fix(pypi): address Qodo review findings for pyproject.toml support

- Fix PEP 621 annotation targeting: use individual TomlLiteral elements
  instead of parent TomlKeyValue so each dependency gets its own highlight
- Fix quick-fix replacement: preserve package name in PEP 508 strings
  (e.g. "anyio==3.6.2" → "anyio==4.0.0" instead of just "==4.0.0")
- Add [project.optional-dependencies] parsing for PEP 621 optional groups
- Update README to reflect optional-dependencies are now analyzed

Implements TC-3853

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Assisted-by: Claude Code

Author: ruromero

README.md

@@ -380,9 +380,9 @@ When modifying the grammar or lexer files, you need to regenerate the parser cla
   You can create an alternative file to `requirements.txt`, for example, a `requirements-dev.txt` or
   a `requirements-test.txt` file where you can add the development or test dependencies there.
 
-  For `pyproject.toml`, only production dependencies from `[project.dependencies]` (PEP 621) and
-  `[tool.poetry.dependencies]` are analyzed. Optional dependencies (`[project.optional-dependencies]`)
-  and Poetry group dependencies (`[tool.poetry.group.*.dependencies]`) are excluded.
+  For `pyproject.toml`, dependencies from `[project.dependencies]` (PEP 621),
+  `[project.optional-dependencies]`, and `[tool.poetry.dependencies]` are analyzed.
+  Poetry group dependencies (`[tool.poetry.group.*.dependencies]`) are excluded.
 
 
 - **Excluding manifest files with patterns**

src/main/java/org/jboss/tools/intellij/componentanalysis/pypi/PyprojectCAAnnotator.java

@@ -80,6 +80,8 @@ protected Map<Dependency, List<PsiElement>> getDependencies(PsiFile file) {
             String tablePath = getTablePath(header);
             if ("project".equals(tablePath)) {
                 parsePep621Dependencies(table, ignoredDeps, resultMap);
+            } else if ("project.optional-dependencies".equals(tablePath)) {
+                parseOptionalDependencies(table, ignoredDeps, resultMap);
             } else if ("tool.poetry.dependencies".equals(tablePath)) {
                 parsePoetryDependencies(table, ignoredDeps, resultMap);
             }
@@ -100,15 +102,17 @@ protected CAUpdateManifestIntentionAction patchManifest(PsiElement element, Depe
 
     @Override
     protected boolean isQuickFixApplicable(PsiElement element) {
-        return element instanceof TomlKeyValue &&
-               element.getContainingFile() != null &&
-               PYPROJECT_TOML.equals(element.getContainingFile().getName());
+        if (element.getContainingFile() == null || !PYPROJECT_TOML.equals(element.getContainingFile().getName())) {
+            return false;
+        }
+        // Poetry: key-value pair like anyio = "^3.6.2"
+        if (element instanceof TomlKeyValue) {
+            return true;
+        }
+        // PEP 621: string literal in dependencies array like "anyio==3.6.2"
+        return element instanceof TomlLiteral;
     }
 
-    /**
-     * Parses PEP 621 [project] dependencies array.
-     * Format: dependencies = ["anyio==3.6.2", "flask>=2.0.3"]
-     */
     private void parsePep621Dependencies(TomlTable projectTable, Set<String> ignoredDeps,
                                           Map<Dependency, List<PsiElement>> resultMap) {
         List<TomlKeyValue> keyValues = PsiTreeUtil.getChildrenOfTypeAsList(projectTable, TomlKeyValue.class);
@@ -131,10 +135,35 @@ private void parsePep621Dependencies(TomlTable projectTable, Set<String> ignored
                 }
                 String version = extractPep508Version(depString);
                 Dependency dp = new Dependency(PYPI, null, name.toLowerCase(), version);
-                // Use the parent TomlKeyValue of the array as element for annotation,
-                // but we need to find or create a suitable element. Use the literal itself
-                // wrapped through the array's parent key-value.
-                resultMap.computeIfAbsent(dp, k -> new LinkedList<>()).add(kv);
+                resultMap.computeIfAbsent(dp, k -> new LinkedList<>()).add(literal);
+            }
+        }
+    }
+
+    /**
+     * Parses PEP 621 [project.optional-dependencies] table.
+     * Format: dev = ["pytest>=7.0", "black"], security = ["certifi>=2023.7"]
+     */
+    private void parseOptionalDependencies(TomlTable optDepsTable, Set<String> ignoredDeps,
+                                            Map<Dependency, List<PsiElement>> resultMap) {
+        List<TomlKeyValue> groups = PsiTreeUtil.getChildrenOfTypeAsList(optDepsTable, TomlKeyValue.class);
+        for (TomlKeyValue group : groups) {
+            TomlValue value = group.getValue();
+            if (!(value instanceof TomlArray array)) {
+                continue;
+            }
+            for (TomlValue element : array.getElements()) {
+                if (!(element instanceof TomlLiteral literal)) {
+                    continue;
+                }
+                String depString = unquote(literal.getText());
+                String name = extractPep508Name(depString);
+                if (name == null || ignoredDeps.contains(name.toLowerCase())) {
+                    continue;
+                }
+                String version = extractPep508Version(depString);
+                Dependency dp = new Dependency(PYPI, null, name.toLowerCase(), version);
+                resultMap.computeIfAbsent(dp, k -> new LinkedList<>()).add(literal);
             }
         }
     }
@@ -280,7 +309,7 @@ private String normalizeKeyName(String keyText) {
         return keyText;
     }
 
-    private static String unquote(String text) {
+    static String unquote(String text) {
         if (text != null && text.length() >= 2) {
             if ((text.startsWith("\"") && text.endsWith("\"")) ||
                     (text.startsWith("'") && text.endsWith("'"))) {

src/main/java/org/jboss/tools/intellij/componentanalysis/pypi/PyprojectCAIntentionAction.java

@@ -40,7 +40,15 @@ protected void updateVersion(@NotNull Project project, Editor editor, PsiFile fi
             return;
         }
 
-        if (element instanceof TomlKeyValue keyValue) {
+        if (element instanceof TomlLiteral literal) {
+            // PEP 621: string literal in dependencies array like "anyio==3.6.2"
+            String depString = PyprojectCAAnnotator.unquote(literal.getText());
+            String name = PyprojectCAAnnotator.extractPep508Name(depString);
+            if (name != null) {
+                replaceVersionLiteral(project, file, literal, name + "==" + version);
+            }
+        } else if (element instanceof TomlKeyValue keyValue) {
+            // Poetry: key-value pair like anyio = "^3.6.2"
             TomlLiteral valueLiteral = findVersionLiteral(keyValue);
             if (valueLiteral != null) {
                 replaceVersionLiteral(project, file, valueLiteral, "==" + version);
@@ -50,12 +58,11 @@ protected void updateVersion(@NotNull Project project, Editor editor, PsiFile fi
 
     private TomlLiteral findVersionLiteral(TomlKeyValue keyValue) {
         if (keyValue.getValue() instanceof TomlLiteral literal) {
-            // Simple string: "anyio==3.6.2" — this is a PEP 508 array entry, version is embedded in the string
-            // For array entries, the whole literal is the dependency string
+            // Poetry simple string: anyio = "^3.6.2"
             return literal;
         }
         if (keyValue.getValue() instanceof TomlInlineTable inlineTable) {
-            // Poetry format: anyio = {version = "^3.6.2"}
+            // Poetry inline table: anyio = {version = "^3.6.2"}
             for (TomlKeyValue entry : PsiTreeUtil.getChildrenOfTypeAsList(inlineTable, TomlKeyValue.class)) {
                 if ("version".equals(entry.getKey().getText()) && entry.getValue() instanceof TomlLiteral) {
                     return (TomlLiteral) entry.getValue();
@@ -94,6 +101,7 @@ private void replaceVersionLiteral(@NotNull Project project, PsiFile file, TomlL
 
     @Override
     public boolean isAvailable(@NotNull Project project, Editor editor, PsiFile file) {
-        return file != null && "pyproject.toml".equals(file.getName()) && element instanceof TomlKeyValue;
+        return file != null && "pyproject.toml".equals(file.getName())
+                && (element instanceof TomlKeyValue || element instanceof TomlLiteral);
     }
 }