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src/Scanner/__Libraries/StellaOps.Scanner.Analyzers.Lang.Python/Internal/Imports/PythonImportGraph.cs

@@ -201,27 +201,19 @@ internal sealed class PythonImportGraph
     /// </summary>
     public IReadOnlyList<string>? GetTopologicalOrder()
     {
-        var inDegree = new Dictionary<string, int>(StringComparer.Ordinal);
+        var dependencyCounts = new Dictionary<string, int>(StringComparer.Ordinal);
         foreach (var module in _modules.Keys)
         {
-            inDegree[module] = 0;
-        }
-
-        foreach (var edges in _edges.Values)
-        {
-            foreach (var edge in edges)
-            {
-                if (inDegree.ContainsKey(edge.To))
-                {
-                    inDegree[edge.To]++;
-                }
-            }
+            var count = _edges.TryGetValue(module, out var edges)
+                ? edges.Count
+                : 0;
+            dependencyCounts[module] = count;
         }
 
         var queue = new Queue<string>();
-        foreach (var (module, degree) in inDegree)
+        foreach (var (module, count) in dependencyCounts)
         {
-            if (degree == 0)
+            if (count == 0)
             {
                 queue.Enqueue(module);
             }
@@ -233,23 +225,27 @@ internal sealed class PythonImportGraph
             var module = queue.Dequeue();
             result.Add(module);
 
-            if (_edges.TryGetValue(module, out var edges))
+            if (!_reverseEdges.TryGetValue(module, out var dependents))
             {
-                foreach (var edge in edges)
+                continue;
+            }
+
+            foreach (var edge in dependents)
+            {
+                if (!dependencyCounts.TryGetValue(edge.From, out var remaining))
                 {
-                    if (inDegree.ContainsKey(edge.To))
-                    {
-                        inDegree[edge.To]--;
-                        if (inDegree[edge.To] == 0)
-                        {
-                            queue.Enqueue(edge.To);
-                        }
-                    }
+                    continue;
+                }
+
+                remaining--;
+                dependencyCounts[edge.From] = remaining;
+                if (remaining == 0)
+                {
+                    queue.Enqueue(edge.From);
                 }
             }
         }
 
-        // If not all modules are in result, there's a cycle
         return result.Count == _modules.Count ? result : null;
     }
 
@@ -437,27 +433,23 @@ internal sealed class PythonImportGraph
     {
         var parts = sourceModulePath.Split('.');
 
-        // Calculate the package to start from
-        // Level 1 (.) = current package
-        // Level 2 (..) = parent package
-        var levelsUp = import.RelativeLevel;
-
-        // If source is not a package (__init__.py), we need to go one more level up
         var sourceVirtualPath = _modules.TryGetValue(sourceModulePath, out var node) ? node.VirtualPath : null;
         var isSourcePackage = sourceVirtualPath?.EndsWith("__init__.py", StringComparison.Ordinal) == true;
 
-        if (!isSourcePackage)
+        // Base package is the containing package of the source module
+        var packageParts = isSourcePackage ? parts : parts[..^1];
+
+        // RelativeLevel counts from the package boundary; level 1 = current package
+        var levelsUp = Math.Max(import.RelativeLevel - 1, 0);
+        if (levelsUp > packageParts.Length)
         {
-            levelsUp++;
+            return null;
         }
 
-        if (levelsUp > parts.Length)
-        {
-            return null; // Invalid relative import (goes beyond top-level package)
-        }
-
-        var baseParts = parts[..^(levelsUp)];
-        var basePackage = string.Join('.', baseParts);
+        var basePartsLength = packageParts.Length - levelsUp;
+        var basePackage = basePartsLength <= 0
+            ? string.Empty
+            : string.Join('.', packageParts.Take(basePartsLength));
 
         if (string.IsNullOrEmpty(import.Module))
         {

src/Scanner/__Libraries/StellaOps.Scanner.Analyzers.Lang.Python/Internal/Imports/PythonSourceImportExtractor.cs

@@ -11,8 +11,9 @@ internal sealed partial class PythonSourceImportExtractor
     private readonly List<PythonImport> _imports = new();
     private bool _inTryBlock;
     private bool _inTypeCheckingBlock;
-    private int _functionDepth;
-    private int _classDepth;
+    private int? _typeCheckingIndent;
+    private readonly Stack<int> _functionIndentStack = new();
+    private readonly Stack<int> _classIndentStack = new();
 
     public PythonSourceImportExtractor(string sourceFile)
     {
@@ -37,11 +38,15 @@ internal sealed partial class PythonSourceImportExtractor
         var lines = content.Split('\n');
         var lineNumber = 0;
         var continuedLine = string.Empty;
+        var parenBuffer = string.Empty;
+        var inParenContinuation = false;
 
-        foreach (var rawLine in lines)
+        foreach (var rawLineOriginal in lines)
         {
             lineNumber++;
-            var line = rawLine.TrimEnd('\r');
+            var rawLine = rawLineOriginal.TrimEnd('\r');
+            var indent = CountIndentation(rawLine);
+            var line = rawLine;
 
             // Handle line continuations
             if (line.EndsWith('\\'))
@@ -54,7 +59,7 @@ internal sealed partial class PythonSourceImportExtractor
             continuedLine = string.Empty;
 
             // Track context
-            UpdateContext(fullLine.TrimStart());
+            UpdateContext(fullLine.TrimStart(), indent);
 
             // Skip comments and empty lines
             var trimmed = fullLine.TrimStart();
@@ -75,6 +80,29 @@ internal sealed partial class PythonSourceImportExtractor
                 continue;
             }
 
+            // Handle parenthesized from-imports spanning multiple lines
+            if (inParenContinuation)
+            {
+                parenBuffer += " " + trimmed;
+                if (trimmed.Contains(')'))
+                {
+                    inParenContinuation = false;
+                    ExtractImports(parenBuffer, lineNumber);
+                    parenBuffer = string.Empty;
+                }
+                continue;
+            }
+
+            if (trimmed.StartsWith("from ", StringComparison.Ordinal) &&
+                trimmed.Contains("import", StringComparison.Ordinal) &&
+                trimmed.Contains('(') &&
+                !trimmed.Contains(')'))
+            {
+                inParenContinuation = true;
+                parenBuffer = trimmed;
+                continue;
+            }
+
             // Try to extract imports
             ExtractImports(trimmed, lineNumber);
         }
@@ -82,8 +110,24 @@ internal sealed partial class PythonSourceImportExtractor
         return this;
     }
 
-    private void UpdateContext(string line)
+    private void UpdateContext(string line, int indent)
     {
+        // unwind function/class stacks based on indentation
+        while (_functionIndentStack.Count > 0 && indent <= _functionIndentStack.Peek())
+        {
+            _functionIndentStack.Pop();
+        }
+
+        while (_classIndentStack.Count > 0 && indent <= _classIndentStack.Peek())
+        {
+            _classIndentStack.Pop();
+        }
+
+        if (_typeCheckingIndent is not null && indent <= _typeCheckingIndent.Value)
+        {
+            _typeCheckingIndent = null;
+        }
+
         // Track try blocks
         if (line.StartsWith("try:") || line == "try")
         {
@@ -94,31 +138,30 @@ internal sealed partial class PythonSourceImportExtractor
             _inTryBlock = false;
         }
 
-        // Track TYPE_CHECKING blocks
-        if (line.Contains("TYPE_CHECKING") && line.Contains("if"))
-        {
-            _inTypeCheckingBlock = true;
-        }
-
         // Track function depth
         if (line.StartsWith("def ") || line.StartsWith("async def "))
         {
-            _functionDepth++;
+            _functionIndentStack.Push(indent);
         }
 
         // Track class depth (for nested classes)
         if (line.StartsWith("class "))
         {
-            _classDepth++;
+            _classIndentStack.Push(indent);
         }
 
-        // Reset context at module level definitions
-        if ((line.StartsWith("def ") || line.StartsWith("class ") || line.StartsWith("async def ")) &&
-            !line.StartsWith("    ") && !line.StartsWith("\t"))
+        // Track TYPE_CHECKING blocks
+        if (line.StartsWith("if", StringComparison.Ordinal) && line.Contains("TYPE_CHECKING", StringComparison.Ordinal))
+        {
+            _typeCheckingIndent = indent;
+        }
+
+        _inTypeCheckingBlock = _typeCheckingIndent is not null && indent > _typeCheckingIndent.Value;
+
+        // Reset TYPE_CHECKING when hitting new top-level if
+        if (_typeCheckingIndent is null && indent == 0 && line.StartsWith("if ", StringComparison.Ordinal))
         {
             _inTypeCheckingBlock = false;
-            _functionDepth = 0;
-            _classDepth = 0;
         }
     }
 
@@ -212,7 +255,7 @@ internal sealed partial class PythonSourceImportExtractor
                 LineNumber: lineNumber,
                 Confidence: PythonImportConfidence.Definitive,
                 IsConditional: _inTryBlock,
-                IsLazy: _functionDepth > 0,
+                IsLazy: _functionIndentStack.Count > 0,
                 IsTypeCheckingOnly: _inTypeCheckingBlock));
         }
     }
@@ -241,7 +284,7 @@ internal sealed partial class PythonSourceImportExtractor
                 LineNumber: lineNumber,
                 Confidence: PythonImportConfidence.Definitive,
                 IsConditional: _inTryBlock,
-                IsLazy: _functionDepth > 0,
+                IsLazy: _functionIndentStack.Count > 0,
                 IsTypeCheckingOnly: _inTypeCheckingBlock));
             return;
         }
@@ -294,7 +337,7 @@ internal sealed partial class PythonSourceImportExtractor
             LineNumber: lineNumber,
             Confidence: PythonImportConfidence.Definitive,
             IsConditional: _inTryBlock,
-            IsLazy: _functionDepth > 0,
+            IsLazy: _functionIndentStack.Count > 0,
             IsTypeCheckingOnly: _inTypeCheckingBlock));
     }
 
@@ -324,7 +367,7 @@ internal sealed partial class PythonSourceImportExtractor
             LineNumber: lineNumber,
             Confidence: PythonImportConfidence.High,
             IsConditional: _inTryBlock,
-            IsLazy: _functionDepth > 0,
+            IsLazy: _functionIndentStack.Count > 0,
             IsTypeCheckingOnly: _inTypeCheckingBlock));
     }
 
@@ -342,7 +385,7 @@ internal sealed partial class PythonSourceImportExtractor
             LineNumber: lineNumber,
             Confidence: PythonImportConfidence.High,
             IsConditional: _inTryBlock,
-            IsLazy: _functionDepth > 0,
+            IsLazy: _functionIndentStack.Count > 0,
             IsTypeCheckingOnly: _inTypeCheckingBlock));
     }
 
@@ -359,10 +402,32 @@ internal sealed partial class PythonSourceImportExtractor
             LineNumber: lineNumber,
             Confidence: PythonImportConfidence.Medium,
             IsConditional: _inTryBlock,
-            IsLazy: _functionDepth > 0,
+            IsLazy: _functionIndentStack.Count > 0,
             IsTypeCheckingOnly: _inTypeCheckingBlock));
     }
 
+    private static int CountIndentation(string line)
+    {
+        var count = 0;
+        foreach (var c in line)
+        {
+            if (c == ' ')
+            {
+                count++;
+            }
+            else if (c == '\t')
+            {
+                count += 4;
+            }
+            else
+            {
+                break;
+            }
+        }
+
+        return count;
+    }
+
     private static int FindCommentStart(string line)
     {
         var inSingleQuote = false;

src/Scanner/__Libraries/StellaOps.Scanner.Analyzers.Lang.Python/Internal/VirtualFileSystem/PythonInputNormalizer.cs

@@ -1,5 +1,6 @@
 using System.Text.Json;
 using System.Text.RegularExpressions;
+using System.Linq;
 
 namespace StellaOps.Scanner.Analyzers.Lang.Python.Internal.VirtualFileSystem;
 
@@ -276,10 +277,10 @@ internal sealed partial class PythonInputNormalizer
                         var version = parts[1].Trim();
                         if (!string.IsNullOrEmpty(version))
                         {
-                            _versionTargets.Add(new PythonVersionTarget(
+                            AddVersionTarget(
                                 version,
                                 "pyvenv.cfg",
-                                PythonVersionConfidence.Definitive));
+                                PythonVersionConfidence.Definitive);
                         }
                     }
                 }
@@ -304,8 +305,7 @@ internal sealed partial class PythonInputNormalizer
             var content = await File.ReadAllTextAsync(path, cancellationToken).ConfigureAwait(false);
 
             // Look for requires-python in [project] section
-            var requiresPythonMatch = RequiresPythonPattern().Match(content);
-            if (requiresPythonMatch.Success)
+            foreach (Match requiresPythonMatch in RequiresPythonPattern().Matches(content))
             {
                 var version = requiresPythonMatch.Groups["version"].Value.Trim().Trim('"', '\'');
                 if (!string.IsNullOrEmpty(version))
@@ -314,17 +314,16 @@ internal sealed partial class PythonInputNormalizer
                                     version.StartsWith(">", StringComparison.Ordinal);
                     version = Regex.Replace(version, @"^[><=!~]+", string.Empty).Trim();
 
-                    _versionTargets.Add(new PythonVersionTarget(
+                    AddVersionTarget(
                         version,
                         "pyproject.toml",
                         PythonVersionConfidence.High,
-                        isMinimum));
+                        isMinimum);
                 }
             }
 
             // Look for python_requires in [tool.poetry] or similar
-            var pythonMatch = PythonVersionTomlPattern().Match(content);
-            if (pythonMatch.Success)
+            foreach (Match pythonMatch in PythonVersionTomlPattern().Matches(content))
             {
                 var version = pythonMatch.Groups["version"].Value.Trim().Trim('"', '\'');
                 if (!string.IsNullOrEmpty(version))
@@ -333,11 +332,11 @@ internal sealed partial class PythonInputNormalizer
                                     version.StartsWith(">=", StringComparison.Ordinal);
                     version = Regex.Replace(version, @"^[\^><=!~]+", string.Empty).Trim();
 
-                    _versionTargets.Add(new PythonVersionTarget(
+                    AddVersionTarget(
                         version,
                         "pyproject.toml",
                         PythonVersionConfidence.High,
-                        isMinimum));
+                        isMinimum);
                 }
             }
         }
@@ -367,11 +366,11 @@ internal sealed partial class PythonInputNormalizer
                     var isMinimum = version.StartsWith(">=", StringComparison.Ordinal);
                     version = Regex.Replace(version, @"^[><=!~]+", string.Empty).Trim();
 
-                    _versionTargets.Add(new PythonVersionTarget(
+                    AddVersionTarget(
                         version,
                         "setup.py",
                         PythonVersionConfidence.High,
-                        isMinimum));
+                        isMinimum);
                 }
             }
         }
@@ -401,11 +400,11 @@ internal sealed partial class PythonInputNormalizer
                     var isMinimum = version.StartsWith(">=", StringComparison.Ordinal);
                     version = Regex.Replace(version, @"^[><=!~]+", string.Empty).Trim();
 
-                    _versionTargets.Add(new PythonVersionTarget(
+                    AddVersionTarget(
                         version,
                         "setup.cfg",
                         PythonVersionConfidence.High,
-                        isMinimum));
+                        isMinimum);
                 }
             }
         }
@@ -433,10 +432,10 @@ internal sealed partial class PythonInputNormalizer
             if (match.Success)
             {
                 var version = match.Groups["version"].Value;
-                _versionTargets.Add(new PythonVersionTarget(
+                AddVersionTarget(
                     version,
                     "runtime.txt",
-                    PythonVersionConfidence.Definitive));
+                    PythonVersionConfidence.Definitive);
             }
         }
         catch (IOException)
@@ -462,10 +461,10 @@ internal sealed partial class PythonInputNormalizer
             if (fromMatch.Success)
             {
                 var version = fromMatch.Groups["version"].Value;
-                _versionTargets.Add(new PythonVersionTarget(
+                AddVersionTarget(
                     version,
                     "Dockerfile",
-                    PythonVersionConfidence.High));
+                    PythonVersionConfidence.High);
                 return;
             }
 
@@ -474,10 +473,10 @@ internal sealed partial class PythonInputNormalizer
             if (envMatch.Success)
             {
                 var version = envMatch.Groups["version"].Value;
-                _versionTargets.Add(new PythonVersionTarget(
+                AddVersionTarget(
                     version,
                     "Dockerfile",
-                    PythonVersionConfidence.Medium));
+                    PythonVersionConfidence.Medium);
             }
         }
         catch (IOException)
@@ -509,10 +508,10 @@ internal sealed partial class PythonInputNormalizer
                     {
                         // Convert py311 to 3.11
                         var formatted = $"{version[0]}.{version[1..]}";
-                        _versionTargets.Add(new PythonVersionTarget(
+                        AddVersionTarget(
                             formatted,
                             "tox.ini",
-                            PythonVersionConfidence.Medium));
+                            PythonVersionConfidence.Medium);
                     }
                 }
             }
@@ -553,10 +552,10 @@ internal sealed partial class PythonInputNormalizer
                     if (match.Success)
                     {
                         var version = match.Groups["version"].Value;
-                        _versionTargets.Add(new PythonVersionTarget(
+                        AddVersionTarget(
                             version,
                             $"lib/{dirName}",
-                            PythonVersionConfidence.Medium));
+                            PythonVersionConfidence.Medium);
                     }
                 }
             }
@@ -659,6 +658,46 @@ internal sealed partial class PythonInputNormalizer
         }
     }
 
+    private void AddVersionTarget(string version, string source, PythonVersionConfidence confidence, bool isMinimum = false)
+    {
+        if (string.IsNullOrWhiteSpace(version) || string.IsNullOrWhiteSpace(source))
+        {
+            return;
+        }
+
+        var normalizedVersion = version.Trim();
+        var normalizedSource = source.Trim();
+
+        var existingIndex = _versionTargets.FindIndex(target =>
+            string.Equals(target.Version, normalizedVersion, StringComparison.OrdinalIgnoreCase) &&
+            string.Equals(target.Source, normalizedSource, StringComparison.OrdinalIgnoreCase));
+
+        if (existingIndex >= 0)
+        {
+            var existing = _versionTargets[existingIndex];
+            var effectiveConfidence = (PythonVersionConfidence)Math.Max((int)existing.Confidence, (int)confidence);
+            var effectiveIsMinimum = existing.IsMinimum || isMinimum;
+
+            if (existing.Confidence == effectiveConfidence && existing.IsMinimum == effectiveIsMinimum)
+            {
+                return;
+            }
+
+            _versionTargets[existingIndex] = new PythonVersionTarget(
+                normalizedVersion,
+                normalizedSource,
+                effectiveConfidence,
+                effectiveIsMinimum);
+            return;
+        }
+
+        _versionTargets.Add(new PythonVersionTarget(
+            normalizedVersion,
+            normalizedSource,
+            confidence,
+            isMinimum));
+    }
+
     private void DetectZipapps()
     {
         if (!Directory.Exists(_rootPath))
@@ -779,7 +818,7 @@ internal sealed partial class PythonInputNormalizer
     [GeneratedRegex(@"requires-python\s*=\s*[""']?(?<version>[^""'\n]+)", RegexOptions.IgnoreCase)]
     private static partial Regex RequiresPythonPattern();
 
-    [GeneratedRegex(@"python\s*=\s*[""'](?<version>[^""']+)[""']", RegexOptions.IgnoreCase)]
+    [GeneratedRegex(@"^\s*python\s*=\s*[""'](?<version>[^""']+)[""']", RegexOptions.IgnoreCase | RegexOptions.Multiline)]
     private static partial Regex PythonVersionTomlPattern();
 
     [GeneratedRegex(@"python_requires\s*=\s*[""'](?<version>[^""']+)[""']", RegexOptions.IgnoreCase)]