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

Directory.Packages.props

@@ -67,7 +67,6 @@
     <PackageVersion Include="Refit.HttpClientFactory" Version="8.0.0" />
     <PackageVersion Include="RockLib.Reflection.Optimized" Version="3.0.0" />
     <PackageVersion Include="Nito.AsyncEx" Version="5.1.2" />
-    <PackageVersion Include="Salaros.ConfigParser" Version="0.3.8" />
     <PackageVersion Include="Semi.Avalonia" Version="11.2.0" />
     <PackageVersion Include="Semver" Version="3.0.0-beta.1" />
     <PackageVersion Include="Sentry" Version="5.5.1" />

StabilityMatrix.Core/Python/PyVenvCfg.cs

@@ -0,0 +1,136 @@
+using System.Text;
+
+namespace StabilityMatrix.Core.Python;
+
+/// <summary>
+/// Ordered, sectionless <c>key = value</c> configuration, as used by pyvenv.cfg.
+/// Keys are case-insensitive. Duplicate keys are preserved in order; setting a
+/// key rewrites every occurrence (fixing stale duplicates) rather than only the
+/// first, which matches how CPython's site.py actually reads the file.
+/// </summary>
+public sealed class PyVenvCfg
+{
+    private readonly List<Entry> _entries;
+
+    private PyVenvCfg(List<Entry> entries) => _entries = entries;
+
+    /// <summary>Parses pyvenv.cfg text without touching the disk.</summary>
+    public static PyVenvCfg Parse(string content)
+    {
+        var entries = new List<Entry>();
+
+        var segments = content.Split('\n');
+        // A trailing empty segment is the artifact of a final newline, not a real line.
+        var lineCount =
+            segments.Length > 0 && segments[^1].Length == 0 ? segments.Length - 1 : segments.Length;
+
+        for (var i = 0; i < lineCount; i++)
+        {
+            var text = segments[i].TrimEnd('\r');
+            var trimmed = text.Trim();
+            var eqIdx = trimmed.IndexOf('=');
+
+            // Lines without '=' are comments/blank lines and are preserved as-is.
+            if (eqIdx < 0)
+            {
+                entries.Add(new Entry(text, null, null));
+                continue;
+            }
+
+            var key = trimmed[..eqIdx].Trim();
+            var value = trimmed[(eqIdx + 1)..].Trim();
+            entries.Add(new Entry(text, key, value));
+        }
+
+        return new PyVenvCfg(entries);
+    }
+
+    /// <summary>
+    /// Loads a pyvenv.cfg file. Fails loudly on non-UTF-8 encodings instead of
+    /// silently mangling the file.
+    /// </summary>
+    public static PyVenvCfg Load(string path)
+    {
+        var bytes = File.ReadAllBytes(path);
+
+        // pyvenv.cfg is UTF-8/ASCII; reject UTF-16 BOMs and NUL bytes, which
+        // indicate the file was read with the wrong encoding.
+        if (
+            bytes.Length >= 2
+            && ((bytes[0] == 0xFF && bytes[1] == 0xFE) || (bytes[0] == 0xFE && bytes[1] == 0xFF))
+        )
+        {
+            throw new InvalidDataException($"pyvenv.cfg is UTF-16 encoded; expected UTF-8/ASCII: {path}");
+        }
+
+        var content = new UTF8Encoding(false).GetString(bytes);
+        if (content.Contains('\0'))
+        {
+            throw new InvalidDataException($"pyvenv.cfg contains NUL bytes; expected UTF-8/ASCII: {path}");
+        }
+
+        return Parse(content);
+    }
+
+    /// <summary>
+    /// Gets the value of the last matching key (CPython is last-wins), or null.
+    /// Setting rewrites every matching key, appending a new key when absent.
+    /// </summary>
+    public string? this[string key]
+    {
+        get
+        {
+            for (var i = _entries.Count - 1; i >= 0; i--)
+            {
+                if (_entries[i].Key is { } k && k.Equals(key, StringComparison.OrdinalIgnoreCase))
+                {
+                    return _entries[i].Value;
+                }
+            }
+
+            return null;
+        }
+        set
+        {
+            ArgumentNullException.ThrowIfNull(value);
+
+            var updated = false;
+            for (var i = 0; i < _entries.Count; i++)
+            {
+                if (_entries[i].Key is { } k && k.Equals(key, StringComparison.OrdinalIgnoreCase))
+                {
+                    _entries[i].Text = $"{key} = {value}";
+                    _entries[i].Value = value;
+                    updated = true;
+                }
+            }
+
+            if (!updated)
+            {
+                _entries.Add(new Entry($"{key} = {value}", key, value));
+            }
+        }
+    }
+
+    /// <summary>Serializes back to pyvenv.cfg text, preserving order and untouched lines.</summary>
+    public override string ToString() => string.Join(Environment.NewLine, _entries.Select(e => e.Text));
+
+    /// <summary>Writes the config back to disk.</summary>
+    public void Save(string path) => File.WriteAllText(path, ToString());
+
+    private sealed class Entry
+    {
+        public Entry(string text, string? key, string? value)
+        {
+            Text = text;
+            Key = key;
+            Value = value;
+        }
+
+        public string Text { get; set; }
+
+        public string? Key { get; }
+
+        public string? Value { get; set; }
+    }
+}

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 +201,17 @@ 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);
+        var cfg = PyVenvCfg.Load(cfgPath);
+        cfg["home"] = pythonDirectory;
+        cfg["base-prefix"] = pythonDirectory;
+        cfg["base-exec-prefix"] = pythonDirectory;
+        cfg["base-executable"] = baseExecutable;
+        cfg.Save(cfgPath);
 
         // 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,
@@ -289,33 +295,47 @@ public async Task<IReadOnlyList<UvPythonInfo>> ListAvailablePythonsAsync(
         {
             var subdirectories = Directory.GetDirectories(uvPythonInstallPath);
             var potentialDirs = subdirectories
-                .Select(dir => new { Path = dir, DirInfo = new DirectoryInfo(dir) })
+                .Select(dir =>
+                {
+                    var info = new DirectoryInfo(dir);
+                    return new
+                    {
+                        Path = dir,
+                        Name = info.Name,
+                        CreationTimeUtc = info.CreationTimeUtc,
+                        Version = ParseUvInstallDirVersion(info.Name),
+                    };
+                })
                 .Where(x =>
-                    x.DirInfo.Name.StartsWith("cpython-", StringComparison.OrdinalIgnoreCase)
-                    || x.DirInfo.Name.StartsWith("pypy-", StringComparison.OrdinalIgnoreCase)
+                    (
+                        x.Name.StartsWith("cpython-", StringComparison.OrdinalIgnoreCase)
+                        || x.Name.StartsWith("pypy-", StringComparison.OrdinalIgnoreCase)
+                    )
+                    && x.Version is { } parsedVersion
+                    && parsedVersion.Major == version.Major
+                    && parsedVersion.Minor == version.Minor
                 )
-                .Where(x => x.DirInfo.Name.Contains($"{version.Major}.{version.Minor}"))
-                .OrderByDescending(x => x.DirInfo.CreationTimeUtc)
+                .OrderByDescending(x => x.CreationTimeUtc)
                 .ToList();
 
             foreach (var potentialDir in potentialDirs)
             {
                 var actualInstallPath = potentialDir.Path;
-                var pyInstallCheck = new PyInstallation(version, actualInstallPath);
+                var actualVersion = potentialDir.Version!.Value;
+                var pyInstallCheck = new PyInstallation(actualVersion, actualInstallPath);
                 if (!pyInstallCheck.Exists())
                     continue;
 
                 Logger.Info($"Fallback discovery found likely installation at: {actualInstallPath}");
-                var inferredKey = Path.GetFileName(actualInstallPath);
-                var inferredSource = inferredKey.Split('-')[0];
+                var inferredSource = potentialDir.Name.Split('-')[0];
                 return new UvPythonInfo(
-                    version,
+                    actualVersion,
                     actualInstallPath,
                     true,
                     inferredSource,
                     null,
                     null,
-                    inferredKey,
+                    potentialDir.Name,
                     null,
                     null
                 );
@@ -330,6 +350,35 @@ public async Task<IReadOnlyList<UvPythonInfo>> ListAvailablePythonsAsync(
         return null;
     }
 
+    /// <summary>
+    /// Parses the version out of a uv Python install directory name
+    /// (e.g. "cpython-3.12.10-windows-x86_64-none"), or null if it doesn't match the expected shape.
+    /// </summary>
+    public static PyVersion? ParseUvInstallDirVersion(string dirName)
+    {
+        var parts = dirName.Split('-');
+        if (parts.Length < 2)
+        {
+            return null;
+        }
+
+        // The version is segment [1]; take its leading "major.minor[.micro]" numeric prefix
+        // so suffixes like "rc1" or "+freethreaded" are tolerated.
+        var segment = parts[1];
+        var prefixLength = 0;
+        while (
+            prefixLength < segment.Length
+            && (char.IsDigit(segment[prefixLength]) || segment[prefixLength] == '.')
+        )
+        {
+            prefixLength++;
+        }
+
+        return prefixLength > 0 && PyVersion.TryParse(segment[..prefixLength], out var parsed)
+            ? parsed
+            : null;
+    }
+
     [GeneratedRegex(
         @"^\s*(?<key>[a-zA-Z0-9_.-]+(?:[\+\-][a-zA-Z0-9_.-]+)?)\s+(?<status_or_path>.+)\s*$",
         RegexOptions.IgnoreCase | RegexOptions.Compiled,

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 +207,17 @@ 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);
+        var cfg = PyVenvCfg.Load(cfgPath);
+        cfg["home"] = pythonDirectory;
+        cfg["base-prefix"] = pythonDirectory;
+        cfg["base-exec-prefix"] = pythonDirectory;
+        cfg["base-executable"] = baseExecutable;
+        cfg.Save(cfgPath);
 
         // Update last set path
         lastSetPyvenvCfgPath = pythonDirectory;

StabilityMatrix.Core/StabilityMatrix.Core.csproj

@@ -62,7 +62,6 @@
       <PackageReference Include="Refit" />
       <PackageReference Include="Refit.HttpClientFactory" />
       <PackageReference Include="RockLib.Reflection.Optimized" />
-      <PackageReference Include="Salaros.ConfigParser" />
       <PackageReference Include="Semver" />
       <PackageReference Include="Sentry.NLog" />
       <PackageReference Include="SharpCompress" />