Merge pull request #2730 from Open-Systems-Pharmacology/develop

Version 12.2

Author: Yuri05

.github/workflows/build-and-publish.yml …hub/workflows/build-and-publish_12.2.yml.github/workflows/build-and-publish.yml renamed to .github/workflows/build-and-publish_12.2.yml .github/workflows/build-and-publish.yml renamed to .github/workflows/build-and-publish_12.2.yml

@@ -1,5 +1,5 @@
-name: Build and Publish
-run-name: Version 12.1.${{ github.run_number }} (${{ github.event.head_commit.message }})
+name: Build and Publish 12.2
+run-name: Version 12.2.${{ github.run_number }} (${{ github.event.head_commit.message }})
 
 on:
   push:
@@ -11,7 +11,7 @@ permissions:
 
 env:
   MAJOR: 12
-  MINOR: 1
+  MINOR: 2
   RUN: ${{ github.run_number }}
 
 jobs:

.github/workflows/build-pr.yml .github/workflows/build-pr_12.2.yml.github/workflows/build-pr.yml renamed to .github/workflows/build-pr_12.2.yml

@@ -1,10 +1,14 @@
-name: Build PR
+name: Build PR 12.2
 
 on:
   pull_request:
     branches:
     - develop
 
+permissions:
+  contents: read
+  packages: read
+
 jobs:
   build-and-test:
     runs-on: windows-latest
@@ -20,7 +24,7 @@ jobs:
           dotnet restore
 
       - name: Build
-        run: dotnet build OSPSuite.Core.sln /p:Version=12.1.9999
+        run: dotnet build OSPSuite.Core.sln /p:Version=12.2.9999
 
       - name : Test
         run: dotnet test .\tests\**\bin\Debug\net472\OSPSuite*Tests.dll -v normal --no-build  --logger:"html;LogFileName=../testLog_Windows.html"

.github/workflows/codeql.yml

@@ -0,0 +1,63 @@
+name: "CodeQL Advanced"
+
+on:
+  push:
+    branches:
+    - develop
+    - main
+  pull_request:
+    branches:
+    - develop
+  workflow_dispatch:
+  schedule:
+    - cron: '40 3 * * 1' # Runs at 03:40 every monday
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    runs-on: windows-latest
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: actions
+          build-mode: none
+        - language: csharp
+          build-mode: manual
+        - language: ruby
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+          submodules: 'true'
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+
+    - if: matrix.build-mode == 'manual'
+      run: |
+        nuget sources add -username Open-Systems-Pharmacology -password ${{ secrets.GITHUB_TOKEN }} -name OSP-GitHub-Packages -source "https://nuget.pkg.github.com/Open-Systems-Pharmacology/index.json"
+        dotnet restore
+        dotnet build OSPSuite.Core.sln /p:Version=12.2.9999
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/coverage.yml .github/workflows/coverage_12.2.yml.github/workflows/coverage.yml renamed to .github/workflows/coverage_12.2.yml

@@ -1,9 +1,13 @@
-name: Code Coverage
+name: Code Coverage 12.2
 
 on:
   schedule:
     - cron: '0 1 * * 4'
 
+permissions:
+  contents: read
+  packages: read
+
 jobs:
   cover:
     runs-on: windows-latest
@@ -19,7 +23,7 @@ jobs:
           dotnet restore
 
       - name: Build
-        run: dotnet build OSPSuite.Core.sln /p:Version=12.1.999
+        run: dotnet build OSPSuite.Core.sln /p:Version=12.2.999
 
 
       - name: Cover and report

OSPSuite.Core.sln

@@ -7,9 +7,10 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "OSPSuite.Core", "src\OSPSui
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{25A7357D-0812-44F3-AF90-244FD752FAE2}"
 	ProjectSection(SolutionItems) = preProject
-		.github\workflows\build-and-publish.yml = .github\workflows\build-and-publish.yml
-		.github\workflows\build-pr.yml = .github\workflows\build-pr.yml
-		.github\workflows\coverage.yml = .github\workflows\coverage.yml
+		.github\workflows\build-and-publish_12.2.yml = .github\workflows\build-and-publish_12.2.yml
+		.github\workflows\build-pr_12.2.yml = .github\workflows\build-pr_12.2.yml
+		.github\workflows\coverage_12.2.yml = .github\workflows\coverage_12.2.yml
+		dotcover.xml = dotcover.xml
 		logo.png = logo.png
 		rakefile.rb = rakefile.rb
 		SolutionInfo.cs = SolutionInfo.cs

README.md

@@ -3,7 +3,7 @@
 Core functionalities of the Open Systems Pharmacology Suite.
 
 ## Code Status
-[![Build status](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/OSPSuite.Core/build-and-publish.yml?logo=nuget&label=Build%20status)](https://github.com/Open-Systems-Pharmacology/OSPSuite.Core/actions/workflows/build-and-publish.yml)
+[![Build status](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/OSPSuite.Core/build-and-publish_12.2.yml?logo=nuget&label=Build%20status)](https://github.com/Open-Systems-Pharmacology/OSPSuite.Core/actions/workflows/build-and-publish_12.2.yml)
 [![Coverage status](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite.Core/branch/develop/graph/badge.svg)](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite.Core)
 
 ## Code of conduct

dotcover.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <CoverageParams>
   <TargetArguments>
-  Tests\OSPSuite.Core.Tests\bin\Debug\net472\OSPSuite.Core.Tests.dll
+  Tests\OSPSuite.Core.Tests\bin\Debug\net8\OSPSuite.Core.Tests.dll
   Tests\OSPSuite.Core.IntegrationTests\bin\Debug\net472\OSPSuite.Core.IntegrationTests.dll
   Tests\OSPSuite.Presentation.Tests\bin\Debug\net472\OSPSuite.Presentation.Tests.dll
   Tests\OSPSuite.Infrastructure.Tests\bin\Debug\net472\OSPSuite.Infrastructure.Tests.dll

rakefile.rb

@@ -28,7 +28,7 @@
 
 task :create_local_nuget, [:arg1, :arg2, :arg3] do |t, args|
   FileUtils.rm_f Dir.glob("./nuget_repo/*.nupkg")
-  versionId = "12.1.0-" + generate_code(5)
+  versionId = "12.2.0-" + generate_code(5)
   puts("Your version is " + versionId.red)
   system("dotnet", "pack", "-p:PackageVersion="+ versionId, "--configuration", "Debug", "--output", "nuget_repo", "--no-build") 
   if args.to_hash.values.include? "m"
@@ -41,7 +41,7 @@
 
 private
 def find_token(file, regex)
-  file_content = str = IO.read(file)
+  file_content = str = File.read(file)
   matches = file_content.match(regex)
 
   if(matches.nil?)

src/OSPSuite.Assets/UIConstants.cs

@@ -5,6 +5,7 @@
 using System.Drawing;
 using System.Linq;
 using System.Text;
+using OSPSuite.Utility.Collections;
 
 namespace OSPSuite.Assets
 {
@@ -232,7 +233,7 @@ public static class Captions
       public static readonly string DeleteSelected = "Delete Selected Records";
       public static readonly string ModulesFolder = "Modules";
       public static readonly string ApplyChangesToUpdateChart = "Apply changes to update chart";
-      public static readonly string Apply = "Apply";
+      public static readonly string ApplyUpdates = "Apply updates";
       public static readonly string AutoUpdateChart = "Auto-update chart";
 
       public static string EditTableParameter(string parameter, bool editable) => $"{(editable ? "Edit" : "Show")} table parameter '{parameter}'";
@@ -471,7 +472,7 @@ public static class Importer
          public static readonly string SaveConfiguration = "Save Configuration";
          public static readonly string ApplyConfiguration = "Load Configuration";
          public static readonly string ActionWillEraseLoadedData = "This action will result in dropping all the loaded sheets. Do you want to continue?";
-         public static readonly string OpenFile = "Select the file you would like to apply configuration on";
+         public static readonly string SelectFileToImport = "Select the file to import";
          public static readonly string GroupByTitle = "Group By";
          public static readonly string SelectToAdd = "Select to add";
          public static readonly string MappingTitle = "Mapping";
@@ -1203,6 +1204,16 @@ public static class Descriptions
             }
          }
 
+         public static string SimulationsAreRunning(IReadOnlyList<string> names)
+         {
+            return $"The following Simulations are currently running: {names.ToString(", ", "'")}, action cannot be performed until they are stopped.";
+         }
+
+         public static string ParameterIdentificationsAreRunning(IReadOnlyList<string> names)
+         {
+            return $"The following Parameter Identifications are currently running: {ObjectTypes.ParameterIdentification.ToLowerInvariant().PluralizeIf(names)} {names.ToString(", ", "'")}, action cannot be performed until they are stopped.";
+         }
+
          public static string ReallyDeleteParameterIdentifications(IReadOnlyList<string> names)
          {
             return $"Really delete {ObjectTypes.ParameterIdentification.ToLowerInvariant().PluralizeIf(names)} {names.ToString(", ", "'")}?";
@@ -1240,11 +1251,30 @@ public static class SensitivityAnalysis
          public static readonly string NoResultsAvailable = "No result available. Please start sensitivity analysis";
          public static readonly string ErrorsDuringPreviousRun = "<b>The last run resulted in one or more errors:</b>";
 
-         public static string SensitivityAnalysisFinished(string duration)
+         public static string SensitivityAnalysisFinished(string duration, IReadOnlyList<string> failedPKParameterCalculations)
          {
+            if (failedPKParameterCalculations.Any())
+            {
+
+               return $"Sensitivity analysis finished in {duration} but failed to calculate sensitivities for:{Environment.NewLine}{buildNestedList(failedPKParameterCalculations)}";
+            }
             return $"Sensitivity analysis finished in {duration}";
          }
 
+         private static string buildNestedList(IReadOnlyList<string> failedPKParameterCalculations)
+         {
+            var sb = new StringBuilder();
+            sb.AppendLine();
+            
+            failedPKParameterCalculations.Each(x =>
+            {
+               sb.Append(" - ");
+               sb.AppendLine(x);
+            });
+            
+            return sb.ToString();
+         }
+
          public static readonly string SensitivityAnalysisCanceled = "Sensitivity analysis canceled";
          public static readonly string NoSensitivityAnalysisRunning = "No visual feedback available. Please start sensitivity analysis.";
          public static readonly string SensitivityHasNotBeenUpdated = "Sensitivity analysis has not been updated";
@@ -1633,9 +1663,28 @@ public static string CannotFindSimulationResultsForOutput(string fullOutputPath)
       public static readonly string TableFormulaWithOffsetUsesNonTableFormulaObject = "Object used in table formula with offset must be based an a table formula";
       public static readonly string ScaleFactorShouldBeGreaterThanZero = "Scale factor should be greater than 0";
 
+      public static string TimeFromRepositoryNotStrictlyMonotone(double valueBefore, double valueAfter, string displayUnit, string repositoryName)
+      {
+         var hint = hintForNotStrictlyMonotone(valueBefore, valueAfter, displayUnit);
+
+         return $"The time column in data set '{repositoryName}' is not strictly monotonically increasing ({hint}).\nEnsure that time always increases (e.g. 0.5, 1, 2, 4 hours).";
+      }
+
+      private static string hintForNotStrictlyMonotone(double valueBefore, double valueAfter, string displayUnit)
+      {
+         return Equals(valueAfter, valueBefore) ? $"{valueBefore} {displayUnit} is duplicated" : $"{valueBefore} {displayUnit} is immediately followed by {valueAfter} {displayUnit}";
+      }
+
+      public static string TimeFromSheetNotStrictlyMonotone(double valueBefore, double valueAfter, string displayUnit, string sheetName)
+      {
+         var hint = hintForNotStrictlyMonotone(valueBefore, valueAfter, displayUnit);
+
+         return $"The time column in sheet '{sheetName}' is not strictly monotonically increasing ({hint}).\nEnsure that time always increases (e.g. 0.5, 1, 2, 4 hours).";
+      }
+
       public static string TimeNotStrictlyMonotone(double valueBefore, double valueAfter, string displayUnit)
       {
-         var hint = Equals(valueAfter, valueBefore) ? $"{valueBefore} {displayUnit} is duplicated" : $"{valueBefore} {displayUnit} is immediately followed by {valueAfter} {displayUnit}";
+         var hint = hintForNotStrictlyMonotone(valueBefore, valueAfter, displayUnit);
 
          return $"The time column is not strictly monotonically increasing ({hint}).\nEnsure that time always increases (e.g. 0.5, 1, 2, 4 hours).";
       }
@@ -2154,6 +2203,8 @@ public static string LargeNumberOfOutputPoints(int numberOfPoints) =>
          $"The selected output resolution will generate {numberOfPoints} points and may severely impact the software performance.\nAre you sure you want to run with these setting? If not, consider changing output resolution in simulations settings";
 
       public static string NeighborhoodWasNotFoundInModel(string neighborhoodName, string buildingBlockName) => $"The neighborhood '{neighborhoodName}' from building block '{buildingBlockName}' was not added to the simulation";
+
+      public static string ExpressionMoleculeNotFoundInSimulation(string moleculeName) => $"The molecule '{moleculeName}' is not part of the simulation structure";
    }
 
    public static class RibbonCategories
@@ -2253,7 +2304,7 @@ public static string CompareObjects(string objectType)
          return $"Compare {objectType}s";
       }
 
-      public static readonly string AutoUpdateChart = "Autoupdate chart";
+      public static readonly string AutoUpdateChart = "Auto-update chart";
       public static readonly string ApplyUpdates = "Apply updates";
    }
 
@@ -2346,6 +2397,16 @@ public static string SetObservedDataParameterCommandDescription(string oldValue,
          return $"{parameterName} set from {oldValue} to {newValue} in {observedDataName}";
       }
 
+      public static string AddManyObservedDataToProjectDescription(IReadOnlyList<string> names, string projectName)
+      {
+         return $"Added observed data: \n\n{string.Join("\n", names)}\n\n to project '{projectName}'";
+      }
+
+      public static string RemoveManyObservedDataToProjectDescription(IReadOnlyList<string> names, string projectName)
+      {
+         return $"Removed observed data: \n\n{string.Join("\n", names)}\n\n from project '{projectName}'";
+      }
+
       public static string AddObservedDataToProjectDescription(string observedDataName, string projectName)
       {
          return AddEntityToContainer(ObjectTypes.ObservedData, observedDataName, ObjectTypes.Project, projectName);
@@ -2650,4 +2711,4 @@ public static class Colors
       public static Color NegativeCorrelation = Color.FromArgb(96, 187, 70);
       public static Color PositiveCorrelation = Color.FromArgb(0, 174, 239);
    }
-}
+}

src/OSPSuite.Core/Chart/CurveChart.cs

@@ -116,7 +116,7 @@ public void RemoveCurve(string curveId)
          updateAxesForRemovedCurve(yAxisType);
       }
 
-      public Curve CreateCurve(DataColumn columnX, DataColumn columnY, string curveName, IDimensionFactory dimensionFactory)
+      public virtual Curve CreateCurve(DataColumn columnX, DataColumn columnY, string curveName, IDimensionFactory dimensionFactory)
       {
          var curve = FindCurveWithSameData(columnX, columnY);
          if (curve != null)