Bump scikit-learn from 1.4.0 to 1.5.0 in /gui/api

.github/scripts/count_loc.py

@@ -13,12 +13,38 @@ def count_lines_in_file(filepath):
     """
     Count lines in a single file.
     Returns tuple: (total_lines, code_lines, comment_lines, blank_lines)
+
+    Supports comment detection for multiple languages:
+    - Python: #
+    - C/C++/Java/JavaScript/Go/Rust: //, /* */
+    - HTML/XML: <!-- -->
+    - Shell: #
+    - CSS: /* */
     """
     total_lines = 0
     code_lines = 0
     comment_lines = 0
     blank_lines = 0
 
+    # Get file extension to determine comment style
+    ext = filepath.suffix.lower()
+
+    # Define comment prefixes for different languages
+    single_line_comments = []
+    if ext in ['.py', '.sh', '.bash', '.yml', '.yaml', '.toml', '.r', '.rb']:
+        single_line_comments = ['#']
+    elif ext in ['.js', '.jsx', '.ts', '.tsx', '.java', '.c', '.cpp', '.cc', '.h', '.hpp', 
+                 '.cs', '.go', '.rs', '.swift', '.kt', '.scala', '.php']:
+        single_line_comments = ['//', '/*', '*/']
+    elif ext in ['.css', '.scss', '.sass', '.less']:
+        single_line_comments = ['/*', '*/']
+    elif ext in ['.html', '.xml', '.svg']:
+        single_line_comments = ['<!--', '-->']
+    elif ext in ['.lua']:
+        single_line_comments = ['--']
+    elif ext in ['.sql']:
+        single_line_comments = ['--', '/*', '*/']
+
     try:
         with open(filepath, 'r', encoding='utf-8', errors='ignore') as f:
             for line in f:
@@ -27,7 +53,7 @@ def count_lines_in_file(filepath):
 
                 if not stripped:
                     blank_lines += 1
-                elif stripped.startswith('#'):
+                elif any(stripped.startswith(comment) for comment in single_line_comments):
                     comment_lines += 1
                 else:
                     code_lines += 1
@@ -44,12 +70,34 @@ def count_loc(root_dir, extensions=None):
     Args:
         root_dir: Root directory to search
         extensions: List of file extensions to include (e.g., ['.py', '.js'])
+                   If None or 'all', counts all common programming language files.
 
     Returns:
         Dictionary with LOC statistics
     """
-    if extensions is None:
-        extensions = ['.py']
+    if extensions is None or (isinstance(extensions, list) and 'all' in extensions):
+        # Count all common programming language files
+        extensions = [
+            '.py',          # Python
+            '.js', '.jsx', '.ts', '.tsx',  # JavaScript/TypeScript
+            '.java',        # Java
+            '.c', '.cpp', '.cc', '.h', '.hpp',  # C/C++
+            '.cs',          # C#
+            '.go',          # Go
+            '.rs',          # Rust
+            '.rb',          # Ruby
+            '.php',         # PHP
+            '.swift',       # Swift
+            '.kt',          # Kotlin
+            '.scala',       # Scala
+            '.r',           # R
+            '.sh', '.bash', # Shell
+            '.html', '.css', '.scss', '.sass',  # Web
+            '.xml', '.svg', # Markup
+            '.sql',         # SQL
+            '.lua',         # Lua
+            '.yml', '.yaml', '.toml', '.json',  # Config
+        ]
 
     root_path = Path(root_dir)
 
@@ -109,7 +157,7 @@ def main():
     parser.add_argument('--root', default='.', help='Root directory to scan')
     parser.add_argument('--json', help='Output JSON file path')
     parser.add_argument('--extensions', nargs='+', default=['.py'], 
-                        help='File extensions to count (default: .py)')
+                        help='File extensions to count (default: .py). Use "all" to count all languages.')
 
     args = parser.parse_args()
 

.github/scripts/run_examples.py

@@ -249,9 +249,9 @@ def main():
         results.append((file_path, success, duration, error))
 
         if success:
-            print(f"{Colors.GREEN}✓{Colors.RESET} ({duration:.2f}s)")
+            print(f"{Colors.GREEN}[OK]{Colors.RESET} ({duration:.2f}s)")
         else:
-            print(f"{Colors.RED}✗{Colors.RESET} ({duration:.2f}s)")
+            print(f"{Colors.RED}[X]{Colors.RESET} ({duration:.2f}s)")
             if error:
                 # Print first line of error
                 error_line = error.split('\n')[0][:80]
@@ -277,7 +277,7 @@ def main():
         print(f"{Colors.BOLD}{Colors.RED}Failed Examples:{Colors.RESET}")
         for file_path, _, duration, error in failed:
             rel_path = file_path.relative_to(examples_dir)
-            print(f"  ✗ {rel_path} ({duration:.2f}s)")
+            print(f"  [X] {rel_path} ({duration:.2f}s)")
             if error:
                 print(f"    {Colors.GRAY}{error[:MAX_ERROR_LENGTH]}{Colors.RESET}")
 

.github/workflows/benchmarks.yml

@@ -45,10 +45,10 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade --timeout 120 --retries 5 pip setuptools wheel
         # Install core dependencies needed for benchmarks
-        pip install numpy scipy networkx matplotlib tqdm pandas
-        pip install pytest pytest-benchmark
+        pip install --timeout 120 --retries 5 numpy scipy networkx matplotlib tqdm pandas
+        pip install --timeout 120 --retries 5 pytest pytest-benchmark
       timeout-minutes: 10
 
     - name: Add py3plex to PYTHONPATH

.github/workflows/code-quality.yml

@@ -25,10 +25,10 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install black ruff isort mypy types-six
+        python -m pip install --upgrade --timeout 120 --retries 5 pip
+        pip install --timeout 120 --retries 5 black ruff isort mypy types-six
         # Install minimal dependencies for type checking
-        pip install numpy scipy networkx matplotlib rdflib tqdm bitarray pandas
+        pip install --timeout 120 --retries 5 numpy scipy networkx matplotlib rdflib tqdm bitarray pandas
       timeout-minutes: 8
 
     - name: Run lint checks via Makefile

.github/workflows/doc-coverage.yml

@@ -14,7 +14,6 @@ jobs:
     timeout-minutes: 10
     permissions:
       contents: read
-      pull-requests: write
 
     steps:
     - name: Checkout code
@@ -53,30 +52,3 @@ jobs:
         echo "COVERAGE=$COVERAGE" >> $GITHUB_ENV
         echo "Documentation coverage: $COVERAGE%"
       timeout-minutes: 1
-
-    - name: Comment coverage on PR
-      if: github.event_name == 'pull_request'
-      uses: actions/github-script@v7
-      with:
-        script: |
-          const fs = require('fs');
-          const coverage = JSON.parse(fs.readFileSync('doc-coverage.json', 'utf8'));
-
-          const comment = `## 📚 Documentation Coverage Report
-
-          | Metric | Count | Coverage |
-          |--------|-------|----------|
-          | Functions | ${coverage.documented_functions}/${coverage.total_functions} | ${coverage.function_coverage.toFixed(1)}% |
-          | Classes | ${coverage.documented_classes}/${coverage.total_classes} | ${coverage.class_coverage.toFixed(1)}% |
-          | **Overall** | **${coverage.documented_functions + coverage.documented_classes}/${coverage.total_items}** | **${coverage.overall_coverage.toFixed(1)}%** |
-
-          ![Badge](${coverage.badge_url})
-          `;
-
-          github.rest.issues.createComment({
-            issue_number: context.issue.number,
-            owner: context.repo.owner,
-            repo: context.repo.repo,
-            body: comment
-          });
-      timeout-minutes: 2

.github/workflows/docs.yml

@@ -26,13 +26,13 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade --timeout 120 --retries 5 pip
         # Install Sphinx and extensions
-        pip install sphinx sphinx-rtd-theme myst-parser m2r2
+        pip install --timeout 120 --retries 5 sphinx sphinx-rtd-theme myst-parser m2r2
         # Install package dependencies for API documentation
-        pip install numpy scipy networkx matplotlib rdflib tqdm bitarray
+        pip install --timeout 120 --retries 5 numpy scipy networkx matplotlib rdflib tqdm bitarray
         # Install py3plex package itself for autodoc to work
-        pip install -e .
+        pip install --timeout 120 --retries 5 -e .
       timeout-minutes: 8
 
     - name: Build Sphinx documentation

.github/workflows/examples.yml

@@ -51,10 +51,10 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade --timeout 120 --retries 5 pip setuptools wheel
         # Install numpy and scipy first to avoid potential conflicts
-        pip install --timeout 120 numpy scipy
-        pip install --timeout 120 -e .
+        pip install --timeout 120 --retries 5 numpy scipy
+        pip install --timeout 120 --retries 5 -e .
         # Verify key dependencies
         python -c "import numpy; print(f'numpy {numpy.__version__}')"
         python -c "import scipy; print(f'scipy {scipy.__version__}')"

.github/workflows/fuzzing.yml

@@ -26,10 +26,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install --upgrade pip --timeout 120
-          pip install --timeout 120 --retries 3 pytest hypothesis
-          pip install --timeout 120 --retries 3 networkx numpy scipy tqdm || true
-          pip install -e . || true
+          pip install --upgrade --timeout 120 --retries 5 pip
+          pip install --timeout 120 --retries 5 pytest hypothesis
+          pip install --timeout 120 --retries 5 networkx numpy scipy tqdm || true
+          pip install --timeout 120 --retries 5 -e . || true
         timeout-minutes: 8
 
       - name: Run property-based fuzzing tests
@@ -67,10 +67,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install --upgrade pip --timeout 120
-          pip install --timeout 120 --retries 3 atheris
-          pip install --timeout 120 --retries 3 networkx numpy scipy tqdm || true
-          pip install -e . || true
+          pip install --upgrade --timeout 120 --retries 5 pip
+          pip install --timeout 120 --retries 5 atheris
+          pip install --timeout 120 --retries 5 networkx numpy scipy tqdm || true
+          pip install --timeout 120 --retries 5 -e . || true
         timeout-minutes: 5
 
       - name: Run quick fuzzing campaign (60 seconds)