the term name - ref = "https://link/to/reference/vocabulary/named/TO" // the reference vocabulary -) -``` - - -
{ Accession = "TO:00042069"\n Name = "yup"\n RefUri = "https://link/to/reference/vocabulary/named/TO" }
Accession
TO:00042069
Name
yup
RefUri
https://link/to/reference/vocabulary/named/TO
- diff --git a/docs/docfx_project/api/.gitignore b/docs/docfx_project/api/.gitignore deleted file mode 100644 index e8079a3..0000000 --- a/docs/docfx_project/api/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -############### -# temp file # -############### -*.yml -.manifest diff --git a/docs/docfx_project/api/index.md b/docs/docfx_project/api/index.md deleted file mode 100644 index 78dc9c0..0000000 --- a/docs/docfx_project/api/index.md +++ /dev/null @@ -1,2 +0,0 @@ -# PLACEHOLDER -TODO: Add .NET projects to the *src* folder and run `docfx` to generate **REAL** *API Documentation*! diff --git a/docs/docfx_project/docfx.json b/docs/docfx_project/docfx.json deleted file mode 100644 index c8d183b..0000000 --- a/docs/docfx_project/docfx.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "metadata": [ - { - "src": [ - { - "files": [ - "**/bin/**/**/*.dll" - ], - "src": "../../src" - } - ], - "dest": "api", - "includePrivateMembers": false, - "disableGitFeatures": false, - "disableDefaultFilter": false, - "noRestore": false, - "namespaceLayout": "flattened", - "memberLayout": "samePage", - "allowCompilationErrors": false - } - ], - "build": { - "globalMetadata": { - "_enableSearch": true, - "_appName": "ARCTokenization" - }, - "fileMetadata": { - "_appTitle": { - "ARCTokenization/*.md": "ARCTokenization Documentation:", - "ControlledVocabulary/*.md": "ControlledVocabulary Documentation:" - } - - }, - "content": [ - { - "files": [ - "api/**.yml", - "api/index.md" - ] - }, - { - "files": [ - "ControlledVocabulary/*.md", - "ARCTokenization/*.md", - "articles/**/toc.yml", - "toc.yml", - "*.md" - ] - } - ], - "resource": [ - { - "files": [ - "images/**" - ] - } - ], - "output": "_site", - "globalMetadataFiles": [], - "fileMetadataFiles": [], - "template": [ - "default", - "modern" - ], - "postProcessors": [ "ExtractSearchIndex" ], - "keepFileLink": false, - "disableGitFeatures": false - } -} \ No newline at end of file diff --git a/docs/docfx_project/index.md b/docs/docfx_project/index.md deleted file mode 100644 index 3ae2506..0000000 --- a/docs/docfx_project/index.md +++ /dev/null @@ -1,4 +0,0 @@ -# This is the **HOMEPAGE**. -Refer to [Markdown](http://daringfireball.net/projects/markdown/) for how to write markdown files. -## Quick Start Notes: -1. Add images to the *images* folder if the file is referencing an image. diff --git a/docs/docfx_project/toc.yml b/docs/docfx_project/toc.yml deleted file mode 100644 index 97b018c..0000000 --- a/docs/docfx_project/toc.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: Home - href: index.md -- name: ControlledVocabulary - items: - - name: Introduction - href: ControlledVocabulary/intro.md - - name: CvParam - href: ControlledVocabulary/CvParam.md -- name: ARCTokenization - items: - - name: Introduction - href: ARCTokenization/intro.md -- name: Api Documentation - href: api/ - homepage: api/index.md diff --git a/docs/index.ipynb b/docs/index.ipynb new file mode 100644 index 0000000..6abed4e --- /dev/null +++ b/docs/index.ipynb @@ -0,0 +1,51 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "dotnet_repl_cellExecutionStartTime": "2024-01-03T14:01:29.7359431+01:00", + "dotnet_repl_cellExecutionEndTime": "2024-01-03T14:01:29.7581085+01:00" + }, + "source": [ + "# ARCTokenization\n", + "\n", + "this is the home of the documentation for 2 libraries:\n", + "\n", + "- [ControlledVocabulary](./ControlledVocabulary/Introduction.html) - a .NET library for modelling and working with controlled vocabularies.\n", + "- [ARCTokenization](./ARCTokenization/Introduction.html) - a library for parsing Research metadata formatted as Annotated Research Contexts ([ARCs](https://github.com/nfdi4plants/ARC-specification)) as tokens of a controlled structural vocabulary." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".NET (F#)", + "language": "F#", + "name": ".net-fsharp" + }, + "language_info": { + "file_extension": ".fs", + "mimetype": "text/x-fsharp", + "name": "F#", + "pygments_lexer": "fsharp", + "version": "6.0" + }, + "polyglot_notebook": { + "defaultKernelName": "fsharp", + "items": [ + { + "name": "fsharp" + } + ] + }, + "dotnet_interactive": { + "defaultKernelName": "fsharp", + "items": [ + { + "name": "fsharp" + } + ] + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} \ No newline at end of file diff --git a/src/ARCTokenization/RELEASE_NOTES.md b/src/ARCTokenization/RELEASE_NOTES.md index 5cfdf8b..f9597df 100644 --- a/src/ARCTokenization/RELEASE_NOTES.md +++ b/src/ARCTokenization/RELEASE_NOTES.md @@ -2,7 +2,8 @@ - Additions: [Add metadata token Mock API](https://github.com/nfdi4plants/ARCTokenization/commit/7ba554848542f46a60bdb82c54d84d186d6e685e) - Bugfixes: - - Fix multiple structural term relations ([#31](https://github.com/nfdi4plants/ARCTokenization/issues/31), [#30](https://github.com/nfdi4plants/ARCTokenization/issues/30)) + - Fix multiple structural term relations [#42](https://github.com/nfdi4plants/ARCTokenization/issues/42) + ### 1.2.0 - (Released 2023-10-26) - Additions: - [Add file system tokenization](https://github.com/nfdi4plants/ARCTokenization/commit/57de162d50c918f1e245f1aa34db0a6b1660ba3b) diff --git a/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo b/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo index b3ce5d6..eaa86c1 100644 --- a/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo +++ b/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo @@ -1,4 +1,4 @@ -!This file was auto generated on 2024-01-02. Do not edit it. All manual changes will be overwritten by the next generator run eventually. +!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually. format-version: 1.2 data-version: init/2023-10-26 saved-by: Kevin Schneider diff --git a/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo b/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo index ffccbff..b567d37 100644 --- a/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo +++ b/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo @@ -1,4 +1,4 @@ -!This file was auto generated on 2024-01-02. Do not edit it. All manual changes will be overwritten by the next generator run eventually. +!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually. format-version: 1.2 data-version: init/2023-07-27 saved-by: Kevin Schneider diff --git a/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo b/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo index c483d40..94052f6 100644 --- a/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo +++ b/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo @@ -1,4 +1,4 @@ -!This file was auto generated on 2024-01-02. Do not edit it. All manual changes will be overwritten by the next generator run eventually. +!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually. format-version: 1.2 data-version: init/2023-07-20 saved-by: Kevin Schneider diff --git a/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo b/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo index aad3c3e..78dda8b 100644 --- a/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo +++ b/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo @@ -1,4 +1,4 @@ -!This file was auto generated on 2024-01-02. Do not edit it. All manual changes will be overwritten by the next generator run eventually. +!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually. format-version: 1.2 data-version: init/2023-07-27 saved-by: Kevin Schneider