Bug Fixes and Workflow Improvements

.gitignore

@@ -64,3 +64,9 @@ run_indexer_with_filtering.py
 
 # Cline files
 memory-bank/
+/deepcode_lab
+/logs
+mcp_agent.config.yaml
+mcp_agent.secrets.yaml
+mcp_agent.config.yaml
+mcp_agent.secrets.yaml

CHANGELOG.md

@@ -0,0 +1,74 @@
+# Changelog
+
+All notable changes to DeepCode will be documented in this file.
+
+## [1.0.6-jm] - 2025-10-19
+
+### Added
+- **Dynamic Model Limit Detection**: New `utils/model_limits.py` module that automatically detects and adapts to any LLM model's token limits and pricing
+- **Loop Detection System**: `utils/loop_detector.py` prevents infinite loops by detecting repeated tool calls, timeouts, and progress stalls
+- **Progress Tracking**: 8-phase progress tracking (5% → 100%) with file-level progress indicators in both UI and terminal
+- **Abort Mechanism**: "Stop Processing" button in UI with global abort flag for clean process termination
+- **Cache Cleanup Scripts**: `start_clean.bat` and `start_clean.ps1` to clear Python cache before starting
+- **Enhanced Error Display**: Real-time error messages in both UI and terminal with timestamps
+- **File Progress Tracking**: Shows files completed/total with estimated time remaining
+
+### Fixed
+- **Critical: False Error Detection**: Fixed overly aggressive error detection that was marking successful operations as failures, causing premature abort and empty file generation
+- **Critical: Empty File Generation**: Files now contain actual code instead of being empty (2-byte files)
+- **Unique Folder Naming**: Each project run now creates `paper_{timestamp}` folders instead of reusing `pdf_output`
+- **PDF Save Location**: PDFs now save to `deepcode_lab/papers/` instead of system temp directory
+- **Duplicate Folder Prevention**: Added session state caching to prevent duplicate folder creation on UI reruns
+- **Token Limit Compliance**: Fixed `max_tokens` to respect model limits dynamically (e.g., gpt-4o-mini's 16,384 token limit)
+- **Empty Plan Detection**: System now fails early with clear error messages when initial plan is empty or invalid
+- **Process Hanging**: Fixed infinite loops and hanging on errors - process now exits cleanly
+- **Token Cost Tracking**: Restored accurate token usage and cost display (was showing $0.0000)
+- **PDF to Markdown Conversion**: Fixed automatic conversion and file location handling
+- **Document Segmentation**: Properly uses configured 50K character threshold from `mcp_agent.config.yaml`
+- **Error Propagation**: Abort mechanism now properly stops process after 10 consecutive real errors
+
+### Changed
+- **Model-Aware Token Management**: Token limits now adapt automatically based on configured model instead of hardcoded values
+- **Cost Calculation**: Dynamic pricing based on actual model rates (OpenAI, Anthropic)
+- **Retry Logic**: Token limits for retries now respect model maximum (87.5% → 95% → 98% of max)
+- **Segmentation Workflow**: Better integration with code implementation phase
+- **Error Handling**: Enhanced error propagation - errors no longer reported as "success"
+- **UI Display**: Shows project folder name after PDF conversion for better visibility
+- **Terminal Logging**: Added timestamps to all progress messages
+
+### Technical Improvements
+- Added document-segmentation server to code implementation workflow for better token management
+- Improved error handling in agent orchestration engine with proper cleanup
+- Enhanced subprocess handling on Windows (hide console windows, prevent hanging)
+- Better LibreOffice detection on Windows using direct path checking
+- Fixed input data format consistency (JSON with `paper_path` key)
+- Added comprehensive logging throughout the pipeline
+- Improved resource cleanup on errors and process termination
+
+### Documentation
+- Translated Chinese comments to English in core workflow files
+- Added inline documentation for new utility modules
+- Created startup scripts with clear usage instructions
+
+### Breaking Changes
+- None - all changes are backward compatible
+
+### Known Issues
+- Terminal may show trailing "Calling Tool..." line after completion (cosmetic display artifact - process completes successfully)
+- Some Chinese comments remain in non-critical files (cli, tools) - translation in progress
+- tiktoken package optional warning (doesn't affect functionality)
+
+### Success Metrics
+- ✅ Complete end-to-end workflow: DOCX upload → PDF conversion → Markdown → Segmentation → Planning → Code generation
+- ✅ Files generated with actual code content (15+ files with proper implementation)
+- ✅ Single folder per project run (no duplicates)
+- ✅ Dynamic token management working across different models
+- ✅ Accurate cost tracking per model
+- ✅ Clean process termination with proper error handling
+
+---
+
+## [1.0.5] - Previous Release
+
+See previous releases for earlier changes.
+

__init__.py

@@ -5,9 +5,10 @@
 ⚡ Transform research papers into working code automatically
 """
 
-__version__ = "1.0.5"
-__author__ = "DeepCode Team"
+__version__ = "1.0.6-jm"
+__author__ = "DeepCode Team, Jany Martelli"
 __url__ = "https://github.com/HKUDS/DeepCode"
+__repo__ = "https://github.com/Jany-M/DeepCode/"
 
 # Import main components for easy access
 from utils import FileProcessor, DialogueLogger

deepcode.py

@@ -50,6 +50,7 @@ def check_dependencies():
     try:
         import subprocess
         import platform
+        import os
 
         subprocess_kwargs = {
             "capture_output": True,
@@ -58,25 +59,56 @@ def check_dependencies():
         }
 
         if platform.system() == "Windows":
-            subprocess_kwargs["creationflags"] = 0x08000000  # Hide console window
+            subprocess_kwargs["creationflags"] = 0x08000000
+            # Also configure startupinfo to hide window
+            startupinfo = subprocess.STARTUPINFO()
+            startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+            startupinfo.wShowWindow = subprocess.SW_HIDE
+            subprocess_kwargs["startupinfo"] = startupinfo
 
         # Try different LibreOffice commands
         libreoffice_found = False
-        for cmd in ["libreoffice", "soffice"]:
-            try:
-                result = subprocess.run([cmd, "--version"], **subprocess_kwargs)
-                if result.returncode == 0:
-                    print(
-                        "✅ LibreOffice is installed (for Office document conversion)"
-                    )
+
+        # On Windows, try standard installation paths first
+        # Just check if file exists to avoid window/hanging issues
+        if platform.system() == "Windows":
+            possible_paths = [
+                r"C:\Program Files\LibreOffice\program\soffice.exe",
+                r"C:\Program Files (x86)\LibreOffice\program\soffice.exe",
+            ]
+
+            # Also check PROGRAMFILES environment variables
+            program_files = os.environ.get("PROGRAMFILES")
+            program_files_x86 = os.environ.get("PROGRAMFILES(X86)")
+
+            if program_files:
+                possible_paths.append(os.path.join(program_files, "LibreOffice", "program", "soffice.exe"))
+            if program_files_x86:
+                possible_paths.append(os.path.join(program_files_x86, "LibreOffice", "program", "soffice.exe"))
+
+            for path in possible_paths:
+                if os.path.exists(path):
+                    print("✅ LibreOffice is installed (for Office document conversion)")
                     libreoffice_found = True
                     break
-            except (
-                subprocess.CalledProcessError,
-                FileNotFoundError,
-                subprocess.TimeoutExpired,
-            ):
-                continue
+
+        # Try standard commands if not found via Windows paths (non-Windows systems)
+        if not libreoffice_found and platform.system() != "Windows":
+            for cmd in ["libreoffice", "soffice"]:
+                try:
+                    result = subprocess.run([cmd, "--version"], **subprocess_kwargs)
+                    if result.returncode == 0:
+                        print(
+                            "✅ LibreOffice is installed (for Office document conversion)"
+                        )
+                        libreoffice_found = True
+                        break
+                except (
+                    subprocess.CalledProcessError,
+                    FileNotFoundError,
+                    subprocess.TimeoutExpired,
+                ):
+                    continue
 
         if not libreoffice_found:
             missing_system_deps.append("LibreOffice")

requirements.txt

@@ -5,8 +5,12 @@ asyncio-mqtt
 docling
 mcp-agent
 mcp-server-git
+openapi
 nest_asyncio
 pathlib2
 PyPDF2>=2.0.0
 reportlab>=3.5.0
 streamlit
+openai
+PyPDF2
+aiohttp