Skyline: Extended keyboard shortcut help

.cursorrules

@@ -1,4 +1,8 @@
 # Cursor project orientation for ProteoWizard (pwiz)
+# 
+# This file provides Cursor-specific behavior guidance.
+# For detailed coding conventions, style guidelines, and testing patterns,
+# see STYLEGUIDE.md - the comprehensive style guide used by all AI tools.
 
 [project]
 name = "ProteoWizard (pwiz)"
@@ -51,6 +55,13 @@ docs = [
 - Use fenced code blocks only for relevant snippets or commands.
 - Default to read-only discovery before edits; then apply focused edits.
 
+[build_and_testing]
+- LLM agents CANNOT build or run this project directly.
+- Build and test operations must be performed by the developer using Visual Studio.
+- When code changes are made, request that the developer build and test the changes.
+- Do not attempt to run quickbuild.bat, bs.bat, or any build commands.
+- Do not attempt to run tests or execute the application.
+
 [file_headers]
 standard_header = """
 /*
@@ -82,95 +93,23 @@ ai_attribution = {
 }
 
 [testing]
-unit_tests = {
-  projects = ["Test", "TestData"]
-  base_classes = ["AbstractUnitTest", "AbstractUnitTestEx"]
-  characteristics = "Fast execution, no UI overhead (no SkylineWindow)"
-  test_project = "General unit tests, may access file system but no UI"
-  testdata_project = "Unit tests with mass spectrometry data files, must access file system"
-}
-functional_tests = {
-  projects = ["TestFunctional", "TestPerf", "TestTutorial"]
-  base_classes = ["AbstractFunctionalTest", "AbstractFunctionalTestEx"]
-  overhead = "Significant - must show/destroy SkylineWindow and drive UI"
-  performance = "Much slower than unit tests (in-memory, no file system/network)"
-  consolidation = "Prefer multiple validations in single test class with one [TestMethod]"
-  helpers = "Use private helper methods for different validation concerns"
-  avoid = "Separate test classes for related functional validations that could share SkylineWindow"
-}
-test_perf = {
-  purpose = "Performance tests with large datasets (>100MB)"
-  requirements = ">100GB free disk space, Downloads folder storage"
-  frequency = "Run less often than standard functional tests"
-}
-test_tutorial = {
-  purpose = "Automated tutorial implementation and screenshot capture"
-  source = "Skyline/Documentation/Tutorials/*"
-  screenshots = "s-01.png, s-02.png, cover.png in language subfolders (en, ja, zh-CHS)"
-  examples = ["TestIrtTutorial for iRT tutorial"]
-}
+# See STYLEGUIDE.md for comprehensive testing guidelines
+reference = "STYLEGUIDE.md"
 
 [style_skyline_csharp]
-control_flow = {
-  single_line_if = false
-  allow_no_braces_single_statement = true
-}
-member_order = [
-  "static_fields",
-  "static_public_methods",
-  "private_instance_fields",
-  "constructors",
-  "public_instance_api",
-  "private_helpers_after_usage"
-]
-naming = {
-  descriptive_names = true
-  avoid_abbreviations = true
-  private_instance_field_prefix = "_"
-  private_static_field_prefix = "_"
-  interface_prefix = "I"
-  type_parameter_prefix = "T"
-  enum_member_style = "snake_case"
-}
-formatting = {
-  preserve_existing_indentation = true
-  avoid_unrelated_reformatting = true
-  tabs_disallowed = true
-}
+# See STYLEGUIDE.md for comprehensive C# coding conventions
+reference = "STYLEGUIDE.md"
 docs = [
   "STYLEGUIDE.md"
 ]
 
 [localization]
-resource_system = {
-  primary_location = "pwiz_tools/Skyline/Properties/Resources.resx"
-  auxiliary_locations = [
-    "pwiz_tools/Skyline/Menus/MenusResources.resx",
-    "pwiz_tools/Skyline/FileUI/FileUIResources.resx",
-    "pwiz_tools/Skyline/Controls/Graphs/GraphResources.resx"
-  ]
-  organization_tool = "pwiz_tools/Skyline/Executables/AssortResources/ResourceAssorter.cs"
-  static_analysis_test = "pwiz_tools/Skyline/Test/CodeInspectionTest.cs"
-}
-guidelines = [
-  "For folder-specific strings (e.g., menu items), add directly to <folder-name>Resources.resx (e.g., MenusResources.resx)",
-  "For general UI strings, add to Properties/Resources.resx and let ResourceAssorter organize them",
-  "ResourceAssorter moves strings from Properties/Resources.resx to appropriate <folder-name>Resources.resx files based on usage context",
-  "Generate resource keys by replacing non-alphanumerics with '_' and trimming",
-  "Prefer context prefixes like SkylineWindow_ or EditMenu_ where appropriate",
-  "CRITICAL: When adding .resx entries, also add corresponding public static string properties to .Designer.cs in ALPHABETICAL ORDER",
-  "Compiler will fail with CS0117 errors if Designer.cs is not updated",
-  "ReSharper static analysis and CodeInspectionTest.cs verify proper resource placement",
-  "AssortResources.exe can clean up misplaced resources if needed"
-]
+# See STYLEGUIDE.md for detailed localization guidelines
+reference = "STYLEGUIDE.md"
 
 [ui_guidelines]
-menu_items = [
-  "All menuMain items and submenus must have mnemonics (e.g., '&Keyboard Shortcuts')",
-  "Use title-case for menu text and action buttons (e.g., 'Keyboard Shortcuts')",
-  "Only menuMain items can have mnemonics and keyboard shortcuts",
-  "Context menus should not have mnemonics or keyboard shortcuts"
-]
+# See STYLEGUIDE.md for detailed UI guidelines
+reference = "STYLEGUIDE.md"
 
 [executables]
 note = "Projects under pwiz_tools/Skyline/Executables are separate solutions (stand-alone tools and utilities). Not built by Skyline.sln; prefer Skyline conventions unless local overrides are required."

README.md

@@ -78,6 +78,15 @@ Full setup and troubleshooting guide: [How to Build Skyline](https://skyline.ms/
 
 Skyline C# coding conventions: see `STYLEGUIDE.md`.
 
+### Threading Guidelines
+
+The project avoids `async`/`await` and .NET Task support in favor of deterministic threading:
+
+- **Use `CommonActionUtil.RunAsync()`** (in Shared projects) or `ActionUtil.RunAsync()` (in Skyline) instead of `Task.Run()` or `async`/`await`
+- **Avoid .NET thread pool** - Use allocated threads for more deterministic behavior and easier debugging
+- **Prefer synchronous operations** on background threads when possible
+- **Thread marshaling** - Use `Invoke()` for UI thread operations from background threads
+
 Executables note: Projects under `pwiz_tools/Skyline/Executables` are separate solutions (most build stand‑alone EXEs or developer tools, some ship with Skyline). They are not built by `Skyline.sln`, but should generally follow the same coding conventions unless a local project override is required. See the Tool Store: https://skyline.ms/tools.url
 
 EditorConfig: Repository-wide `.editorconfig` enforces core C# naming/formatting so separate solutions (including `pwiz_tools/Skyline/Executables`) inherit consistent style in Visual Studio.

STYLEGUIDE.md

@@ -2,6 +2,8 @@
 
 This guide captures Skyline-specific C# conventions to keep AI- and human-authored code consistent with `pwiz_tools/Skyline`.
 
+**Universal AI Guidelines**: This file serves as the comprehensive style guide for all AI tools (Cursor, Claude Code, GitHub Copilot, ChatGPT, etc.). The `.cursorrules` file references this document to avoid duplication.
+
 ## Control flow
 - If statements must not be single-line. If braces are omitted, keep the condition and body on separate lines.
 
@@ -73,6 +75,7 @@ EditorConfig
 - If a specific Executables project needs different rules, add a minimal project-level `.editorconfig` or project `.DotSettings` override local to that solution only.
 
 ## Resource strings (localization)
+- **CRITICAL: ALL user-facing text must be in .resx files - NO string literals in .cs files**
 - Add new UI strings for menus/dialogs/pages to `pwiz_tools/Skyline/Menus/MenusResources.resx`.
 - Strings will be translated to Chinese/Japanese via our translation process; use clear, concise English.
 - Generate resource keys from the English text in a ReSharper-like way:

pwiz_tools/Shared/Common/Common.csproj

@@ -17,6 +17,7 @@
     <OldToolsVersion>3.5</OldToolsVersion>
     <UpgradeBackupLocation />
     <TargetFrameworkProfile />
+    <RuntimeIdentifiers>win;win-x64;win-x86</RuntimeIdentifiers>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x86' ">
     <DebugSymbols>true</DebugSymbols>
@@ -586,6 +587,11 @@
     <None Include="Resources\maximize.bmp" />
     <None Include="Resources\MatchCase.bmp" />
   </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="Microsoft.Web.WebView2">
+      <Version>1.0.2420.47</Version>
+    </PackageReference>
+  </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\MSGraph\MSGraph.csproj">
       <Project>{26CFD1FF-F4F7-4F66-B5B4-E686BDB9B34E}</Project>

pwiz_tools/Shared/Common/DataBinding/Controls/Editor/DocumentationViewer.cs

@@ -1,6 +1,7 @@
 /*
  * Original author: Nicholas Shulman <nicksh .at. u.washington.edu>,
  *                  MacCoss Lab, Department of Genome Sciences, UW
+ * AI assistance: Cursor (Claude Sonnet 4) <cursor .at. anysphere.co>
  *
  * Copyright 2016 University of Washington - Seattle, WA
  *
@@ -17,31 +18,156 @@
  * limitations under the License.
  */
 using System;
-using System.Windows.Forms;
+using Microsoft.Web.WebView2.Core;
+using pwiz.Common.GUI;
 using pwiz.Common.SystemUtil;
 
 namespace pwiz.Common.DataBinding.Controls.Editor
 {
     public partial class DocumentationViewer : CommonFormEx
     {
+        private string _documentationHtml = string.Empty;
+        private string _webView2Html = string.Empty;
+
+        /// <summary>
+        /// Static property to set the WebView2 environment directory for test scenarios.
+        /// Tests should set this before creating a DocumentationViewer and reset to null when done.
+        /// </summary>
+        public static string TestWebView2EnvironmentDirectory { get; set; }
+
         public DocumentationViewer(bool showInTaskBar)
         {
             InitializeComponent();
 
-            // WINDOWS 10 UPDATE HACK: Because Windows 10 update version 1803 causes unparented non-ShowInTaskbar windows to leak GDI and User handles
+            // WINDOWS 10 UPDATE HACK: Because Windows 10 update version 1803 causes un-parented non-ShowInTaskbar windows to leak GDI and User handles
             ShowInTaskbar = showInTaskBar;
         }
 
-        public String DocumentationHtml
+        public bool IsWebView2Initialized { get; private set; }
+
+        public string DocumentationHtml
+        {
+            get => _documentationHtml;
+            set
+            {
+                _documentationHtml = value;
+
+                if (IsWebView2Initialized)
+                    NavigateToHtml();
+            }
+        }
+
+        protected override void OnHandleCreated(EventArgs e)
+        {
+            InitializeWebView2();
+
+            base.OnHandleCreated(e);
+        }
+
+        private void InitializeWebView2()
+        {
+            try
+            {
+                // Initialize WebView2 environment on UI thread to avoid COM threading issues
+                var environment = InitWebView2Environment();
+                var task = webView2.EnsureCoreWebView2Async(environment);
+
+                // Initialize WebView2 on a background thread
+                CommonActionUtil.RunAsync(() =>
+                {
+                    try
+                    {
+                        // Initialize WebView2 with the environment
+                        task.Wait();
+                        IsWebView2Initialized = true;
+
+                        // Navigate to the HTML if it was set before initialization
+                        if (!string.IsNullOrEmpty(_documentationHtml))
+                        {
+                            RunUIAsync(NavigateToHtml);
+                        }
+                    }
+                    catch (Exception ex)
+                    {
+                        RunUIAsync(() => CommonAlertDlg.ShowException(this, ex));
+                    }
+                });
+            }
+            catch (Exception ex)
+            {
+                CommonAlertDlg.ShowException(this, ex);
+            }
+        }
+
+        private CoreWebView2Environment InitWebView2Environment()
+        {
+            if (string.IsNullOrEmpty(TestWebView2EnvironmentDirectory))
+                return null;
+
+            // Create environment with custom user data folder on UI thread
+            return CoreWebView2Environment.CreateAsync(null, TestWebView2EnvironmentDirectory).Result;
+        }
+
+        private void RunUIAsync(Action act)
+        {
+            CommonActionUtil.SafeBeginInvoke(this, act);
+        }
+
+        private void NavigateToHtml()
         {
-            get { return webBrowser1.DocumentText; } 
-            set { webBrowser1.DocumentText = value; }
+            if (IsWebView2Initialized && !string.IsNullOrEmpty(_documentationHtml))
+            {
+                webView2.NavigateToString(_documentationHtml);
+            }
         }
 
-        protected override void OnFormClosed(FormClosedEventArgs e)
+        #region Test helpers
+
+        /// <summary>
+        /// Gets the HTML content currently displayed in the WebView2 control.
+        /// This is useful for testing to verify that the content was actually rendered.
+        /// </summary>
+        public string GetWebView2HtmlContent(int minLen = 1)
         {
-            base.OnFormClosed(e);
-            Dispose();
+            // Wait for the HTML content of the control to stabilize as matching the documentation HTML
+            // Normalize line endings for comparison since WebView2 may normalize \r\n to \n
+            if (_webView2Html.Length >= minLen)
+                return _webView2Html;
+
+            if (!IsWebView2Initialized || webView2?.CoreWebView2 == null)
+                return string.Empty;
+
+            try
+            {
+                // Execute JavaScript to get the document's HTML content
+                var task = webView2.CoreWebView2.ExecuteScriptAsync(@"document.documentElement.outerHTML");
+                CommonActionUtil.RunAsync(() =>
+                {
+                    try
+                    {
+                        var encodedHtml = task.Result;
+                        // Decode Unicode escape sequences (e.g., \u003C -> <)
+                        var decodedHtml = System.Text.RegularExpressions.Regex.Unescape(encodedHtml);
+                        // Remove leading and trailing quotation marks from JavaScript string
+                        var rawHtml = decodedHtml.Trim('"');
+                        // Normalize line endings to match WebView2's normalization
+                        _webView2Html = rawHtml;
+                    }
+                    catch (Exception ex)
+                    {
+                        // Log cleanup errors for debugging but don't throw
+                        System.Diagnostics.Debug.WriteLine($@"Failed to get WebView2 outerHtml: {ex}");
+                    }
+                });
+            }
+            catch (Exception ex)
+            {
+                // Log cleanup errors for debugging but don't throw
+                System.Diagnostics.Debug.WriteLine($@"Failed to execute script on WebView2: {ex}");
+            }
+            return string.Empty;
         }
+
+        #endregion
     }
 }