Merge changes from main into feature branch

.config/dotnet-tools.json

@@ -3,7 +3,7 @@
   "isRoot": true,
   "tools": {
     "fable": {
-      "version": "4.16.0",
+      "version": "4.22.0",
       "commands": [
         "fable"
       ]

ARCtrl.sln

@@ -10,6 +10,8 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 		.github\workflows\build-test.yml = .github\workflows\build-test.yml
 		build.cmd = build.cmd
 		build.sh = build.sh
+		Directory.Build.props = Directory.Build.props
+		Directory.Packages.props = Directory.Packages.props
 		.config\dotnet-tools.json = .config\dotnet-tools.json
 		global.json = global.json
 		package.json = package.json
@@ -24,6 +26,11 @@ EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "ARCtrl.FileSystem", "src\FileSystem\ARCtrl.FileSystem.fsproj", "{F47E23C3-8415-4725-9E85-57271694DEB3}"
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{6DA2330B-D407-4FB1-AF05-B0184034EC44}"
+	ProjectSection(SolutionItems) = preProject
+		src\ARCtrl\ARCtrl.Javascript.fsproj = src\ARCtrl\ARCtrl.Javascript.fsproj
+		src\ARCtrl\ARCtrl.Python.fsproj = src\ARCtrl\ARCtrl.Python.fsproj
+		src\Package.Metadata.props = src\Package.Metadata.props
+	EndProjectSection
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "Build", "build\Build.fsproj", "{5EAFB0CD-1168-4FCA-AA61-E96AD6C85819}"
 EndProject

Directory.Build.props

@@ -0,0 +1,20 @@
+<Project>
+    <!-- Make F# support Central Package Management -->
+    <PropertyGroup>
+        <DisableImplicitSystemValueTupleReference>true</DisableImplicitSystemValueTupleReference>
+        <DisableImplicitFSharpCoreReference>true</DisableImplicitFSharpCoreReference>
+    </PropertyGroup>
+    <!-- Use lock files --><!--
+    <PropertyGroup Condition="'$(GITHUB_ACTIONS)' == 'true'">
+        <ContinuousIntegrationBuild>true</ContinuousIntegrationBuild>
+    </PropertyGroup>
+    <PropertyGroup>
+        <RestorePackagesWithLockFile>true</RestorePackagesWithLockFile>
+        <RestoreLockedMode Condition="'$(ContinuousIntegrationBuild)' == 'true'">true</RestoreLockedMode>
+    </PropertyGroup>-->
+	<PropertyGroup>
+		<!-- Make all the projects use the highest warning level -->
+		<WarningLevel>3</WarningLevel>
+	</PropertyGroup>
+
+</Project>

Directory.Packages.props

@@ -0,0 +1,22 @@
+<Project>
+  <PropertyGroup>
+    <ManagePackageVersionsCentrally>true</ManagePackageVersionsCentrally>
+  </PropertyGroup>
+  <ItemGroup>
+    <PackageVersion Include="Fable.Core"            Version="4.3.0" />
+    <PackageVersion Include="Fable.Package.SDK"     Version="1.1.0" />
+    <PackageVersion Include="FSharp.Core"           Version="[8.0.1,)" />
+    <PackageVersion Include="Thoth.Json.Core"       Version="0.4.0" />
+    <PackageVersion Include="Thoth.Json.JavaScript" Version="0.3.0" />
+    <PackageVersion Include="Thoth.Json.Python"     Version="0.4.0" />
+    <PackageVersion Include="Thoth.Json.Newtonsoft" Version="0.2.0" />
+    <PackageVersion Include="FsSpreadsheet"         Version="6.3.0-alpha.4" />
+    <PackageVersion Include="YAMLicious"            Version="0.0.1" />
+    <PackageVersion Include="DynamicObj"            Version="4.0.0" />
+    <PackageVersion Include="Fable.SimpleHttp"      Version="3.5.0" />
+    <PackageVersion Include="Fable.Fetch"           Version="2.6.0" />
+    <PackageVersion Include="Fable.Node"            Version="1.2.0" />
+    <PackageVersion Include="Fable.Pyxpecto"        Version="1.2.0" />
+    <PackageVersion Include="NJsonSchema"           Version="10.8.0" />
+  </ItemGroup>
+</Project>

RELEASE_NOTES.md

@@ -1,3 +1,36 @@
+### 2.1.0+99b2659 (Released 2024-10-2)
+* Additions:
+    * [[#28cfd13](https://github.com/nfdi4plants/ARCtrl/commit/28cfd133152fa3cdc6606b4ccb7cda3c340e8f62)] add rocrate project
+    * [[#f71faea](https://github.com/nfdi4plants/ARCtrl/commit/f71faea334538425d5f92e81c650b1cdd46446ef)] rocrate datamodel wip based on inheritance and single interface
+    * [[#ef15f35](https://github.com/nfdi4plants/ARCtrl/commit/ef15f35779606a1bfcaecdadfc7532886466ec46)] implement first POC of ISA ROCrate profile
+    * [[#168ead8](https://github.com/nfdi4plants/ARCtrl/commit/168ead84ca93dc0fae911e760673ef6e33180447)] add test project
+    * [[#2cea57c](https://github.com/nfdi4plants/ARCtrl/commit/2cea57cc1415310e36f5931ef376ea183b85fb71)] update solution
+    * [[#ccd1805](https://github.com/nfdi4plants/ARCtrl/commit/ccd18053a83c80f4ca4b7a2ac7008a4a0cf3d348)] Unify Inheritance to ROCrateObject
+    * [[#95cab6f](https://github.com/nfdi4plants/ARCtrl/commit/95cab6f0f85f71a7adea887a25bd47c714e5af35)] wip ro-crate tests
+    * [[#9ef48d7](https://github.com/nfdi4plants/ARCtrl/commit/9ef48d75f5439d3a71ca943941b70c5af3ff9261)] only use primary constructor
+    * [[#9deffb7](https://github.com/nfdi4plants/ARCtrl/commit/9deffb7ea81f76c067de5618f2b3388303402191)] Add basic tests for I/S/A ROCrateObjects
+    * [[#4b4a2fc](https://github.com/nfdi4plants/ARCtrl/commit/4b4a2fcc3bd32b31ec5aa3b4f1127883f7af83fc)] temp workaround in tests for https://github.com/CSBiology/DynamicObj/issues/25
+    * [[#f67e78b](https://github.com/nfdi4plants/ARCtrl/commit/f67e78b068350a8e1aecf80fa8b9dd4646fb9ddd)] Use unblocking version of DynamicObj, introduce runTestProject target
+    * [[#4e91e9d](https://github.com/nfdi4plants/ARCtrl/commit/4e91e9dcc5b34747a2e4a16f33aee1a227eb08ef)] finish basic property tests for isa profile types
+    * [[#8b4368a](https://github.com/nfdi4plants/ARCtrl/commit/8b4368aed9a9705a78f95ec752143b1620fb0408)] Merge pull request #426 from nfdi4plants/ro-crate-data-model
+    * [[#fdc4773](https://github.com/nfdi4plants/ARCtrl/commit/fdc4773125fb37bf7140476460a117e575e420ae)] add tryGetColumnByHeaderBy member and static + tests
+    * [[#1a5c4d6](https://github.com/nfdi4plants/ARCtrl/commit/1a5c4d64cdd3c591a2c7af73c4bdb7a9261c5ffb)] Update ArcTable.Tests.fs
+    * [[#29d1bb2](https://github.com/nfdi4plants/ARCtrl/commit/29d1bb250a2fc6ee4253e8a94f820f03bf87a09d)] update to thoth.json.core 0.4.0 and use temporary FsSpreadsheet implementations for js and py
+    * [[#2e47979](https://github.com/nfdi4plants/ARCtrl/commit/2e479798a7812233b109da566db68246fc9df7a2)] start working on ro-crate-json parsing
+    * [[#f6afa53](https://github.com/nfdi4plants/ARCtrl/commit/f6afa53b83b8003f16c7881a8bd7ea958466c5fb)] first buildable version after fable restructure
+    * [[#755879d](https://github.com/nfdi4plants/ARCtrl/commit/755879dbf3d30d1305ae8645fdf84338ce89c26a)] move duplicate project references into props files
+    * [[#93030e9](https://github.com/nfdi4plants/ARCtrl/commit/93030e915329c23b4b4f8cddc5b622312de6cedb)] Make use of Fable.Package.SDK
+    * [[#99b2659](https://github.com/nfdi4plants/ARCtrl/commit/99b2659d1dd5c3815693f4df85691f9bead3e26d)] rename json IO implementations folder to reduce ambiguity in py and javascript packages
+* Deletions:
+    * [[#c71b8a3](https://github.com/nfdi4plants/ARCtrl/commit/c71b8a301fbdf95531a9ba0d33f8e6d0d238adc9)] correct interface implementation on ROCrateObject, remove interface implementation from Dataset
+    * [[#c429686](https://github.com/nfdi4plants/ARCtrl/commit/c4296864a7443a990257f7eb47fed92458fa0a7b)] remove javascript and pyton packages from main solution
+    * [[#3586dee](https://github.com/nfdi4plants/ARCtrl/commit/3586dee6a736d3ad2ed9e79778e3ea136c638eac)] remove restorelockedmode flag
+* Bugfixes:
+    * [[#9d526b8](https://github.com/nfdi4plants/ARCtrl/commit/9d526b82df1d7ac04283cbe23c9832f1d5818771)] add LabProcess tests, fix schematype of ROCrateObject base constructor
+    * [[#192812d](https://github.com/nfdi4plants/ARCtrl/commit/192812d43569270845883ca116de9931dea6ba62)] fix error messages of ROCrate testing utils
+    * [[#43d65db](https://github.com/nfdi4plants/ARCtrl/commit/43d65db3fb121a4832e771541880c1fe79cfe89c)] various test fixes for Fable logic transition
+    * [[#8552f9e](https://github.com/nfdi4plants/ARCtrl/commit/8552f9ea7b2183c4cb382049c71793918d4128b3)] fix fable ready packaging and/by update package tags
+
 ### 2.0.1+5e6cc32 (Released 2024-8-29)
 * Bugfixes:
     * [[#bfaaaf6](https://github.com/nfdi4plants/ARCtrl/commit/bfaaaf614a1a2dc788a1b7de17761b5867aa9fee)] fix single dot in paths being interpreted as folder

build/Build.Packages.props

@@ -0,0 +1,18 @@
+<Project>
+  <PropertyGroup>
+    <ManagePackageVersionsCentrally>true</ManagePackageVersionsCentrally>
+  </PropertyGroup>
+  <ItemGroup>
+      <PackageVersion Include="BlackFox.Fake.BuildTask" Version="0.1.3" />
+      <PackageVersion Include="Fake.Api.Github" Version="6.0.0" />
+      <PackageVersion Include="Fake.Core.Process" Version="6.0.0" />
+      <PackageVersion Include="Fake.Core.ReleaseNotes" Version="6.0.0" />
+      <PackageVersion Include="Fake.Core.Target" Version="6.0.0" />
+      <PackageVersion Include="Fake.DotNet.Cli" Version="6.0.0" />
+      <PackageVersion Include="Fake.DotNet.MSBuild" Version="6.0.0" />
+      <PackageVersion Include="Fake.IO.FileSystem" Version="6.0.0" />
+      <PackageVersion Include="Fake.JavaScript.Npm" Version="6.0.0" />
+      <PackageVersion Include="Fake.Tools.Git" Version="6.0.0" />
+      <PackageVersion Include="Fake.Extensions.Release" Version="0.3.0" />      
+  </ItemGroup>
+</Project>

build/Build.fsproj

@@ -5,6 +5,7 @@
     <OutputType>Exe</OutputType>
   </PropertyGroup>
   <ItemGroup>
+    <None Include="Build.Packages.props" />
     <Content Include="release_package.json" />
     <Compile Include="Helpers.fs" />
     <Compile Include="MessagePrompts.fs" />
@@ -19,17 +20,20 @@
     <Compile Include="ReleaseTasks.fs" />
     <Compile Include="Build.fs" />
   </ItemGroup>
+
   <ItemGroup>
-    <PackageReference Include="BlackFox.Fake.BuildTask" Version="0.1.3" />
-    <PackageReference Include="Fake.Api.Github" Version="6.0.0" />
-    <PackageReference Include="Fake.Core.Process" Version="6.0.0" />
-    <PackageReference Include="Fake.Core.ReleaseNotes" Version="6.0.0" />
-    <PackageReference Include="Fake.Core.Target" Version="6.0.0" />
-    <PackageReference Include="Fake.DotNet.Cli" Version="6.0.0" />
-    <PackageReference Include="Fake.DotNet.MSBuild" Version="6.0.0" />
-    <PackageReference Include="Fake.IO.FileSystem" Version="6.0.0" />
-    <PackageReference Include="Fake.JavaScript.Npm" Version="6.0.0" />
-    <PackageReference Include="Fake.Tools.Git" Version="6.0.0" />
-    <PackageReference Include="Fake.Extensions.Release" Version="0.3.0" />
+    <PackageReference Include="BlackFox.Fake.BuildTask" />
+    <PackageReference Include="Fake.Api.Github" />
+    <PackageReference Include="Fake.Core.Process" />
+    <PackageReference Include="Fake.Core.ReleaseNotes" />
+    <PackageReference Include="Fake.Core.Target" />
+    <PackageReference Include="Fake.DotNet.Cli" />
+    <PackageReference Include="Fake.DotNet.MSBuild" />
+    <PackageReference Include="Fake.IO.FileSystem" />
+    <PackageReference Include="Fake.JavaScript.Npm" />
+    <PackageReference Include="Fake.Tools.Git" />
+    <PackageReference Include="Fake.Extensions.Release" />
   </ItemGroup>
+
+  <Import Project="Build.Packages.props" />
 </Project>

build/PackageTasks.fs

@@ -22,7 +22,7 @@ module BundleDotNet =
         System.IO.Directory.CreateDirectory(ProjectInfo.netPkgDir) |> ignore
         !! "src/**/*.*proj"
         -- "src/bin/*"
-        |> Seq.iter (Fake.DotNet.DotNet.pack (fun p ->
+        |> Seq.iter (Fake.DotNet.DotNet.pack (fun p ->           
             let msBuildParams =
                 {p.MSBuildParams with 
                     Properties = ([
@@ -56,8 +56,10 @@ let packDotNetSwate = BuildTask.create "packDotNetSwate" [clean; build; RunTests
 
 module BundleJs =
     let bundle (versionTag: string) =
-        Fake.JavaScript.Npm.run "bundlejs" (fun o -> o)
+        run dotnet $"fable src/ARCtrl/ARCtrl.Javascript.fsproj -o {ProjectInfo.npmPkgDir}" ""
+
         GenerateIndexJs.ARCtrl_generate ProjectInfo.npmPkgDir
+
         Fake.IO.File.readAsString "build/release_package.json"
         |> fun t ->
             let t = t.Replace(ProjectInfo.stableVersionTag, versionTag)
@@ -86,7 +88,7 @@ let packJSPrerelease = BuildTask.create "PackJSPrerelease" [setPrereleaseTag; cl
 module BundlePy =
     let bundle (versionTag: string) =
 
-        run dotnet $"fable src/ARCtrl -o {ProjectInfo.pyPkgDir}/arctrl --lang python" ""
+        run dotnet $"fable src/ARCtrl/ARCtrl.Python.fsproj -o {ProjectInfo.pyPkgDir}/arctrl --lang python" ""
         run python "-m poetry install --no-root" ProjectInfo.pyPkgDir
         GenerateIndexPy.ARCtrl_generate (ProjectInfo.pyPkgDir + "/arctrl")
 

build/TestTasks.fs

@@ -22,7 +22,7 @@ module RunTests =
         Trace.traceImportant "Start native JavaScript tests"
         for path in ProjectInfo.jsTestProjects do
             // transpile library for native access
-            run dotnet $"fable src/ARCtrl -o {path}/ARCtrl" ""
+            run dotnet $"fable src/ARCtrl/ARCtrl.Javascript.fsproj -o {path}/ARCtrl" ""
             GenerateIndexJs.ARCtrl_generate($"{path}/ARCtrl")
             run npx $"mocha {path} --timeout 20000" "" 
     }
@@ -40,7 +40,7 @@ module RunTests =
         Trace.traceImportant "Start native Python tests"
         for path in ProjectInfo.pyTestProjects do
             // transpile library for native access
-            run dotnet $"fable src/ARCtrl -o {path}/ARCtrl --lang python" ""
+            run dotnet $"fable src/ARCtrl/ARCtrl.Python.fsproj -o {path}/ARCtrl --lang python" ""
             GenerateIndexPy.ARCtrl_generate($"{path}/ARCtrl")
             run python $"-m pytest {path}" "" 
     }