Fix: pyvenv.cfg corruption and wrong Python distribution selection when multiple Python versions are installed (3.13 after 3.12)

StabilityMatrix.Core/Python/PyVenvConfigHelper.cs

@@ -0,0 +1,96 @@
+using System.Text;
+using NLog;
+
+namespace StabilityMatrix.Core.Python;
+
+/// <summary>
+/// Helper for reading and writing pyvenv.cfg files.
+/// pyvenv.cfg is a simple key = value format without INI sections,
+/// so we manipulate it directly instead of using a section-based INI parser.
+/// </summary>
+public static class PyVenvConfigHelper
+{
+    private static readonly Logger Logger = LogManager.GetCurrentClassLogger();
+
+    /// <summary>
+    /// Write or update the path keys in a pyvenv.cfg file.
+    /// Sets home, base-prefix, base-exec-prefix to <paramref name="pythonDirectory"/>
+    /// and base-executable to <paramref name="baseExecutable"/>.
+    /// Other existing keys are preserved in their original order.
+    /// </summary>
+    public static void WritePyVenvCfg(string cfgPath, string pythonDirectory, string baseExecutable)
+    {
+        var lines = File.ReadAllLines(cfgPath);
+        var sb = new StringBuilder();
+        var hasHome = false;
+        var hasBasePrefix = false;
+        var hasBaseExecPrefix = false;
+        var hasBaseExecutable = false;
+
+        foreach (var line in lines)
+        {
+            var trimmed = line.Trim();
+            var eqIdx = trimmed.IndexOf('=');
+
+            // Preserve lines without an = sign (comments, blank lines, etc.)
+            if (eqIdx < 0)
+            {
+                sb.AppendLine(line);
+                continue;
+            }
+
+            var key = trimmed.Substring(0, eqIdx).TrimEnd();
+
+            if (key.Equals("home", StringComparison.OrdinalIgnoreCase))
+            {
+                sb.AppendLine($"home = {pythonDirectory}");
+                hasHome = true;
+            }
+            else if (key.Equals("base-prefix", StringComparison.OrdinalIgnoreCase))
+            {
+                sb.AppendLine($"base-prefix = {pythonDirectory}");
+                hasBasePrefix = true;
+            }
+            else if (key.Equals("base-exec-prefix", StringComparison.OrdinalIgnoreCase))
+            {
+                sb.AppendLine($"base-exec-prefix = {pythonDirectory}");
+                hasBaseExecPrefix = true;
+            }
+            else if (key.Equals("base-executable", StringComparison.OrdinalIgnoreCase))
+            {
+                sb.AppendLine($"base-executable = {baseExecutable}");
+                hasBaseExecutable = true;
+            }
+            else
+            {
+                sb.AppendLine(line);
+            }
+        }
+
+        // Append any missing keys
+        if (!hasHome)
+        {
+            sb.AppendLine($"home = {pythonDirectory}");
+        }
+        if (!hasBasePrefix)
+        {
+            sb.AppendLine($"base-prefix = {pythonDirectory}");
+        }
+        if (!hasBaseExecPrefix)
+        {
+            sb.AppendLine($"base-exec-prefix = {pythonDirectory}");
+        }
+        if (!hasBaseExecutable)
+        {
+            sb.AppendLine($"base-executable = {baseExecutable}");
+        }
+
+        File.WriteAllText(cfgPath, sb.ToString());
+
+        Logger.Debug(
+            "Wrote pyvenv.cfg: home={PyDir}, base-executable={PyExe}",
+            pythonDirectory,
+            baseExecutable
+        );
+    }
+}

StabilityMatrix.Core/Python/PyVenvRunner.cs

@@ -3,7 +3,6 @@
 using System.Text;
 using System.Text.Json;
 using NLog;
-using Salaros.Configuration;
 using StabilityMatrix.Core.Exceptions;
 using StabilityMatrix.Core.Extensions;
 using StabilityMatrix.Core.Helper;
@@ -202,25 +201,12 @@ private void SetPyvenvCfg(string pythonDirectory, bool force = false)
 
         Logger.Info("Updating pyvenv.cfg with embedded Python directory {PyDir}", pythonDirectory);
 
-        // Insert a top section
-        var topSection = "[top]" + Environment.NewLine;
-        var cfg = new ConfigParser(topSection + File.ReadAllText(cfgPath));
-
-        // Need to set all path keys - home, base-prefix, base-exec-prefix, base-executable
-        cfg.SetValue("top", "home", pythonDirectory);
-        cfg.SetValue("top", "base-prefix", pythonDirectory);
-
-        cfg.SetValue("top", "base-exec-prefix", pythonDirectory);
-
-        cfg.SetValue(
-            "top",
-            "base-executable",
-            Path.Combine(pythonDirectory, Compat.IsWindows ? "python.exe" : RelativePythonPath)
+        var baseExecutable = Path.Combine(
+            pythonDirectory,
+            Compat.IsWindows ? "python.exe" : RelativePythonPath
         );
 
-        // Convert to string for writing, strip the top section
-        var cfgString = cfg.ToString()!.Replace(topSection, "");
-        File.WriteAllText(cfgPath, cfgString);
+        PyVenvConfigHelper.WritePyVenvCfg(cfgPath, pythonDirectory, baseExecutable);
 
         // Update last set path
         lastSetPyvenvCfgPath = pythonDirectory;

StabilityMatrix.Core/Python/UvManager.cs

@@ -149,15 +149,21 @@ public async Task<IReadOnlyList<UvPythonInfo>> ListAvailablePythonsAsync(
             return pythons.AsReadOnly();
         }
 
+        // When only installed Pythons are requested, exclude entries with no path (not installed).
+        // Also guard against null paths reaching PyInstallation constructor which throws ArgumentException.
         var filteredPythons = uvPythonListEntries
-            .Where(e => e.Path == null || e.Path.StartsWith(uvPythonInstallPath))
+            .Where(e =>
+                installedOnly
+                    ? e.Path != null && e.Path.StartsWith(uvPythonInstallPath)
+                    : e.Path == null || e.Path.StartsWith(uvPythonInstallPath)
+            )
             .Where(e =>
                 settingsManager.Settings.ShowAllAvailablePythonVersions
                 || (!e.Version.Contains("a") && !e.Version.Contains("b"))
             )
             .Select(e => new UvPythonInfo
             {
-                InstallPath = Path.GetDirectoryName(e.Path) ?? string.Empty,
+                InstallPath = e.Path != null ? (Path.GetDirectoryName(e.Path) ?? string.Empty) : string.Empty,
                 Version = e.VersionParts,
                 Architecture = e.Arch,
                 IsInstalled = e.Path != null,
@@ -287,14 +293,24 @@ public async Task<IReadOnlyList<UvPythonInfo>> ListAvailablePythonsAsync(
         Logger.Debug($"Attempting fallback path discovery in central directory: {uvPythonInstallPath}");
         try
         {
+            // Build a version prefix that won't accidentally match higher minor/patch versions.
+            // e.g. "3.12." so that "cpython-3.12.10" matches but "cpython-3.13.12" does not.
+            var versionPrefix = $"{version.Major}.{version.Minor}.";
+
             var subdirectories = Directory.GetDirectories(uvPythonInstallPath);
             var potentialDirs = subdirectories
                 .Select(dir => new { Path = dir, DirInfo = new DirectoryInfo(dir) })
                 .Where(x =>
                     x.DirInfo.Name.StartsWith("cpython-", StringComparison.OrdinalIgnoreCase)
                     || x.DirInfo.Name.StartsWith("pypy-", StringComparison.OrdinalIgnoreCase)
                 )
-                .Where(x => x.DirInfo.Name.Contains($"{version.Major}.{version.Minor}"))
+                .Where(x =>
+                    x.DirInfo.Name.Contains(versionPrefix)
+                    || x.DirInfo.Name.EndsWith(
+                        $"-{version.Major}.{version.Minor}",
+                        StringComparison.OrdinalIgnoreCase
+                    )
+                )
                 .OrderByDescending(x => x.DirInfo.CreationTimeUtc)
                 .ToList();
 

StabilityMatrix.Core/Python/UvVenvRunner.cs

@@ -3,7 +3,6 @@
 using System.Text;
 using System.Text.Json;
 using NLog;
-using Salaros.Configuration;
 using StabilityMatrix.Core.Exceptions;
 using StabilityMatrix.Core.Extensions;
 using StabilityMatrix.Core.Helper;
@@ -208,25 +207,12 @@ private void SetPyvenvCfg(string pythonDirectory, bool force = false)
 
         Logger.Info("Updating pyvenv.cfg with embedded Python directory {PyDir}", pythonDirectory);
 
-        // Insert a top section
-        var topSection = "[top]" + Environment.NewLine;
-        var cfg = new ConfigParser(topSection + File.ReadAllText(cfgPath));
-
-        // Need to set all path keys - home, base-prefix, base-exec-prefix, base-executable
-        cfg.SetValue("top", "home", pythonDirectory);
-        cfg.SetValue("top", "base-prefix", pythonDirectory);
-
-        cfg.SetValue("top", "base-exec-prefix", pythonDirectory);
-
-        cfg.SetValue(
-            "top",
-            "base-executable",
-            Path.Combine(pythonDirectory, Compat.IsWindows ? "python.exe" : RelativePythonPath)
+        var baseExecutable = Path.Combine(
+            pythonDirectory,
+            Compat.IsWindows ? "python.exe" : RelativePythonPath
         );
 
-        // Convert to string for writing, strip the top section
-        var cfgString = cfg.ToString()!.Replace(topSection, "");
-        File.WriteAllText(cfgPath, cfgString);
+        PyVenvConfigHelper.WritePyVenvCfg(cfgPath, pythonDirectory, baseExecutable);
 
         // Update last set path
         lastSetPyvenvCfgPath = pythonDirectory;