Merge upstream/dev and resolve conflicts in concore.py

Author: Sahil-u07

concore.py

@@ -1,18 +1,26 @@
 import time
 import logging
 import os
+import atexit
 from ast import literal_eval
 import sys
 import re
 import zmq
 import numpy as np
-import atexit
 import signal
 
 logging.basicConfig(
     level=logging.INFO,
-    format='%(levelname)s - %(message)s'
-) # Added for ZeroMQ
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', 
+    force=True 
+)
+
+#these lines mute the noisy library
+logging.getLogger('matplotlib').setLevel(logging.WARNING)
+logging.getLogger('PIL').setLevel(logging.WARNING)
+logging.getLogger('urllib3').setLevel(logging.WARNING) 
+logging.getLogger('requests').setLevel(logging.WARNING) 
+
 
 # if windows, create script to kill this process 
 # because batch files don't provide easy way to know pid of last command
@@ -193,26 +201,50 @@ def safe_literal_eval(filename, defaultValue):
 # ===================================================================
 # Parameter Parsing
 # ===================================================================
+def parse_params(sparams: str) -> dict:
+    params = {}
+    if not sparams:
+        return params
+
+    s = sparams.strip()
+
+    #full dict literal
+    if s.startswith("{") and s.endswith("}"):
+        try:
+            val = literal_eval(s)
+            if isinstance(val, dict):
+                return val
+        except (ValueError, SyntaxError):
+            pass
+
+    for item in s.split(";"):
+        if "=" in item:
+            key, value = item.split("=", 1)  # split only once
+            key=key.strip()
+            value=value.strip()
+            #try to convert to python type (int, float, list, etc.)
+            # Use literal_eval to preserve backward compatibility (integers/lists)
+            # Fallback to string for unquoted values (paths, URLs)
+            try:
+                params[key] = literal_eval(value)
+            except (ValueError, SyntaxError):
+                params[key] = value
+    return params
+
 try:
     sparams_path = concore_params_file
     if os.path.exists(sparams_path):
         with open(sparams_path, "r") as f:
-            sparams = f.read()
+            sparams = f.read().strip()
         if sparams: # Ensure sparams is not empty
             # Windows sometimes keeps quotes
             if sparams[0] == '"' and sparams[-1] == '"':  #windows keeps "" need to remove
                 sparams = sparams[1:-1]
 
-            # Convert key=value;key2=value2 to Python dict format
-            if sparams != '{' and not (sparams.startswith('{') and sparams.endswith('}')): # Check if it needs conversion
-                logging.debug("converting sparams: "+sparams)
-                sparams = "{'"+re.sub(';',",'",re.sub('=',"':",re.sub(' ','',sparams)))+"}"
-                logging.debug("converted sparams: " + sparams)
-            try:
-                params = literal_eval(sparams)
-            except Exception as e:
-                logging.warning(f"bad params content: {sparams}, error: {e}")
-                params = dict()
+            # Parse params using clean function instead of regex
+            logging.debug("parsing sparams: "+sparams)
+            params = parse_params(sparams)
+            logging.debug("parsed params: " + str(params))
         else:
             params = dict()
     else:

concore_cli/commands/run.py

@@ -5,10 +5,17 @@
 from rich.panel import Panel
 from rich.progress import Progress, SpinnerColumn, TextColumn
 
+def _find_mkconcore_path():
+    for parent in Path(__file__).resolve().parents:
+        candidate = parent / "mkconcore.py"
+        if candidate.exists():
+            return candidate
+    return None
+
 def run_workflow(workflow_file, source, output, exec_type, auto_build, console):
     workflow_path = Path(workflow_file).resolve()
     source_path = Path(source).resolve()
-    output_path = Path(output)
+    output_path = Path(output).resolve()
 
     if not source_path.exists():
         raise FileNotFoundError(f"Source directory '{source}' not found")
@@ -24,6 +31,10 @@ def run_workflow(workflow_file, source, output, exec_type, auto_build, console):
     console.print(f"[cyan]Type:[/cyan] {exec_type}")
     console.print()
 
+    mkconcore_path = _find_mkconcore_path()
+    if mkconcore_path is None:
+        raise FileNotFoundError("mkconcore.py not found. Please install concore from source.")
+
     with Progress(
         SpinnerColumn(),
         TextColumn("[progress.description]{task.description}"),
@@ -33,7 +44,8 @@ def run_workflow(workflow_file, source, output, exec_type, auto_build, console):
 
         try:
             result = subprocess.run(
-                [sys.executable, 'mkconcore.py', str(workflow_path), str(source_path), str(output_path), exec_type],
+                [sys.executable, str(mkconcore_path), str(workflow_path), str(source_path), str(output_path), exec_type],
+                cwd=mkconcore_path.parent,
                 capture_output=True,
                 text=True,
                 check=True

concore_cli/commands/validate.py

@@ -3,6 +3,7 @@
 from rich.panel import Panel
 from rich.table import Table
 import re
+import xml.etree.ElementTree as ET
 
 def validate_workflow(workflow_file, console):
     workflow_path = Path(workflow_file)
@@ -22,15 +23,34 @@ def validate_workflow(workflow_file, console):
             errors.append("File is empty")
             return show_results(console, errors, warnings, info)
 
+        # strict XML syntax check
+        try:
+            ET.fromstring(content)
+        except ET.ParseError as e:
+            errors.append(f"Invalid XML: {str(e)}")
+            return show_results(console, errors, warnings, info)
+        
         try:
             soup = BeautifulSoup(content, 'xml')
         except Exception as e:
             errors.append(f"Invalid XML: {str(e)}")
             return show_results(console, errors, warnings, info)
 
-        if not soup.find('graphml'):
+        root = soup.find('graphml')
+        if not root:
             errors.append("Not a valid GraphML file - missing <graphml> root element")
             return show_results(console, errors, warnings, info)
+            
+        # check the graph attributes
+        graph = soup.find('graph')
+        if not graph:
+             errors.append("Missing <graph> element")
+        else:
+             edgedefault = graph.get('edgedefault')
+             if not edgedefault:
+                 errors.append("Graph missing required 'edgedefault' attribute")
+             elif edgedefault not in ['directed', 'undirected']:
+                 errors.append(f"Invalid edgedefault value '{edgedefault}' (must be 'directed' or 'undirected')")
 
         nodes = soup.find_all('node')
         edges = soup.find_all('edge')
@@ -47,8 +67,19 @@ def validate_workflow(workflow_file, console):
 
         node_labels = []
         for node in nodes:
+            #check the node id
+            node_id = node.get('id')
+            if not node_id:
+                errors.append("Node missing required 'id' attribute")
+                #skip further checks for this node to avoid noise
+                continue
+
             try:
+                #robust find: try with namespace prefix first, then without
                 label_tag = node.find('y:NodeLabel')
+                if not label_tag:
+                    label_tag = node.find('NodeLabel')
+                
                 if label_tag and label_tag.text:
                     label = label_tag.text.strip()
                     node_labels.append(label)
@@ -60,13 +91,13 @@ def validate_workflow(workflow_file, console):
                         if len(parts) != 2:
                             warnings.append(f"Node '{label}' has invalid format")
                         else:
-                            node_id, filename = parts
+                            nodeId_part, filename = parts
                             if not filename:
                                 errors.append(f"Node '{label}' has no filename")
                             elif not any(filename.endswith(ext) for ext in ['.py', '.cpp', '.m', '.v', '.java']):
                                 warnings.append(f"Node '{label}' has unusual file extension")
                 else:
-                    warnings.append(f"Node {node.get('id', 'unknown')} has no label")
+                    warnings.append(f"Node {node_id} has no label")
             except Exception as e:
                 warnings.append(f"Error parsing node: {str(e)}")
 
@@ -91,6 +122,9 @@ def validate_workflow(workflow_file, console):
         for edge in edges:
             try:
                 label_tag = edge.find('y:EdgeLabel')
+                if not label_tag:
+                    label_tag = edge.find('EdgeLabel')
+                    
                 if label_tag and label_tag.text:
                     if edge_label_regex.match(label_tag.text.strip()):
                         zmq_edges += 1