Version 12.3

.github/workflows/build-and-test.yml

@@ -0,0 +1,20 @@
+name: Build and Test 12.3
+
+on:
+  pull_request:
+    branches:
+    - develop
+  push:
+    branches:
+    - develop
+
+permissions:
+  contents: read
+  packages: read
+
+jobs:
+  build:
+    uses: Open-Systems-Pharmacology/Workflows/.github/workflows/test-csharp.yml@main
+    secrets: inherit
+    with:
+      temp-version: "12.3.9999"

.github/workflows/build-nightly_12.2.yml → .github/workflows/build-nightly_12.3.yml

@@ -1,17 +1,11 @@
-name: Build Nightly 12.2
-run-name: Version 12.2.${{ github.run_number }}
+name: Build Nightly 12.3
+run-name: Version 12.3.${{ github.run_number }}
 
 on:
   workflow_dispatch:
   schedule:
     - cron: '0 2 * * *'
 
-
-env:
-  MAJOR: 12
-  MINOR: 2
-  RUN: ${{ github.run_number }}
-
 permissions:
   contents: read
   packages: read
@@ -57,15 +51,15 @@ jobs:
 
       - name: define env variables
         run: |
-          echo "APP_VERSION=${{ env.MAJOR }}.${{ env.MINOR }}.${{ env.RUN }}" | Out-File -FilePath $env:GITHUB_ENV -Append
+          echo "APP_VERSION=12.3.${{ github.run_number }}" | Out-File -FilePath $env:GITHUB_ENV -Append
 
       - name: Build
         run: |
           rake "update_go_license[ApplicationStartup.cs, ${{ secrets.GO_DIAGRAM_KEY }}]"
-          dotnet build MoBi.sln /p:Version=${{env.APP_VERSION}}
+          dotnet build /p:Version=${{env.APP_VERSION}}
 
       - name : Test
-        run: dotnet test .\tests\**\bin\Debug\net472\MoBi*Tests.dll -v normal --no-build  --logger:"html;LogFileName=../testLog_Windows.html"
+        run: dotnet test -v normal --no-build  --logger:"html;LogFileName=../testLog_Windows.html"
 
       - name: Sign MoBi.exe with CodeSignTool
         uses: Open-Systems-Pharmacology/Workflows/.github/actions/codesigner-SSL@main
@@ -93,6 +87,7 @@ jobs:
           file_path: ./setup/deploy/MoBi.${{ env.APP_VERSION }}.msi
 
       - name: Push test log as artifact
+        if: always()
         uses: actions/upload-artifact@v4
         with:
           name: testLog_Windows
@@ -124,4 +119,4 @@ jobs:
             -H "Accept: application/vnd.github+json" \
             -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
             -H "X-GitHub-Api-Version: 2022-11-28" \
-            "https://api.github.com/repos/${{ github.repository }}/actions/runs/${{ github.run_id }}/cancel"
+            "https://api.github.com/repos/${{ github.repository }}/actions/runs/${{ github.run_id }}/cancel"

.github/workflows/build-nightly_v13.yml

@@ -0,0 +1,20 @@
+name: Build Nightly 13.0
+run-name: Version 13.0.${{ github.run_number }}
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: read
+
+jobs:
+  check-branch:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Validate source branch
+      run: |
+        if [ "${{ github.ref_name }}" != "v13" ]; then
+          echo "::error::Please call the workflow from the v13 branch"
+          exit 1
+        fi

.github/workflows/coverage_12.2.yml → .github/workflows/coverage.yml

@@ -1,4 +1,4 @@
-name: Code Coverage 12.2
+name: Code Coverage 12.3
 
 on:
     schedule:
@@ -23,7 +23,7 @@ jobs:
           dotnet restore
 
       - name: Build
-        run: dotnet build MoBi.sln /p:Version=12.2.9999
+        run: dotnet build MoBi.sln /p:Version=12.3.9999
 
 
       - name: Cover and report

.github/workflows/nightly-badge.yml

@@ -15,7 +15,7 @@ name: Badge for Nightly Build
 on:
   workflow_run:
     workflows:
-      - "Build Nightly 12.2"
+      - "Build Nightly 12.3"
     types:
       - completed
 
@@ -26,4 +26,4 @@ jobs:
   badge:
     uses: Open-Systems-Pharmacology/Workflows/.github/workflows/nightly-badge.yml@main
     with:
-      nightly-build-workflow: "build-nightly_12.2.yml"
+      nightly-build-workflow: "build-nightly_12.3.yml"

.gitignore

@@ -258,3 +258,4 @@ src/**/licenses.licx
 
 *.ncrunchproject
 /MoBi.v3.ncrunchsolution
+/src/MoBi/Properties/launchSettings.json

MoBi.sln

@@ -1,7 +1,7 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 17
-VisualStudioVersion = 17.0.31912.275
+# Visual Studio Version 18
+VisualStudioVersion = 18.1.11312.151
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "MoBi", "src\MoBi\MoBi.csproj", "{B831E5E2-431A-4627-B58C-3CE3F5002E42}"
 EndProject
@@ -21,9 +21,10 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution
 	ProjectSection(SolutionItems) = preProject
 		.gitattributes = .gitattributes
 		.gitignore = .gitignore
-		.github\workflows\build-and-test_12.2.yml = .github\workflows\build-and-test_12.2.yml
-		.github\workflows\build-nightly_12.2.yml = .github\workflows\build-nightly_12.2.yml
-		.github\workflows\coverage_12.2.yml = .github\workflows\coverage_12.2.yml
+		.github\workflows\build-nightly_12.3.yml = .github\workflows\build-nightly_12.3.yml
+		.github\workflows\build-and-test.yml = .github\workflows\build-and-test.yml
+		.github\workflows\nightly-badge.yml = .github\workflows\nightly-badge.yml
+		.github\workflows\coverage.yml = .github\workflows\coverage.yml
 		postclean.bat = postclean.bat
 		rakefile.rb = rakefile.rb
 		README.md = README.md

README.md

@@ -20,7 +20,7 @@ may define a new scenario, situation, or individual. Refine a Reaction(s) networ
 where it should be considered.
 
 ## Code Status
-[![Build status](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/MoBi/nightly-badge.yml?logo=GitHub&label=Build%20status)](https://github.com/Open-Systems-Pharmacology/MoBi/actions/workflows/build-nightly_12.2.yml)
+[![Build status](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/MoBi/nightly-badge.yml?logo=GitHub&label=Build%20status)](https://github.com/Open-Systems-Pharmacology/MoBi/actions/workflows/build-nightly_12.3.yml)
 [![Coverage status](https://codecov.io/gh/Open-Systems-Pharmacology/MoBi/branch/develop/graph/badge.svg)](https://codecov.io/gh/Open-Systems-Pharmacology/MoBi)
 
 ## Code of conduct

rakefile.rb

@@ -112,7 +112,7 @@ def src_dir_for(configuration)
    packages_dir =  src_dir_for("Debug")
 
    all_users_dir = ENV['ALLUSERSPROFILE']
-   all_users_application_dir = File.join(all_users_dir, manufacturer, product_name, '12.2')
+   all_users_application_dir = File.join(all_users_dir, manufacturer, product_name, '12.3')
 
    copy_dependencies solution_dir,  all_users_application_dir do
       copy_files 'Data', ['xml', 'mbdt']

src/MoBi.Assets/AppConstants.cs

@@ -1686,6 +1686,9 @@ public static class Captions
          public static readonly string GoToSource = "Go to Source";
          public static readonly string AddOutputSelection = "Add Output";
          public static readonly string AddingParametersToASimulationIsNotSupported = "Adding parameters to a simulation is not supported";
+         public static readonly string DefaultParameterView = "Default parameter view";
+         public static readonly string RenameDependentObjects = "Rename dependent objects";
+         public static readonly string WarnForNonFiniteQuantities = "Warn for non-finite quantities";
          public static string SelectTheBuildingBlockWhereEntitiesWillBeAddedOrUpdated(string typeBeingAdded) => $"Select the building block where {typeBeingAdded} will be added or updated";
          public static readonly string SelectBuildingBlock = "Select Building Block";
          public static readonly string MakeDefault = "Make defaults";
@@ -2255,6 +2258,7 @@ public static string HasEquivalentNeighborhood(string firstNeighborPath, string
       public static readonly IReadOnlyList<string> DefaultObservedDataCategories = new[] { Constants.ObservedData.MOLECULE, Constants.ObservedData.COMPARTMENT, Constants.ObservedData.ORGAN };
       public static readonly string Clone = "Clone";
       public static readonly string Endosome = "Endosome";
+      public static readonly string EventsContainerName = "Events";
 
       public static string PathType(string pathTypeAsString)
       {

src/MoBi.Assets/MoBi.Assets.csproj

@@ -10,7 +10,7 @@
     <OutputPath>bin\$(Configuration)</OutputPath>
     <DocumentationFile>bin\$(Configuration)\$(TargetFramework)\$(AssemblyName).xml</DocumentationFile>
     <NoWarn>1591, 3246</NoWarn>
-    <Version Condition="'$(Version)' == ''">12.2.0</Version>
+    <Version Condition="'$(Version)' == ''">12.3.0</Version>
   </PropertyGroup>
 
   <ItemGroup>
@@ -22,9 +22,9 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.2.26" /> 
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.2.26" />
-    <PackageReference Include="OSPSuite.Core" Version="12.2.26" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.3.32" /> 
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.3.32" />
+    <PackageReference Include="OSPSuite.Core" Version="12.3.32" />
   </ItemGroup>
 
   <ItemGroup>

src/MoBi.BatchTool/MoBi.BatchTool.csproj

@@ -12,7 +12,7 @@
     <NoWarn>1591, 3246</NoWarn>
     <ApplicationIcon>MoBi.ico</ApplicationIcon>
     <Description>MoBi.BatchTool</Description>
-    <Version Condition="'$(Version)' == ''">12.2.0</Version>
+    <Version Condition="'$(Version)' == ''">12.3.0</Version>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">
@@ -53,7 +53,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.2.26" />
+    <PackageReference Include="OSPSuite.Core" Version="12.3.32" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.15" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.73" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.75" GeneratePathProperty="true" />

src/MoBi.BatchTool/Services/BatchUserSettings.cs

@@ -40,6 +40,7 @@ public class BatchUserSettings : IUserSettings
       public ParameterIdentificationFeedbackEditorSettings ParameterIdentificationFeedbackEditorSettings { get; set; }
       public SensitivityAnalysisFeedbackEditorSettings SensitivityAnalysisFeedbackEditorSettings { get; set; }
       public MergeConflictViewSettings MergeConflictViewSettings { get; set; }
+      public ParameterGroupingModeIdForParameterAnalyzable DefaultParameterGroupingModeForPIAndSA { get; set; }
       public string PKSimPath { get; set; }
 
       public string IconSizeGeneral { get; set; }
@@ -93,5 +94,6 @@ public BatchUserSettings()
       public int MaximumNumberOfCoresToUse { get; set; }
       public int NumberOfBins { get; set; }
       public int NumberOfIndividualsPerBin { get; set; }
+      public bool WarnForNonFiniteQuantities { get; set; }
    }
 }

src/MoBi.Core/Commands/BuildingBlockChangeCommandBase.cs

@@ -13,14 +13,14 @@ public abstract class BuildingBlockChangeCommandBase : MoBiReversibleCommand, IW
       public abstract Module Module { get; }
    }
 
-   public abstract class BuildingBlockChangeCommandBase<T> : BuildingBlockChangeCommandBase where T :  class, IBuildingBlock
+   public abstract class BuildingBlockChangeCommandBase<T> : BuildingBlockChangeCommandBase where T : class, IBuildingBlock
    {
       public bool ShouldIncrementVersion { get; set; }
       public bool HasChangedModuleType { get; private set; }
-      public PKSimModuleConversion ConversionOption { get; set; }  = PKSimModuleConversion.SetAsExtensionModule;
+      public PKSimModuleConversion ConversionOption { get; set; } = PKSimModuleConversion.SetAsExtensionModule;
 
       protected T _buildingBlock;
-      protected string _buildingBlockId;
+      protected readonly string _buildingBlockId;
 
       protected BuildingBlockChangeCommandBase(T buildingBlock)
       {
@@ -32,17 +32,17 @@ protected BuildingBlockChangeCommandBase(T buildingBlock)
 
       protected override void ExecuteWith(IMoBiContext context)
       {
+         if (_buildingBlock == null)
+            return;
+
          var originalPkSimModuleState = _buildingBlock.IsPkSimModule();
-         if (_buildingBlock == null) return;
          var buildingBlockVersionUpdater = context.Resolve<IBuildingBlockVersionUpdater>();
          buildingBlockVersionUpdater.UpdateBuildingBlockVersion(_buildingBlock, ShouldIncrementVersion, ConversionOption);
          HasChangedModuleType = originalPkSimModuleState != _buildingBlock.IsPkSimModule();
       }
 
-      protected override void ClearReferences()
-      {
+      protected override void ClearReferences() => 
          _buildingBlock = default;
-      }
 
       public override void RestoreExecutionData(IMoBiContext context)
       {

src/MoBi.Core/Commands/SetConstantFormulaValueCommand.cs

@@ -1,7 +1,7 @@
 using MoBi.Assets;
-using OSPSuite.Core.Commands.Core;
 using MoBi.Core.Domain.Model;
 using MoBi.Core.Helper;
+using OSPSuite.Core.Commands.Core;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Builder;
 using OSPSuite.Core.Domain.Formulas;
@@ -21,15 +21,15 @@ public class SetConstantFormulaValueCommand : BuildingBlockChangeCommandBase<IBu
       protected string FormulaId { get; private set; }
 
       /// <summary>
-      /// Sets a constant value into a constant value formula
+      ///    Sets a constant value into a constant value formula
       /// </summary>
       /// <param name="constantFormula">The constant formula being edited</param>
       /// <param name="newValue">The new value being applied to the formula</param>
       /// <param name="displayUnit">The new value new display unit</param>
       /// <param name="oldUnit">The old value display unit</param>
       /// <param name="buildingBlock">The building block that this formula is a member of</param>
       /// <param name="formulaOwner">The entity that owns the formula</param>
-      public SetConstantFormulaValueCommand(ConstantFormula constantFormula, double newValue, Unit displayUnit, Unit oldUnit, IBuildingBlock buildingBlock, IEntity formulaOwner):base(buildingBlock)
+      public SetConstantFormulaValueCommand(ConstantFormula constantFormula, double newValue, Unit displayUnit, Unit oldUnit, IBuildingBlock buildingBlock, IEntity formulaOwner) : base(buildingBlock)
       {
          _constantFormula = constantFormula;
          _newValue = newValue;
@@ -60,10 +60,10 @@ protected override void ExecuteWith(IMoBiContext context)
          base.ExecuteWith(context);
 
          Description = AppConstants.Commands.SetConstantValueFormula(
-            ObjectType, 
-            formatForDisplay(_newValue, _displayUnit), 
+            ObjectType,
+            formatForDisplay(_newValue, _displayUnit),
             formatForDisplay(_constantFormula.Value, _oldDisplayUnit),
-            _owner == null? string.Empty : _owner.EntityPath());
+            _owner == null ? string.Empty : _owner.EntityPath());
 
          _constantFormula.Value = _newValue;
       }
@@ -75,6 +75,7 @@ private string formatForDisplay(double newValue, Unit displayUnit)
 
       public override void RestoreExecutionData(IMoBiContext context)
       {
+         base.RestoreExecutionData(context);
          _constantFormula = context.Get<ConstantFormula>(FormulaId);
          _owner = context.Get<IEntity>(_ownerId);
       }

src/MoBi.Core/Domain/Extensions/ContainerExtensions.cs

@@ -38,12 +38,12 @@ public static IContainer WithTag(this IContainer container, string tag)
 
       public static IEnumerable<T> GetChildrenSortedByName<T>(this IContainer container, Func<T, bool> pred) where T : class, IEntity
       {
-         return container.GetChildren(pred).OrderBy(x => x.Name);
+         return container.GetChildren(pred).OrderBy(x => x.Name, new IndexedNameComparer());
       }
 
       public static IEnumerable<T> GetChildrenSortedByName<T>(this IContainer container) where T : class, IEntity
       {
-         return container.GetChildren<T>().OrderBy(x => x.Name);
+         return container.GetChildrenSortedByName<T>(x => true);
       }
    }
 }