Replace MiKTeX/LaTeX reporting with Markdown + QuestPDF (#325)

* Replace MiKTeX/LaTeX reporting with Markdown + QuestPDF

Removes the dependency on OSPSuite.TeXReporting and MiKTeX, replacing
it with a simpler, pure .NET solution:

- Markdown reports with embedded SVG charts (viewable in VS Code, GitHub)
- PDF reports via QuestPDF (no external tools required)
- Custom SVG chart generator for 2D line charts with log/linear scale
- Report format switchable via ReportFormat enum

New files:
- Reporting/Charts/SvgChartGenerator.cs - SVG line chart generation
- Reporting/Markdown/* - Markdown builder pattern implementation
- Reporting/Pdf/PdfReportDocument.cs - QuestPDF document
- Services/MarkdownReportingTask.cs, PdfReportingTask.cs

Removed:
- All *TeXBuilder.cs files
- *Reporter.cs files
- OSPSuite.TeXReporting dependency from all projects

Closes #183

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Restore fixProductNameForWindows11 method for tests

The method was removed during cross-platform refactoring but is
needed by OperatingSystemInfoSpecs tests that use reflection to
call it.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Revert OperatingSystemInfo to original Windows-specific implementation

Keep the original Windows-specific OperatingSystemInfo that uses
Registry, WMI, and SystemInformation APIs. Update Core and Tests
projects to target net8.0-windows.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Trigger update

* Address PR comments

* Refactor test to use real MarkdownBuilderRepository

Replace TestMarkdownBuilderRepository with the real MarkdownBuilderRepository
and all production builders. This improves test coverage by exercising the
actual builder implementations rather than duplicating their logic.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add MissingFileComparisonResult handling in Markdown and PDF reports

- Create MissingFileComparisonResultMarkdownBuilder to properly report
  missing file details including which folder contains the file and
  which folder is missing it
- Add ComposeMissingFileResult in PdfReportDocument to display the
  missing file validation message in PDF reports
- Register the new builder in ValidatorRegister
- Add builder to test setup

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix PR review findings: table escaping, null checks, and test refactoring

- Escape pipe characters in MarkdownReportContext.AppendTable to prevent
  broken markdown tables when cell values contain '|'
- Add null validation for installationValidationResult and RunSummary in
  both MarkdownReportingTask and PdfReportingTask before accessing StartTime
- Refactor MarkdownReportingSpecs to use ContextForIntegration, resolving
  IMarkdownReportingTask from the DI container instead of manually
  constructing all builders

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Refactor ValidationReportingTask to use ReportOptions parameter

Replace DefaultFormat property with ReportOptions parameter that includes:
- ReportFormat as flags enum (None, Markdown, Pdf, All)
- OpenReport boolean
- Convenience properties ExportToMarkdown and ExportToPdf

This allows generating both Markdown and PDF reports in a single call
by using ReportFormat.All.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Bump to version 13. ALso use correct builder

* Fix Markdown bold formatting by removing trailing space from ValidationResult caption

The trailing space in the caption prevented proper bold formatting in Markdown
output (**Result of the validation: ** instead of **Result of the validation:**).

* Only generate charts for invalid outputs in Markdown and PDF reports

Valid outputs with matching curves don't need charts. Removing the
valid-outputs-with-data loop prevents generating thousands of
unnecessary pages when a file has many outputs but only a few are invalid.

* Ensures that we export the expected format

* Add all valid curves back

* Use report-specific filenames for PDF output

Pass reportName parameter to reportOutputPath so PDF filenames reflect
the actual report type (FolderComparison vs InstallationValidation).

* Extract shared helpers, disable start without report format, add tests

- Extract ChartDataFactory.CreateFor() to eliminate duplicate
  createChartData methods in OutputComparisonResultMarkdownBuilder
  and PdfReportDocument
- Extract ColorExtensions.ToHexString() to replace colorToHex in
  SvgChartGenerator, toQuestColor in PdfReportDocument, and inline
  hex formatting in MarkdownReportContext
- Fix PDF run summary labels: start/end time now have their own
  labels instead of reusing BatchRunDuration for the start time
- Disable start button in MainView and SimulationComparisonView
  when neither PDF nor Markdown report format is selected
- Replace Enumerable.Select allocation with Enumerable.Repeat in
  MarkdownReportContext.AppendTable separator row
- Add MarkdownReportContextSpecs unit tests covering headings,
  tables, colored status, bold formatting, and content accumulation
- Add observations to MarkdownReportingSpecs for SVG chart,
  validation state, and deviation section

* Replace hardcoded strings with resources and add null guards

- Add localized resource keys to Assets.Reporting: StartTime, EndTime,
  Yes, No, OSLabel, FileWasContainedInFolder, ButWasMissingInFolder,
  ValidationPerformedIn
- Replace all hardcoded English strings in PdfReportDocument with
  Assets.Reporting resources for consistent localization
- Add constructor null guards in PdfReportDocument for validationResult,
  comparisonResult, and svgChartGenerator
- Add null guard for comparisonResult in both PdfReportingTask and
  MarkdownReportingTask CreateReport overloads

* Ensure enable state is reset

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Co-authored-by: msevestre <msevestre@users.noreply.github.com>

Author: msevestre

.gitignore

@@ -246,3 +246,5 @@ ModelManifest.xml
 # FAKE - F# Make
 .fake/
 *.ncrunchsolution
+
+.claude/settings.local.json

src/InstallationValidator.Core/Assets/Captions.cs

@@ -52,6 +52,8 @@ public static string ValidationDescription
       public static readonly string IgnoreRemovedCurves= "Ignore removed curves";
       public static readonly string ReallyCancelFolderComparison = "Really cancel folder comparison?";
       public static readonly string ExclusionList = "Exclusion List";
+      public static readonly string ExportToPdf = "Export to PDF";
+      public static readonly string ExportToMarkdown = "Export to Markdown";
    }
 
    public static class Logs
@@ -187,8 +189,13 @@ public static class Reporting
       public static readonly string OverallValidationResult = "Overall Validation Result";
       public static readonly string FailedValidations = "Failed Validations";
       public static readonly string InputConfigurationFolder = "Input Configuration Folder";
+      public static readonly string StartTime = "Start time";
+      public static readonly string EndTime = "End time";
       public static readonly string BatchRunDuration = "Run Duration";
-      public static readonly string ValidationResult = "Result of the validation: ";
+      public static readonly string Yes = "Yes";
+      public static readonly string No = "No";
+      public static readonly string OSLabel = "OS";
+      public static readonly string ValidationResult = "Result of the validation:";
       public static readonly string Simulation = "Simulation";
       public static readonly string Deviation = "Deviation";
       public static readonly string OutputPath = "Output Path";
@@ -213,6 +220,10 @@ public static string InstallationValidationPerformedIn(string startTime, string
 
       public static string ComparisonFolder(string folderName) => $"{folderName} Folder";
 
+      public static string FileWasContainedInFolder(string fileName) => $"{fileName} was contained in folder:";
+      public static readonly string ButWasMissingInFolder = "but was missing in folder:";
+      public static string ValidationPerformedIn(string duration) => $"Validation performed in {duration}";
+
       public static string MissingFileValidationMessage(string fileName, string folderContainingFile, string folderWithoutFile) =>
          $"{fileName} was contained in folder:{Environment.NewLine}{folderContainingFile}{Environment.NewLine}but was missing in folder:{Environment.NewLine}{folderWithoutFile}";
    }

src/InstallationValidator.Core/Domain/OperatingSystemInfo.cs

@@ -10,7 +10,6 @@ namespace InstallationValidator.Core.Domain
    public class OperatingSystemInfo
    {
       private const string WINDOWS_REG_KEY = @"SOFTWARE\Microsoft\Windows NT\CurrentVersion";
-
       public string ComputerName { get; } = Environment.MachineName;
       public string Architecture => Environment.Is64BitOperatingSystem ? "x64" : "x32";
 
@@ -103,4 +102,4 @@ public bool IsRunningOnVirtualMachine
 
       public bool IsRunningOnTerminalSession => SystemInformation.TerminalServerSession;
    }
-}
+}

src/InstallationValidator.Core/InstallationValidator.Core.csproj

@@ -1,7 +1,9 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net472</TargetFramework>
+    <TargetFramework>net8.0-windows</TargetFramework>
+    <UseWindowsForms>true</UseWindowsForms>
+    <EnableWindowsTargeting>true</EnableWindowsTargeting>
     <GenerateAssemblyProductAttribute>false</GenerateAssemblyProductAttribute>
     <GenerateAssemblyCompanyAttribute>false</GenerateAssemblyCompanyAttribute>
     <PackageTags>open-systems-pharmacology, ospsuite-components</PackageTags>
@@ -10,7 +12,7 @@
     <OutputPath>bin\$(Configuration)</OutputPath>
     <DocumentationFile>bin\$(Configuration)\$(TargetFramework)\$(AssemblyName).xml</DocumentationFile>
     <NoWarn>1591</NoWarn>
-    <Version Condition="'$(Version)' == ''">12.3.0</Version>
+    <Version Condition="'$(Version)' == ''">13.0.0</Version>
     <IncludeSourceRevisionInInformationalVersion>false</IncludeSourceRevisionInInformationalVersion>
   </PropertyGroup>
 
@@ -24,15 +26,19 @@
 
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.3.1" />
-    <PackageReference Include="OSPSuite.Infrastructure" Version="12.3.1" />
-    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="12.3.1" />
-    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="12.3.1" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.3.1" />
-    <PackageReference Include="OSPSuite.TeXReporting" Version="3.0.1.1" />
-    <PackageReference Include="OSPSuite.Utility" Version="4.1.1.1" />
-    <PackageReference Include="OSPSuite.Core" Version="12.3.1" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.3.1" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="13.0.87" />
+    <PackageReference Include="OSPSuite.DevExpress" Version="21.2.15.1" />
+    <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.76" />
+    <PackageReference Include="OSPSuite.Infrastructure" Version="13.0.87" />
+    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="13.0.87" />
+    <PackageReference Include="OSPSuite.Presentation" Version="13.0.87" />
+    <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.79" />
+    <PackageReference Include="OSPSuite.Utility" Version="4.1.1.5" />
+    <PackageReference Include="OSPSuite.Core" Version="13.0.87" />
+    <PackageReference Include="OSPSuite.Assets" Version="13.0.87" />
+    <PackageReference Include="QuestPDF" Version="2024.3.0" />
+    <PackageReference Include="Microsoft.Win32.Registry" Version="5.0.0" />
+    <PackageReference Include="System.Management" Version="8.0.0" />
   </ItemGroup>
 
   <ItemGroup>
@@ -42,9 +48,5 @@
     </None>
   </ItemGroup>
 
-  <ItemGroup>
-    <Reference Include="System.Management" />
-    <Reference Include="System.Windows.Forms" />
-  </ItemGroup>
 
 </Project>

src/InstallationValidator.Core/Presentation/DTO/ReportOptionsDTO.cs

@@ -0,0 +1,8 @@
+namespace InstallationValidator.Core.Presentation.DTO
+{
+   public class ReportOptionsDTO
+   {
+      public bool ExportToPdf { get; set; } = true;
+      public bool ExportToMarkdown { get; set; }
+   }
+}

src/InstallationValidator.Core/Presentation/MainPresenter.cs

@@ -28,6 +28,7 @@ public class MainPresenter : AbstractDisposablePresenter<IMainView, IMainPresent
       private readonly IInstallationValidatorConfiguration _configuration;
       private readonly IValidationReportingTask _validationReportingTask;
       private readonly FolderDTO _outputFolderDTO = new FolderDTO(folderMustExist: false);
+      private readonly ReportOptionsDTO _reportOptionsDTO = new ReportOptionsDTO();
       private CancellationTokenSource _cancellationTokenSource;
       private bool _validationRunning;
 
@@ -40,6 +41,7 @@ public MainPresenter(IMainView view, IDialogCreator dialogCreator, IBatchStarter
          _validationReportingTask = validationReportingTask;
          _outputFolderDTO.FolderPath = configuration.DefaultOutputPath;
          view.BindTo(_outputFolderDTO);
+         view.BindToReportOptions(_reportOptionsDTO);
       }
 
       public void SelectOutputFolder()
@@ -86,7 +88,7 @@ public async Task<InstallationValidationResult> StartInstallationValidation()
             validationResult.RunSummary = runSummary;
 
             this.LogLine(Logs.StartingReport);
-            await _validationReportingTask.CreateReport(validationResult, _outputFolderDTO.FolderPath, openReport: true);
+            await _validationReportingTask.CreateReport(validationResult, _outputFolderDTO.FolderPath, new ReportOptions(reportFormatFromDTO(), openReport: true));
             this.LogLine();
 
             this.LogLine(Logs.ValidationCompleted);
@@ -109,6 +111,14 @@ public async Task<InstallationValidationResult> StartInstallationValidation()
          }
       }
 
+      private ReportFormat reportFormatFromDTO()
+      {
+         var format = ReportFormat.None;
+         if (_reportOptionsDTO.ExportToPdf) format |= ReportFormat.Pdf;
+         if (_reportOptionsDTO.ExportToMarkdown) format |= ReportFormat.Markdown;
+         return format;
+      }
+
       private void updateValidationRunningState(bool running)
       {
          _validationRunning = running;

src/InstallationValidator.Core/Presentation/SimulationComparisonPresenter.cs

@@ -35,6 +35,7 @@ public class SimulationComparisonPresenter : AbstractDisposablePresenter<ISimula
       private readonly IBatchComparisonTask _batchComparisonTask;
       private readonly IValidationReportingTask _validationReportingTask;
       private readonly FolderComparisonDTO _folderComparisonDTO;
+      private readonly ReportOptionsDTO _reportOptionsDTO = new ReportOptionsDTO();
 
       public SimulationComparisonPresenter(ISimulationComparisonView view, IInstallationValidatorConfiguration configuration, IDialogCreator dialogCreator,
          IBatchComparisonTask batchComparisonTask, IValidationReportingTask validationReportingTask) : base(view)
@@ -45,6 +46,7 @@ public SimulationComparisonPresenter(ISimulationComparisonView view, IInstallati
          _validationReportingTask = validationReportingTask;
          _folderComparisonDTO = new FolderComparisonDTO();
          view.BindTo(_folderComparisonDTO);
+         view.BindToReportOptions(_reportOptionsDTO);
       }
 
       public void Handle(AppendTextToLogEvent eventToHandle)
@@ -70,7 +72,7 @@ public async Task StartComparison()
             this.LogLine();
 
             this.LogLine(Logs.StartingReport);
-            await _validationReportingTask.CreateReport(comparisonResult, _folderComparisonDTO.FirstFolder.FolderPath, _folderComparisonDTO.SecondFolder.FolderPath, openReport: true);
+            await _validationReportingTask.CreateReport(comparisonResult, _folderComparisonDTO.FirstFolder.FolderPath, _folderComparisonDTO.SecondFolder.FolderPath, new ReportOptions(reportFormatFromDTO(), openReport: true));
             this.LogLine();
 
             this.LogLine(Logs.ComparisonCompleted);
@@ -102,6 +104,14 @@ private ComparisonSettings comparisonSettingsFromDTO()
          };
       }
 
+      private ReportFormat reportFormatFromDTO()
+      {
+         var format = ReportFormat.None;
+         if (_reportOptionsDTO.ExportToPdf) format |= ReportFormat.Pdf;
+         if (_reportOptionsDTO.ExportToMarkdown) format |= ReportFormat.Markdown;
+         return format;
+      }
+
       private void updateComparisonRunningState(bool running)
       {
          _comparisonRunning = running;

src/InstallationValidator.Core/Presentation/Views/IMainView.cs

@@ -6,6 +6,7 @@ namespace InstallationValidator.Core.Presentation.Views
    public interface IMainView : ILoggerView, IView<IMainPresenter>
    {
       void BindTo(FolderDTO outputFolderDTO);
+      void BindToReportOptions(ReportOptionsDTO reportOptionsDTO);
       void ValidationIsRunning(bool validationRunning);
    }
 }

src/InstallationValidator.Core/Presentation/Views/ISimulationComparisonView.cs

@@ -7,5 +7,6 @@ public interface ISimulationComparisonView : ILoggerView, IView<ISimulationCompa
    {
       void ComparisonIsRunning(bool comparisonRunning);
       void BindTo(FolderComparisonDTO folderComparisonDTO);
+      void BindToReportOptions(ReportOptionsDTO reportOptionsDTO);
    }
 }