Skyline: More tutorial screenshot improvements (#3291)

* Skyline: More tutorial screenshot improvements
- added the ability to us the Git HEAD PNG file as the old image
- added rectangle annotation to ScreenshotProcessingExtensions
- made ANNOTATION_COLOR public and used as the default for grid highlight annotations
- tweaks to annotation and scaling in TestLibraryExplorerTutorial and TestMs1Tutorial
- implemented MultiFormActivator for Skyline and the ScreenshotPreviewForm

pwiz_tools/Shared/CommonUtil/SystemUtil/PathEx.cs

@@ -202,9 +202,26 @@ public static string FindExistingRelativeFile(string relativeFilePath, string fi
             return null;
         }
 
+        /// <summary>
+        /// Apparently this was added to Path in .NET 5 and later. Several places in the project have
+        /// now implemented this with either RemovePrefix or some other method.
+        /// </summary>
+        /// <param name="relativePathTo">The base path to make the path relative to</param>
+        /// <param name="path">The full path to make relative</param>
+        /// <returns>The relative path from the base path to the given path</returns>
+        public static string GetRelativePath(string relativePathTo, string path)
+        {
+            if (!relativePathTo.EndsWith(Path.DirectorySeparatorChar.ToString()))
+                relativePathTo += Path.DirectorySeparatorChar;
+            return RemovePrefix(path, relativePathTo);
+        }
+
         /// <summary>
         /// If the path starts with the prefix, then skip over the prefix; 
-        /// otherwise, return the original path.
+        /// otherwise, return the original path. This works well as a method of getting a relative
+        /// path in combination with <see cref="GetCommonRoot(System.Collections.Generic.IEnumerable{string})"/>, since
+        /// it is guaranteed to return a directory path ending with a Path.DirectorySeparatorChar, but not in
+        /// cases where a path to a directory lacks a terminating separator. In those cases, use <see cref="GetRelativePath"/>.
         /// </summary>
         public static string RemovePrefix(string path, string prefix)
         {

pwiz_tools/Skyline/TestTutorial/CustomReportsTutorialTest.cs

@@ -367,11 +367,11 @@ protected bool DoQualityControlSummaryReports()
                 using var g = Graphics.FromImage(bmp);
                 g.SmoothingMode = SmoothingMode.AntiAlias;
 
-                g.DrawBoxOnColumn(documentGridForm, 3, 10, Color.Red);
-                g.DrawBoxOnColumn(documentGridForm, 5, 10, Color.Red);
-                g.DrawBoxOnColumn(documentGridForm, 6, 10, Color.Red);
+                g.DrawBoxOnColumn(documentGridForm, 3, 10);
+                g.DrawBoxOnColumn(documentGridForm, 5, 10);
+                g.DrawBoxOnColumn(documentGridForm, 6, 10);
 
-                g.DrawEllipseOnCell(documentGridForm, 1, 3, Color.Red);
+                g.DrawEllipseOnCell(documentGridForm, 1, 3);
                 g.DrawEllipseOnCell(documentGridForm, 3, 3, Color.Orange);
                 g.DrawEllipseOnCell(documentGridForm, 1, 5, Color.Orange);
                 g.DrawEllipseOnCell(documentGridForm, 3, 5, Color.Orange);

pwiz_tools/Skyline/TestTutorial/LibraryExplorerTutorialTest.cs

@@ -103,6 +103,7 @@ protected override void DoTest()
             ViewLibraryDlg viewLibraryDlg = ShowDialog<ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
             var matchedPepsDlg = WaitForOpenForm<AddModificationsDlg>();
             OkDialog(matchedPepsDlg, matchedPepsDlg.CancelDialog);
+            RunUIForScreenShot(() => viewLibraryDlg.Size = new Size(775, 463));
             PauseForScreenShot<ViewLibraryDlg>("Library Explorer", 5);
 
             // Types text in Peptide textbox in the Spectral Library Explorer Window

pwiz_tools/Skyline/TestTutorial/Ms1FullScanFilteringTutorial.cs

@@ -497,7 +497,11 @@ protected override void DoTest()
             PauseForScreenShot<AlignmentForm>("Retention time alignment form", tutorialPage++);
 
             OkDialog(alignmentForm, alignmentForm.Close);
-            PauseForScreenShot("Status bar clipped from main window - 4/50 pep 4/51 prec 10/153 tran", tutorialPage++, null, ClipSelectionStatus);
+            PauseForScreenShot("Status bar clipped from main window - 4/50 pep 4/51 prec 10/153 tran", tutorialPage++, null, bmp =>
+            {
+                bmp = ClipSelectionStatus(bmp);
+                return bmp.DrawAnnotationRectOnBitmap(new RectangleF(0.23F, 0, 0.23F, 1), 2).Inflate(1.5F);
+            });
 
             string TIP_NAME = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[TIP3].Name;
             string TIB_NAME = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[TIB_L].Name;

pwiz_tools/Skyline/TestUtil/GitFileHelper.cs

@@ -0,0 +1,151 @@
+/*
+ * Original author: Brendan MacLean <brendanx .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2024 University of Washington - Seattle, WA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+using System;
+using System.Collections.Generic;
+using System.Diagnostics;
+using System.IO;
+using pwiz.Common.SystemUtil;
+
+namespace pwiz.SkylineTestUtil
+{
+    internal static class GitFileHelper
+    {
+        /// <summary>
+        /// Retrieves the committed binary content of a file in a Git repository.
+        /// </summary>
+        /// <param name="fullPath">The fully qualified path of the file.</param>
+        /// <returns>The committed binary content of the file.</returns>
+        public static byte[] GetGitFileBinaryContent(string fullPath)
+        {
+            return RunGitCommand(GetPathInfo(fullPath), "show HEAD:{RelativePath}", process =>
+            {
+                using var memoryStream = new MemoryStream();
+                process.StandardOutput.BaseStream.CopyTo(memoryStream);
+                return memoryStream.ToArray();
+            });
+        }
+
+        /// <summary>
+        /// Gets a list of changed file paths under a specific directory.
+        /// </summary>
+        /// <param name="directoryPath">The fully qualified directory path.</param>
+        /// <returns>An enumerable of file paths that have been modified, added, or deleted.</returns>
+        public static IEnumerable<string> GetChangedFilePaths(string directoryPath)
+        {
+            var output = RunGitCommand(GetPathInfo(directoryPath), "status --porcelain \"{RelativePath}\"", process =>
+                process.StandardOutput.ReadToEnd());
+
+            using var reader = new StringReader(output);
+            while (reader.ReadLine() is { } line)
+            {
+                // 'git status --porcelain' format: XY path/to/file
+                var filePath = line.Substring(3).Replace('/', Path.DirectorySeparatorChar);
+                yield return Path.Combine(GetPathInfo(directoryPath).Root, filePath);
+            }
+        }
+
+        /// <summary>
+        /// Executes a Git command in the specified repository and returns the standard output as a string.
+        /// </summary>
+        /// <param name="pathInfo">The PathInfo object for the target path.</param>
+        /// <param name="commandTemplate">The Git command template with placeholders (e.g., {RelativePath}).</param>
+        /// <param name="processOutput">A function that takes a running process and returns the necessary output</param>
+        /// <returns>Output of type T from the process.</returns>
+        private static T RunGitCommand<T>(PathInfo pathInfo, string commandTemplate, Func<Process, T> processOutput)
+        {
+            var command = commandTemplate.Replace("{RelativePath}", pathInfo.RelativePath);
+            var processInfo = new ProcessStartInfo("git", command)
+            {
+                RedirectStandardOutput = true,
+                RedirectStandardError = true,
+                UseShellExecute = false,
+                CreateNoWindow = true,
+                WorkingDirectory = pathInfo.Root
+            };
+
+            using var process = new Process();
+            process.StartInfo = processInfo;
+            process.Start();
+
+            var output = processOutput(process);
+            var error = process.StandardError.ReadToEnd();
+            process.WaitForExit();
+
+            if (process.ExitCode != 0)
+            {
+                throw new Exception($"Git error: {error}");
+            }
+
+            return output;
+        }
+
+        /// <summary>
+        /// Retrieves the root directory of the Git repository containing the given directory.
+        /// </summary>
+        /// <param name="startPath">The directory or file path to start searching from.</param>
+        /// <returns>The root directory of the Git repository, or null if not found.</returns>
+        private static string GetGitRepositoryRoot(string startPath)
+        {
+            var currentDirectory = File.Exists(startPath)
+                ? Path.GetDirectoryName(startPath)
+                : startPath;
+
+            while (!string.IsNullOrEmpty(currentDirectory))
+            {
+                if (Directory.Exists(Path.Combine(currentDirectory, ".git")))
+                {
+                    return currentDirectory;
+                }
+
+                currentDirectory = Directory.GetParent(currentDirectory)?.FullName;
+            }
+
+            return null; // No Git repository found
+        }
+
+        /// <summary>
+        /// Retrieves path information for a given file or directory, including the repository root and relative path.
+        /// </summary>
+        /// <param name="fullPath">The fully qualified file or directory path.</param>
+        /// <returns>A PathInfo object containing the repository root and the relative path.</returns>
+        private static PathInfo GetPathInfo(string fullPath)
+        {
+            if (!File.Exists(fullPath) && !Directory.Exists(fullPath))
+            {
+                throw new FileNotFoundException($"The path '{fullPath}' does not exist.");
+            }
+
+            var repoRoot = GetGitRepositoryRoot(fullPath);
+            if (repoRoot == null)
+            {
+                throw new InvalidOperationException($"The path '{fullPath}' is not part of a Git repository.");
+            }
+
+            var relativePath = PathEx.GetRelativePath(repoRoot, fullPath).Replace(Path.DirectorySeparatorChar, '/');
+            return new PathInfo { Root = repoRoot, RelativePath = relativePath };
+        }
+
+        private struct PathInfo
+        {
+            public string Root { get; set; }
+            public string RelativePath { get; set; }
+        }
+    }
+
+}

pwiz_tools/Skyline/TestUtil/MultiFormActivator.cs

@@ -38,6 +38,15 @@ public MultiFormActivator(params Form[] formsToActivate)
             }
         }
 
+        public void Reset(params Form[] formsToActivate)
+        {
+            Clear();
+            foreach (var form in formsToActivate)
+            {
+                AddForm(form);
+            }
+        }
+
         public void AddForm(Form form)
         {
             lock (_formsToActivate)
@@ -47,18 +56,22 @@ public void AddForm(Form form)
             }
         }
 
-        public void AddRange(IEnumerable<Form> forms)
-        {
-            // Add only forms that do not parent another form. Track and activate only the
-            // deepest child forms. They are the ones that will get activated and bringing them
-            // forward will drag their parents with them.
-            var listForms = forms.ToArray();
-            var setParents = new HashSet<IntPtr>(listForms
-                .Where(f => f.Parent != null)
-                .Select(f => f.Parent.Handle));
-            foreach (var form in listForms.Where(f => !setParents.Contains(f.Handle)))
-                AddForm(form);
-        }
+        // This approach causes cross-thread exceptions
+        // public void AddRange(IEnumerable<Form> forms)
+        // {
+        //     lock (_formsToActivate)
+        //     {
+        //         // Add only forms that do not parent another form. Track and activate only the
+        //         // deepest child forms. They are the ones that will get activated and bringing them
+        //         // forward will drag their parents with them.
+        //         var listForms = forms.ToArray();
+        //         var setParents = new HashSet<IntPtr>(listForms
+        //             .Where(f => f.Parent != null)
+        //             .Select(f => f.Parent.Handle));
+        //         foreach (var form in listForms.Where(f => !setParents.Contains(f.Handle)))
+        //             AddForm(form);
+        //     }
+        // }
 
         public void RemoveForm(Form form)
         {
@@ -73,7 +86,7 @@ public void Clear()
         {
             lock (_formsToActivate)
             {
-                foreach (var form in _formsToActivate)
+                foreach (var form in _formsToActivate.ToArray())
                     RemoveForm(form);
             }
         }
@@ -85,7 +98,7 @@ private void FormActivated(object sender, EventArgs e)
 
             lock (_formsToActivate)
             {
-                foreach (var form in _formsToActivate.Where(form => !ReferenceEquals(form, activatedForm) && form.Visible))
+                foreach (var form in _formsToActivate.Where(form => !ReferenceEquals(form, activatedForm)))
                 {
                     ActionUtil.RunAsync(() => ShowForm(form, activatedFormHandle));
                 }
@@ -95,13 +108,20 @@ private void FormActivated(object sender, EventArgs e)
         private void ShowForm(Form form, IntPtr referenceFormHandle)
         {
             // Must be done on the form's thread
-            form.Invoke((Action)(() => form.BringWindowToSameLevelWithoutActivating(referenceFormHandle)));
+            form.Invoke((Action)(() =>
+            {
+                if (form.Visible)
+                    form.BringWindowToSameLevelWithoutActivating(referenceFormHandle);
+            }));
         }
 
         public void Dispose()
         {
-            while (_formsToActivate.Any())
-                RemoveForm(_formsToActivate.First());
+            lock (_formsToActivate)
+            {
+                while (_formsToActivate.Any())
+                    RemoveForm(_formsToActivate.First());
+            }
         }
     }
 }

pwiz_tools/Skyline/TestUtil/Properties/Resources.resx

@@ -130,6 +130,9 @@
   <data name="DiskFailure" type="System.Resources.ResXFileRef, System.Windows.Forms">
     <value>..\Resources\DiskFailure.png;System.Drawing.Bitmap, System.Drawing, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a</value>
   </data>
+  <data name="gitsource" type="System.Resources.ResXFileRef, System.Windows.Forms">
+    <value>..\Resources\gitsource.png;System.Drawing.Bitmap, System.Drawing, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a</value>
+  </data>
   <data name="hand_cur" type="System.Resources.ResXFileRef, System.Windows.Forms">
     <value>..\Resources\hand-cur.bmp;System.Drawing.Bitmap, System.Drawing, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a</value>
   </data>

pwiz_tools/Skyline/TestUtil/Properties/TestUtilSettings.settings

@@ -17,11 +17,11 @@
     <Setting Name="ShowTextButtons" Type="System.Boolean" Scope="User">
       <Value Profile="(Default)">False</Value>
     </Setting>
-    <Setting Name="ShowWebImage" Type="System.Boolean" Scope="User">
-      <Value Profile="(Default)">False</Value>
-    </Setting>
     <Setting Name="ManualSizePreview" Type="System.Boolean" Scope="User">
       <Value Profile="(Default)">False</Value>
     </Setting>
+    <Setting Name="OldImageSource" Type="System.Int32" Scope="User">
+      <Value Profile="(Default)">0</Value>
+    </Setting>
   </Settings>
 </SettingsFile>