Memory MCP; Add skill tool; Deployment script improvement; Update readme

.gitignore

@@ -1,4 +1,6 @@
 workspace/
+config_*.json
+workspace_*/
 emma_paper/
 final_outputs/
 *.wav

README.md

@@ -1,7 +1,39 @@
+<div align="center">
+<br>
 
-# Toolomics
+<img src="./docs/images/logo_toolomics.png" width="22%" style="border-radius: 8px;" alt="Toolomics Logo">
 
-*A suite of tools from the Holobiomics Lab for Agents, organized as a set of MCP servers.*
+</div>
+
+<h1 align="center">Toolomics</h1>
+
+<p align="center">
+    <em>A suite of MCP-based Tools from the HolobiomicsLab. Used by AI-Agents such as ***Mimosa-AI***</em>
+</p>
+
+<p align="center">
+    <img src="https://img.shields.io/github/license/HolobiomicsLab/Toolomics?style=flat-square&logo=opensourceinitiative&logoColor=white&color=4caf82" alt="license">
+    <img src="https://img.shields.io/github/last-commit/HolobiomicsLab/Toolomics?style=flat-square&logo=git&logoColor=white&color=4caf82" alt="last-commit">
+    <img src="https://img.shields.io/github/languages/count/HolobiomicsLab/Toolomics?style=flat-square&color=4caf82" alt="repo-language-count">
+</p>
+
+<p align="center">
+    <a href="https://github.com/HolobiomicsLab/Toolomics/stargazers">
+        <img src="https://img.shields.io/github/stars/HolobiomicsLab/Toolomics?style=social" alt="GitHub Stars">
+    </a>
+    <a href="https://opensource.org/licenses/Apache-2.0">
+        <img src="https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square" alt="License: Apache 2.0">
+    </a>
+</p>
+
+---
+
+> ***Toolomics*** — deploys containerized tools, manages isolated instances, and enables file sharing across AI agents for bioinformatics, metabolomics, molecular docking, and beyond.
+
+**Use cases:**
+- Deploy MCP servers for browser automation, PDF processing, and data extraction
+- Run isolated, multi-instance agent workspaces with automatic resource management
+- Orchestrate containerized bioinformatics pipelines (XCMS, RStudio, Redis) with zero config
 
 ## Install & deploy tools
 

config_86517947.json

@@ -5,63 +5,73 @@
         "enabled": false
     },
     {
-        "path": "mcp_host/pdf/server.py",
+        "path": "mcp_host/memory/server.py",
         "port": 5001,
         "enabled": false
     },
     {
-        "path": "mcp_host/html/server.py",
+        "path": "mcp_host/pdf/server.py",
         "port": 5002,
+        "enabled": true
+    },
+    {
+        "path": "mcp_host/html/server.py",
+        "port": 5003,
         "enabled": false
     },
     {
         "path": "mcp_host/graph_rag/server.py",
-        "port": 5003,
+        "port": 5004,
         "enabled": false
     },
     {
         "path": "mcp_host/browser/server.py",
-        "port": 5004,
+        "port": 5005,
         "enabled": false
     },
     {
         "path": "mcp_host/image_analysis/server.py",
-        "port": 5013,
+        "port": 5006,
         "enabled": true
     },
     {
         "path": "mcp_host/csv/server.py",
-        "port": 5006,
+        "port": 5007,
         "enabled": true
     },
+    {
+        "path": "mcp_host/skills/server.py",
+        "port": 5008,
+        "enabled": false
+    },
     {
         "path": "mcp_host/txt_editor/server.py",
-        "port": 5007,
+        "port": 5009,
         "enabled": true
     },
     {
         "path": "mcp_host/python_editor/server.py",
-        "port": 5008,
+        "port": 5010,
         "enabled": true
     },
     {
         "path": "mcp_host/Rscript/docker-compose.yml",
-        "port": 5009,
+        "port": 5011,
         "enabled": false
     },
     {
         "path": "mcp_host/shell/docker-compose.yml",
-        "port": 5010,
+        "port": 5012,
         "enabled": true
     },
     {
         "path": "mcp_host/browser/searxng/docker-compose.yml",
-        "port": 5011,
+        "port": 5013,
         "enabled": false
     },
     {
         "path": "mcp_host/decimer/docker-compose.yml",
-        "port": 5012,
+        "port": 5014,
         "enabled": false
     }
 ]

deploy.py

@@ -480,22 +480,9 @@ def load_config(self) -> Dict[str, dict]:
         if self.config_path.stat().st_size == 0:
             logger.warning(f"Config file {self.config_path} is empty.")
             return {}
-
-        # Check if file is corrupted by reading first character
-        try:
-            with open(self.config_path, 'rb') as f:
-                first_byte = f.read(1)
-                if first_byte and first_byte != b'[':
-                    logger.error(f"Config file {self.config_path} is corrupted (starts with {first_byte!r} instead of b'[')") 
-                    logger.warning(f"Deleting corrupted config file to regenerate fresh")
-                    self.config_path.unlink()
-                    return {}
-        except Exception as e:
-            logger.error(f"Error checking config file: {e}")
-            return {}
 
         try:
-            with open(self.config_path, 'r', encoding='utf-8') as f:
+            with open(self.config_path, 'r', encoding='utf-8-sig') as f:  # utf-8-sig handles BOM
                 # Acquire shared lock for reading
                 try:
                     fcntl.flock(f.fileno(), fcntl.LOCK_SH)
@@ -525,7 +512,7 @@ def load_config(self) -> Dict[str, dict]:
                         else:
                             raise ValueError("Can't parse config.json file")
 
-                    logger.debug(f"Successfully loaded {len(config_dict)} items from config")
+                    logger.info(f"Successfully loaded {len(config_dict)} items from config (enabled: {sum(1 for v in config_dict.values() if v.get('enabled'))})")
                     return config_dict
                 finally:
                     # Release lock
@@ -534,17 +521,28 @@ def load_config(self) -> Dict[str, dict]:
                     except:
                         pass
 
-        except (json.JSONDecodeError, KeyError, IndexError) as e:
+        except (json.JSONDecodeError, KeyError, IndexError, ValueError) as e:
             logger.error(f"Error loading config from {self.config_path}: {e}")
             # Try to read the file again to see what's actually there
             try:
                 file_size = self.config_path.stat().st_size
                 with open(self.config_path, 'rb') as f:
                     raw_bytes = f.read(100)
-                    logger.error(f"File size: {file_size}, first 100 bytes: {raw_bytes}")
+                    logger.error(f"File size: {file_size}, first 100 bytes: {raw_bytes!r}")
             except Exception as debug_e:
                 logger.error(f"Could not read file for debugging: {debug_e}")
-            logger.warning(f"Returning empty config due to parse error. File will be regenerated.")
+
+            # Backup the corrupted file instead of silently regenerating
+            backup_path = self.config_path.with_suffix('.json.backup')
+            try:
+                import shutil
+                shutil.copy2(self.config_path, backup_path)
+                logger.warning(f"Backed up corrupted config to: {backup_path}")
+            except Exception as backup_e:
+                logger.warning(f"Could not backup config: {backup_e}")
+
+            logger.warning(f"Config file appears corrupted. Will regenerate fresh config.")
+            logger.warning(f"If you had enabled services, please re-enable them after checking {backup_path}")
             return {}
 
     def save_config(self, config: Dict[str, dict]) -> None:
@@ -622,7 +620,7 @@ def assign_ports(self, server_files: List[Path], compose_files: List[Path] = Non
 
                 config[server_str] = {'port': next_host_port, 'enabled': False}
                 used_ports.add(next_host_port)
-                logger.info(f"Assigned host port {next_host_port} to {server_str} (enabled by default)")
+                logger.info(f"Assigned host port {next_host_port} to {server_str} (disabled - edit config to enable)")
                 next_host_port += 1
 
         # Assign ports to docker-compose files
@@ -640,7 +638,7 @@ def assign_ports(self, server_files: List[Path], compose_files: List[Path] = Non
 
                     config[compose_str] = {'port': next_host_port, 'enabled': False}
                     used_ports.add(next_host_port)
-                    logger.info(f"Assigned host port {next_host_port} to {compose_str} (enabled by default)")
+                    logger.info(f"Assigned host port {next_host_port} to {compose_str} (disabled - edit config to enable)")
                     next_host_port += 1
 
         self.save_config(config)