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Fixes #2081 PKSim CLI filter simulation #2082

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merged 4 commits into from
Feb 1, 2022
Merged

Fixes #2081 PKSim CLI filter simulation #2082

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d85df61
Fixes #2081 PKSim CLI filter simulation
msevestre Feb 1, 2022
95f2bb6
Better comments
msevestre Feb 1, 2022
de82223
Fixes build
msevestre Feb 1, 2022
ccde3cc
Fixes build
msevestre Feb 1, 2022
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6 changes: 2 additions & 4 deletions src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
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Expand Up @@ -26,10 +26,8 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="11.0.62" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.62" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.60" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.60" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.72" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.72" />
</ItemGroup>

<ItemGroup>
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6 changes: 2 additions & 4 deletions src/PKSim.Assets/PKSim.Assets.csproj
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Expand Up @@ -26,10 +26,8 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Assets" Version="11.0.62" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.62" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.60" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.60" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.72" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.72" />
</ItemGroup>

<ItemGroup>
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3 changes: 3 additions & 0 deletions src/PKSim.Assets/PKSimConstants.cs
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Expand Up @@ -906,6 +906,9 @@ public static string MapToSnapshotNotSupportedWithoutContext(string snapshotType

public static string CannotFindSimulationInSnapshot(string simulationName, string project) => CannotFindBuildingBlockInSnapshot(ObjectTypes.Simulation, simulationName, project);

public static string SimulationUsedInPlotsAreNotExported(IReadOnlyList<string> simulationNames, string project)
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Making sure that simulation used in plots are also referenced here. This is just a simple validation step.

=> $"{ObjectTypes.Simulation.PluralizeIf(simulationNames)} {simulationNames.ToString(", ", "'")} used in plots {"is".PluralizeIf(simulationNames)} not found in the list of exported simulations for {ObjectTypes.Project} {project}";

public static string CannotFindSimulationParameterInSnapshot(string parameterPath, string simulationName, string project) =>
$"Could not find {ObjectTypes.Parameter} with path '{parameterPath}' in {ObjectTypes.Simulation} '{simulationName}' defined in snapshot {project}.";

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3 changes: 1 addition & 2 deletions src/PKSim.BatchTool/PKSim.BatchTool.csproj
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Expand Up @@ -63,8 +63,7 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
<PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
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3 changes: 1 addition & 2 deletions src/PKSim.CLI.Core/PKSim.CLI.Core.csproj
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Expand Up @@ -28,8 +28,7 @@

<ItemGroup>
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
</ItemGroup>

<ItemGroup>
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5 changes: 5 additions & 0 deletions src/PKSim.CLI.Core/RunOptions/QualificationRunOptions.cs
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Expand Up @@ -16,5 +16,10 @@ public class QualificationRunOptions
/// Should simulation be performed as part of the run?
/// </summary>
public bool Run { get; set; }

/// <summary>
/// Specifies if project files (snapshot and PK-Sim project file should be exported)
/// </summary>
public bool ExportProjectFiles { get; set; }
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Should we export the project files or not. Default will be not because I don't think we need to export those for the qualification

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ok, let's keep it like this.
If this option can be passed to the QualificationRunner later I'm perfectly fine with that :)

}
}
29 changes: 21 additions & 8 deletions src/PKSim.CLI.Core/Services/QualificationRunner.cs
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Expand Up @@ -102,7 +102,9 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
{
OutputFolder = projectOutputFolder,
//We run the output, this is for the old matlab implementation where we need xml. Otherwise, we only need pkml export
ExportMode = runOptions.Run ? SimulationExportMode.Xml | SimulationExportMode.Csv : SimulationExportMode.Pkml
ExportMode = runOptions.Run ? SimulationExportMode.Xml | SimulationExportMode.Csv : SimulationExportMode.Pkml,

Simulations = config.Simulations
};

//Using absolute path for simulation folder. We need them to be relative
Expand All @@ -124,13 +126,16 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
await _jsonSerializer.Serialize(mapping, config.MappingFile);
_logger.AddDebug($"Project mapping for '{project.Name}' exported to '{config.MappingFile}'", project.Name);

var projectFile = Path.Combine(config.TempFolder, $"{project.Name}{CoreConstants.Filter.PROJECT_EXTENSION}");
_workspacePersistor.SaveSession(_workspace, projectFile);
_logger.AddDebug($"Project saved to '{projectFile}'", project.Name);
if (runOptions.ExportProjectFiles)
{
var projectFile = Path.Combine(config.TempFolder, $"{project.Name}{CoreConstants.Filter.PROJECT_EXTENSION}");
_workspacePersistor.SaveSession(_workspace, projectFile);
_logger.AddDebug($"Project saved to '{projectFile}'", project.Name);

var snapshotFile = Path.Combine(config.TempFolder, $"{project.Name}{Constants.Filter.JSON_EXTENSION}");
await _snapshotTask.ExportModelToSnapshotAsync(project, snapshotFile);
_logger.AddDebug($"Project snapshot saved to '{snapshotFile}'", project.Name);
var snapshotFile = Path.Combine(config.TempFolder, $"{project.Name}{Constants.Filter.JSON_EXTENSION}");
await _snapshotTask.ExportModelToSnapshotAsync(project, snapshotFile);
_logger.AddDebug($"Project snapshot saved to '{snapshotFile}'", project.Name);
}

var end = DateTime.UtcNow;
var timeSpent = end - begin;
Expand All @@ -140,7 +145,15 @@ public async Task RunBatchAsync(QualificationRunOptions runOptions)
private PlotMapping[] retrievePlotDefinitionsFrom(Project snapshotProject, QualifcationConfiguration configuration)
{
var plotMappings = configuration.SimulationPlots?.SelectMany(x => retrievePlotDefinitionsForSimulation(x, snapshotProject));
return plotMappings?.ToArray() ?? Array.Empty<PlotMapping>();
var plotMappingsArray = plotMappings?.ToArray() ?? Array.Empty<PlotMapping>();
var exportedSimulations = configuration.Simulations?.ToArray() ?? Array.Empty<string>();
var unmappedSimulations = plotMappingsArray.Select(x => x.Simulation).Distinct().Where(x => !exportedSimulations.Contains(x)).ToList();

//All simulations referenced in the the plot mapping are also exported. We are good
if (!unmappedSimulations.Any())
return plotMappingsArray;

throw new QualificationRunException(SimulationUsedInPlotsAreNotExported(unmappedSimulations, snapshotProject.Name));
}

private void validateInputs(Project snapshotProject, QualifcationConfiguration configuration)
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9 changes: 7 additions & 2 deletions src/PKSim.CLI/Commands/QualificationRunCommand.cs
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Expand Up @@ -19,13 +19,17 @@ public class QualificationRunCommand : CLICommand<QualificationRunOptions>
[Option('r', "run", Required = false, HelpText = "Should the qualification runner also run the simulation or simply export the qualification report for further processing. Default is false")]
public bool Run { get; set; } = false;

[Option('e', "exp", Required = false, HelpText = "Should the qualification runner also export the project files (snapshot and PK-Sim project file). Default is false")]
public bool ExportProjectFiles { get; set; } = false;

public override QualificationRunOptions ToRunOptions()
{
return new QualificationRunOptions
{
ConfigurationFile = ConfigurationFile,
Validate = Validate,
Run = Run
Run = Run,
ExportProjectFiles = ExportProjectFiles
};
}

Expand All @@ -35,7 +39,8 @@ public override string ToString()
LogDefaultOptions(sb);
sb.AppendLine($"Validate: {Validate}");
sb.AppendLine($"Configuration file: {ConfigurationFile}");
sb.AppendLine($"Run Simulations: {Run}");
sb.AppendLine($"Run simulations: {Run}");
sb.AppendLine($"Export project files: {ExportProjectFiles}");
return sb.ToString();
}
}
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6 changes: 2 additions & 4 deletions src/PKSim.CLI/PKSim.CLI.csproj
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Expand Up @@ -61,10 +61,8 @@
<ItemGroup>
<PackageReference Include="CommandLineParser" Version="2.8.0" />
<PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.1.0" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.72" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
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12 changes: 4 additions & 8 deletions src/PKSim.Core/PKSim.Core.csproj
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Expand Up @@ -30,14 +30,10 @@
<ItemGroup>
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.62" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.60" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
<PackageReference Include="OSPSuite.Assets" Version="11.0.72" />
<PackageReference Include="OSPSuite.Assets.Images" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.72" />
<PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
</ItemGroup>

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24 changes: 8 additions & 16 deletions src/PKSim.Infrastructure/PKSim.Infrastructure.csproj
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Expand Up @@ -41,22 +41,14 @@
<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.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.62" />
<PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.62" />
<PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.60" />
<PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.60" />
<PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure.Castle" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure.Export" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure.Import" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="11.0.72" />
<PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="11.0.72" />
<PackageReference Include="OSPSuite.Presentation.Serialization" Version="11.0.72" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
</ItemGroup>

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10 changes: 5 additions & 5 deletions src/PKSim.Infrastructure/Services/ImportObservedDataTask.cs
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Expand Up @@ -306,13 +306,13 @@ public IEnumerable<string> PredefinedValuesFor(string name)
return Enumerable.Empty<string>();
}

public IReadOnlyList<string> DefaultMetaDataCategories => CoreConstants.ObservedData.DefaultProperties;
public IReadOnlyList<string> DefaultMetaDataCategories { get; } = CoreConstants.ObservedData.DefaultProperties;

public IReadOnlyList<string> ReadOnlyMetaDataCategories => new List<string> { };
public IReadOnlyList<string> ReadOnlyMetaDataCategories { get; } = new List<string> { };

public bool MolWeightAlwaysEditable { get; } = false;
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@georgeDaskalakis I changed this stuff here. Also when you always return a constant, use {get;} instead 0f => false. A bit faster...


public bool MolWeightEditable => false;

public bool MolWeightVisible => true;
public bool MolWeightVisible { get; }= true;

private IEnumerable<string> predefinedGenders => predefinedValuesFor(addPredefinedGenderValues);

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3 changes: 1 addition & 2 deletions src/PKSim.Matlab/PKSim.Matlab.csproj
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Expand Up @@ -27,8 +27,7 @@

<ItemGroup>
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
</ItemGroup>

<ItemGroup>
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6 changes: 2 additions & 4 deletions src/PKSim.Presentation/PKSim.Presentation.csproj
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Expand Up @@ -29,10 +29,8 @@
<ItemGroup>
<PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" />
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.60" />
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<PackageReference Include="OSPSuite.Presentation" Version="11.0.72" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
</ItemGroup>

<ItemGroup>
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3 changes: 1 addition & 2 deletions src/PKSim.R/PKSim.R.csproj
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Expand Up @@ -50,8 +50,7 @@

<ItemGroup>
<PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
<PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.51" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModel" Version="4.0.0.45" GeneratePathProperty="true" />
<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
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9 changes: 3 additions & 6 deletions src/PKSim.UI/PKSim.UI.csproj
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Expand Up @@ -51,12 +51,9 @@
<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" />
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<PackageReference Include="OSPSuite.UI" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.60" />
<PackageReference Include="OSPSuite.UI" Version="11.0.60" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
<PackageReference Include="OSPSuite.Presentation" Version="11.0.72" />
<PackageReference Include="OSPSuite.UI" Version="11.0.72" />
<PackageReference Include="OSPSuite.Core" Version="11.0.72" />
</ItemGroup>

<ItemGroup>
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6 changes: 2 additions & 4 deletions src/PKSim/PKSim.csproj
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Expand Up @@ -76,15 +76,13 @@
</ItemGroup>

<ItemGroup>
<PackageReference Include="OSPSuite.Core" Version="11.0.62" />
<PackageReference Include="OSPSuite.Core" Version="11.0.60" />
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<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
<PackageReference Include="System.Data.SQLite.Core" Version="1.0.112" GeneratePathProperty="true" />
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<PackageReference Include="OSPSuite.TeXReporting" Version="3.0.0.4" GeneratePathProperty="true" />

</ItemGroup>
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3 changes: 1 addition & 2 deletions tests/PKSim.Matlab.Tests/PKSim.Matlab.Tests.csproj
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Expand Up @@ -23,8 +23,7 @@
</PackageReference>
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
<PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
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<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
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3 changes: 1 addition & 2 deletions tests/PKSim.R.Tests/PKSim.R.Tests.csproj
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Expand Up @@ -23,8 +23,7 @@
</PackageReference>
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.0.0" />
<PackageReference Include="OSPSuite.BDDHelper" Version="4.0.0.1" />
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<PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.8" GeneratePathProperty="true" />
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