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update core #2633

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merged 2 commits into from
May 23, 2023
Merged

update core #2633

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113680c
update core
rwmcintosh May 23, 2023
3b2907c
Merge branch 'OSMOSES' into update-core
rwmcintosh May 23, 2023
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4 changes: 2 additions & 2 deletions src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
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Expand Up @@ -26,8 +26,8 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets.Images" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Assets.Images" Version="12.0.183" />
</ItemGroup>

<ItemGroup>
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4 changes: 2 additions & 2 deletions src/PKSim.Assets/PKSim.Assets.csproj
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Expand Up @@ -26,8 +26,8 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets.Images" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Assets.Images" Version="12.0.183" />
</ItemGroup>

<ItemGroup>
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4 changes: 2 additions & 2 deletions src/PKSim.BatchTool/PKSim.BatchTool.csproj
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Expand Up @@ -59,8 +59,8 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
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4 changes: 2 additions & 2 deletions src/PKSim.CLI.Core/PKSim.CLI.Core.csproj
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Expand Up @@ -27,9 +27,9 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
</ItemGroup>

<ItemGroup>
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6 changes: 3 additions & 3 deletions src/PKSim.CLI/PKSim.CLI.csproj
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Expand Up @@ -61,9 +61,9 @@
<ItemGroup>
<PackageReference Include="CommandLineParser" Version="2.8.0" />
<PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.1.0" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.183" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
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5 changes: 3 additions & 2 deletions src/PKSim.Core/Model/PKSimSpatialStructureFactory.cs
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@@ -1,4 +1,5 @@
using System.Linq;
using OSPSuite.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
using OSPSuite.Core.Domain.Formulas;
Expand Down Expand Up @@ -49,7 +50,7 @@ public PKSimSpatialStructureFactory(

public SpatialStructure CreateFor(Individual individual, Simulation simulation)
{
var spatialStructure = Create().WithName(simulation.Name);
var spatialStructure = Create();
var organism = _objectBaseFactory.Create<Organism>();
spatialStructure.AddTopContainer(organism);

Expand Down Expand Up @@ -126,6 +127,6 @@ private void addModelStructureTo(IContainer container, OriginData originData, Mo
}
}

protected override SpatialStructure CreateSpatialStructure() => _objectBaseFactory.Create<PKSimSpatialStructure>();
protected override SpatialStructure CreateSpatialStructure() => _objectBaseFactory.Create<PKSimSpatialStructure>().WithName(DefaultNames.SpatialStructure);
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In some cases we are counting on the service to create something with a meaningful default name, but ObjectBaseFactory can't do that

}
}
8 changes: 4 additions & 4 deletions src/PKSim.Core/PKSim.Core.csproj
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Expand Up @@ -31,10 +31,10 @@
<ItemGroup>
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets.Images" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Assets.Images" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.183" />
<PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
</ItemGroup>

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3 changes: 2 additions & 1 deletion src/PKSim.Core/Services/EventBuildingBlockCreator.cs
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@@ -1,5 +1,6 @@
using System.Collections.Generic;
using System.Linq;
using OSPSuite.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
using OSPSuite.Core.Domain.Descriptors;
Expand Down Expand Up @@ -60,7 +61,7 @@ public EventGroupBuildingBlock CreateFor(Simulation simulation)
try
{
_simulation = simulation;
_eventGroupBuildingBlock = _objectBaseFactory.Create<EventGroupBuildingBlock>().WithName(simulation.Name);
_eventGroupBuildingBlock = _objectBaseFactory.Create<EventGroupBuildingBlock>().WithName(DefaultNames.EventBuildingBlock);
_cloneManagerForBuildingBlock.FormulaCache = _eventGroupBuildingBlock.FormulaCache;

createApplications(_simulation.CompoundPropertiesList);
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5 changes: 3 additions & 2 deletions src/PKSim.Core/Services/MoleculesAndReactionsCreator.cs
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@@ -1,6 +1,7 @@
using System;
using System.Collections.Generic;
using System.Linq;
using OSPSuite.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
using OSPSuite.Utility.Extensions;
Expand Down Expand Up @@ -91,10 +92,10 @@ IInteractionTask interactionTask
_passiveTransports = _module.PassiveTransports;

_moleculeBuildingBlock = _objectBaseFactory.Create<MoleculeBuildingBlock>()
.WithName(simulation.Name);
.WithName(DefaultNames.MoleculeBuildingBlock);

_reactionBuildingBlock = _objectBaseFactory.Create<ReactionBuildingBlock>()
.WithName(simulation.Name);
.WithName(DefaultNames.ReactionBuildingBlock);

addIndividualMolecules(simulation.CompoundPropertiesList);

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2 changes: 1 addition & 1 deletion src/PKSim.Core/Services/PKSimInitialConditionsCreator.cs
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Expand Up @@ -55,7 +55,7 @@ public InitialConditionsBuildingBlock CreateFor(Module module, Simulation simula
allAvailableInitialConditions.Each(msv => msv.IsPresent = true);
}

return defaultInitialConditions.WithName(simulation.Name);
return defaultInitialConditions;
}

private IEnumerable<ObjectPath> moleculesInvolvedInExpression(Individual individual, IndividualMolecule molecule,
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3 changes: 2 additions & 1 deletion src/PKSim.Core/Services/PKSimParameterValuesCreator.cs
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@@ -1,3 +1,4 @@
using OSPSuite.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
using OSPSuite.Core.Domain.Services;
Expand Down Expand Up @@ -40,7 +41,7 @@ public ParameterValuesBuildingBlock CreateFor(Simulation simulation)
individual.AllUndefinedMolecules().Each(molecule => updateMoleculeParametersValues(molecule, individual));

updateSimulationParameters(simulation);
return _defaultValues.WithName(simulation.Name);
return _defaultValues.WithName(DefaultNames.ParameterValues);
}
finally
{
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1 change: 1 addition & 0 deletions src/PKSim.Core/Services/SimulationConfigurationTask.cs
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@@ -1,3 +1,4 @@
using OSPSuite.Assets;
using OSPSuite.Core;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
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3 changes: 2 additions & 1 deletion src/PKSim.Infrastructure/ORM/Queries/ModelObserverQuery.cs
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@@ -1,5 +1,6 @@
using System;
using System.Linq;
using OSPSuite.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
using OSPSuite.Core.Domain.Descriptors;
Expand Down Expand Up @@ -44,7 +45,7 @@ public ModelObserverQuery(

public ObserverBuildingBlock AllObserversFor(MoleculeBuildingBlock moleculeBuildingBlock, Simulation simulation)
{
var observerBuildingBlock = _objectBaseFactory.Create<ObserverBuildingBlock>().WithName(simulation.Name);
var observerBuildingBlock = _objectBaseFactory.Create<ObserverBuildingBlock>().WithName(DefaultNames.ObserverBuildingBlock);
addStandardObserversTo(simulation, observerBuildingBlock, moleculeBuildingBlock);

addSimulationObservers(simulation, observerBuildingBlock);
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3 changes: 2 additions & 1 deletion src/PKSim.Infrastructure/ORM/Queries/ModelPassiveTransportQuery.cs
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@@ -1,5 +1,6 @@
using System.Collections.Generic;
using System.Linq;
using OSPSuite.Assets;
using OSPSuite.Core.Domain;
using OSPSuite.Core.Domain.Builder;
using OSPSuite.Core.Domain.Services;
Expand Down Expand Up @@ -30,7 +31,7 @@ public ModelPassiveTransportQuery(IObjectBaseFactory objectBaseFactory,
public PassiveTransportBuildingBlock AllPassiveTransportsFor(Simulation simulation)
{
var passiveTransportBuilderCollection = _objectBaseFactory.Create<PassiveTransportBuildingBlock>()
.WithName(simulation.Name);
.WithName(DefaultNames.PassiveTransportBuildingBlock);

var modelProperties = simulation.ModelProperties;
var compoundNames = simulation.AllBuildingBlocks<Compound>().AllNames().ToList();
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18 changes: 9 additions & 9 deletions src/PKSim.Infrastructure/PKSim.Infrastructure.csproj
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Expand Up @@ -41,15 +41,15 @@
<PackageReference Include="Microsoft.Extensions.Logging.Abstractions" Version="3.1.0" />
<PackageReference Include="Newtonsoft.Json.Schema" Version="3.0.13" />
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure.Castle" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure.Export" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="12.0.180" />
<PackageReference Include="OSPSuite.Presentation.Serialization" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure.Castle" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure.Export" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="12.0.183" />
<PackageReference Include="OSPSuite.Presentation.Serialization" Version="12.0.183" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
</ItemGroup>

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4 changes: 2 additions & 2 deletions src/PKSim.Matlab/PKSim.Matlab.csproj
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Expand Up @@ -26,9 +26,9 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
</ItemGroup>

<ItemGroup>
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6 changes: 3 additions & 3 deletions src/PKSim.Presentation/PKSim.Presentation.csproj
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Expand Up @@ -30,11 +30,11 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.183" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
</ItemGroup>

<ItemGroup>
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4 changes: 2 additions & 2 deletions src/PKSim.R/PKSim.R.csproj
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Expand Up @@ -49,9 +49,9 @@


<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
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8 changes: 4 additions & 4 deletions src/PKSim.UI.Starter/PKSim.UI.Starter.csproj
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Expand Up @@ -23,10 +23,10 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Presentation" Version="12.0.180" />
<PackageReference Include="OSPSuite.UI" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Infrastructure" Version="12.0.180" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.183" />
<PackageReference Include="OSPSuite.UI" Version="12.0.183" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.Infrastructure" Version="12.0.183" />
</ItemGroup>

</Project>
8 changes: 4 additions & 4 deletions src/PKSim.UI/PKSim.UI.csproj
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Expand Up @@ -60,14 +60,14 @@
<ItemGroup>
<PackageReference Include="Microsoft.Extensions.Logging" Version="3.1.0" />
<PackageReference Include="Microsoft.Extensions.Logging.Debug" Version="3.1.0" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.DataBinding" Version="3.0.0.4" />
<PackageReference Include="OSPSuite.DataBinding.DevExpress" Version="6.0.0.2" />
<PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.180" />
<PackageReference Include="OSPSuite.UI" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.183" />
<PackageReference Include="OSPSuite.UI" Version="12.0.183" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
</ItemGroup>

<ItemGroup>
Expand Down
6 changes: 3 additions & 3 deletions src/PKSim/PKSim.csproj
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Expand Up @@ -76,14 +76,14 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.112" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.180" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.Presentation" Version="12.0.183" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" GeneratePathProperty="true" />
</ItemGroup>

Expand Down
4 changes: 2 additions & 2 deletions tests/PKSim.Matlab.Tests/PKSim.Matlab.Tests.csproj
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Expand Up @@ -22,9 +22,9 @@
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
</PackageReference>
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
Expand Down
4 changes: 2 additions & 2 deletions tests/PKSim.R.Tests/PKSim.R.Tests.csproj
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Expand Up @@ -22,9 +22,9 @@
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
</PackageReference>
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
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2 changes: 1 addition & 1 deletion tests/PKSim.Tests/PKSim.Tests.csproj
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Expand Up @@ -21,7 +21,7 @@
</PackageReference>
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
<PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
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6 changes: 3 additions & 3 deletions tests/PKSim.UI.Tests/PKSim.UI.Tests.csproj
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Expand Up @@ -29,10 +29,10 @@
</PackageReference>
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
<PackageReference Include="nunit" Version="3.13.2" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.180" />
<PackageReference Include="OSPSuite.Assets" Version="12.0.183" />
<PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
<PackageReference Include="OSPSuite.Core" Version="12.0.180" />
<PackageReference Include="OSPSuite.UI" Version="12.0.180" />
<PackageReference Include="OSPSuite.Core" Version="12.0.183" />
<PackageReference Include="OSPSuite.UI" Version="12.0.183" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.112" GeneratePathProperty="true" />
<None Include="..\..\src\Db\PKSimDB.sqlite" Link="PKSimDB.sqlite">
Expand Down