fix copilot review issues: add init files, fix function signatures, add comments to except clauses, improve edge counting

Author: Sahil-u07

concore_cli/__init__.py

@@ -1,11 +1,6 @@
 import click
 from rich.console import Console
-from rich.table import Table
-from rich.panel import Panel
-from rich import print as rprint
 import sys
-import os
-from pathlib import Path
 
 from .commands.init import init_project
 from .commands.run import run_workflow
@@ -55,10 +50,11 @@ def validate(workflow_file):
 
 @cli.command()
 @click.argument('workflow_file', type=click.Path(exists=True))
+@click.option('--source', '-s', default='src', help='Source directory')
 @click.option('--json', 'output_json', is_flag=True, help='Output in JSON format')
-def inspect(workflow_file, output_json):
+def inspect(workflow_file, source, output_json):
     try:
-        inspect_workflow(workflow_file, console, output_json)
+        inspect_workflow(workflow_file, source, output_json, console)
     except Exception as e:
         console.print(f"[red]Error:[/red] {str(e)}")
         sys.exit(1)

concore_cli/cli.py

@@ -6,15 +6,15 @@
 from collections import defaultdict
 import re
 
-def inspect_workflow(workflow_file, console, output_json=False):
+def inspect_workflow(workflow_file, source_dir, output_json, console):
     workflow_path = Path(workflow_file)
 
     if output_json:
-        return _inspect_json(workflow_path)
+        return _inspect_json(workflow_path, source_dir)
 
-    _inspect_rich(workflow_path, console)
+    _inspect_rich(workflow_path, source_dir, console)
 
-def _inspect_rich(workflow_path, console):
+def _inspect_rich(workflow_path, source_dir, console):
     console.print()
     console.print(f"[bold cyan]Workflow:[/bold cyan] {workflow_path.name}")
     console.print()
@@ -60,7 +60,7 @@ def _inspect_rich(workflow_path, console):
                     else:
                         lang_counts['Other'] += 1
 
-                    src_dir = workflow_path.parent / 'src'
+                    src_dir = workflow_path.parent / source_dir
                     if not (src_dir / filename).exists():
                         missing_files.append(filename)
 
@@ -77,11 +77,11 @@ def _inspect_rich(workflow_path, console):
 
         for edge in edges:
             label_tag = edge.find('y:EdgeLabel')
-            if label_tag and label_tag.text:
-                if edge_label_regex.match(label_tag.text.strip()):
-                    zmq_count += 1
-                else:
-                    file_count += 1
+            label_text = label_tag.text.strip() if label_tag and label_tag.text else ""
+            if label_text and edge_label_regex.match(label_text):
+                zmq_count += 1
+            else:
+                file_count += 1
 
         if zmq_count > 0:
             edges_branch.add(f"ZMQ: {zmq_count}")
@@ -126,7 +126,7 @@ def _inspect_rich(workflow_path, console):
                         }
                         lang = lang_map.get(ext, 'Other')
 
-                        src_dir = workflow_path.parent / 'src'
+                        src_dir = workflow_path.parent / source_dir
                         status = "✓" if (src_dir / filename).exists() else "✗"
 
                         table.add_row(node_id, filename, lang, status)
@@ -166,7 +166,7 @@ def _inspect_rich(workflow_path, console):
     except Exception as e:
         console.print(f"[red]Inspection failed:[/red] {str(e)}")
 
-def _inspect_json(workflow_path):
+def _inspect_json(workflow_path, source_dir):
     import json
 
     try:
@@ -175,6 +175,10 @@ def _inspect_json(workflow_path):
 
         soup = BeautifulSoup(content, 'xml')
 
+        if not soup.find('graphml'):
+            print(json.dumps({'error': 'Not a valid GraphML file'}, indent=2))
+            return
+        
         nodes = soup.find_all('node')
         edges = soup.find_all('edge')
 
@@ -202,7 +206,7 @@ def _inspect_json(workflow_path):
                     lang = lang_map.get(ext, 'other')
                     lang_counts[lang] += 1
 
-                    src_dir = workflow_path.parent / 'src'
+                    src_dir = workflow_path.parent / source_dir
                     exists = (src_dir / filename).exists()
                     if not exists:
                         missing_files.append(filename)
@@ -223,13 +227,13 @@ def _inspect_json(workflow_path):
             target = edge.get('target')
 
             label_tag = edge.find('y:EdgeLabel')
+            label_text = label_tag.text.strip() if label_tag and label_tag.text else ""
             edge_type = 'file'
-            if label_tag and label_tag.text:
-                if edge_label_regex.match(label_tag.text.strip()):
-                    edge_type = 'zmq'
-                    zmq_count += 1
-                else:
-                    file_count += 1
+            if label_text and edge_label_regex.match(label_text):
+                edge_type = 'zmq'
+                zmq_count += 1
+            else:
+                file_count += 1
 
             edge_list.append({
                 'source': source,

concore_cli/commands/__init__.py

@@ -1,5 +1,4 @@
 from rich.table import Table
-from rich.panel import Panel
 import psutil
 import os
 
@@ -18,7 +17,8 @@ def show_status(console):
                 if 'concore' in cmdline.lower() and proc.info['pid'] != current_pid:
                     concore_processes.append(proc)
         except (psutil.NoSuchProcess, psutil.AccessDenied):
-            pass
+            # Process may have exited or be inaccessible; safe to ignore
+            continue
 
     if not concore_processes:
         console.print("[yellow]No running concore processes found[/yellow]")
@@ -38,7 +38,8 @@ def show_status(console):
 
             table.add_row(pid, name, cmd)
         except (psutil.NoSuchProcess, psutil.AccessDenied):
-            pass
+            # Process may have exited between iterations
+            continue
 
     console.print(table)
     console.print()

concore_cli/commands/inspect.py

@@ -19,8 +19,9 @@ def stop_all(console):
                     proc.terminate()
                     stopped += 1
                     console.print(f"[green]✓[/green] Stopped process {proc.info['pid']}")
-        except (psutil.NoSuchProcess, psutil.AccessDenied) as e:
-            pass
+        except (psutil.NoSuchProcess, psutil.AccessDenied):
+            # Process already exited or access denied; continue
+            continue
 
     if stopped == 0:
         console.print("[yellow]No processes to stop[/yellow]")

concore_cli/commands/status.py

@@ -28,3 +28,4 @@ concore = "concore_cli.cli:cli"
 
 [tool.setuptools]
 packages = ["concore_cli", "concore_cli.commands"]
+py-modules = ["mkconcore"]