merge: bring private changes to dev

Latest changes from main including .flake8 configuration and all repokit module updates with fixes for adopt command, auth integration, and improved error handling.

Author: djdarcy

.flake8

@@ -0,0 +1,54 @@
+[flake8]
+# Treat most style issues as warnings rather than errors
+# This prevents CI/CD from failing on style issues while still showing them
+
+# Maximum line length (slightly more lenient than default)
+max-line-length = 88
+
+# Treat these as warnings instead of errors
+# E501: line too long
+# F401: imported but unused  
+# F541: f-string is missing placeholders
+# W293: blank line contains whitespace
+# W291: trailing whitespace
+# E128: continuation line under-indented for visual indent
+# E302: expected 2 blank lines, found 1
+warn-symbols = E501,F401,F541,W293,W291,E128,E302
+
+# Only treat serious issues as errors
+select = E9,F63,F7,F82
+
+# Ignore the following (treat as warnings or ignore completely)
+ignore = 
+    # Line length (we set max-line-length above)
+    E501,
+    # Whitespace issues (cosmetic)
+    W291,W293,
+    # Import issues (non-critical)
+    F401,
+    # f-string issues (minor)
+    F541,
+    # Indentation issues (cosmetic)
+    E128,
+    # Blank line issues (cosmetic)  
+    E302
+
+# Files to exclude from checking
+exclude = 
+    .git,
+    __pycache__,
+    *.pyc,
+    .venv,
+    venv,
+    .tox,
+    dist,
+    build,
+    *.egg-info,
+    private/,
+    test_runs/,
+    revisions/old_*,
+    **/repo-manager-worktree-fix.py
+
+# Show statistics
+statistics = True
+count = True

repokit/auth_integration.py

@@ -12,35 +12,36 @@
 from pathlib import Path
 from typing import Dict, Any, Optional, Tuple
 
+
 class AuthenticationHandler:
     """
     Handles authentication with remote services.
     """
-    
+
     def __init__(self, verbose: int = 0):
         """
         Initialize the authentication handler.
-        
+
         Args:
             verbose: Verbosity level (0=normal, 1=info, 2=debug)
         """
         self.verbose = verbose
         self.logger = logging.getLogger("repokit.auth")
-        
+
         # Default locations for credentials
         self.user_home = Path.home()
         self.default_creds_path = self.user_home / ".repokit" / "credentials.json"
-        
+
         # Initialize with empty credentials
         self.credentials = {}
-    
+
     def load_credentials(self, credentials_file: Optional[str] = None) -> bool:
         """
         Load credentials from a file.
-        
+
         Args:
             credentials_file: Path to credentials file (or None to use default)
-            
+
         Returns:
             True if loaded successfully, False otherwise
         """
@@ -52,48 +53,50 @@ def load_credentials(self, credentials_file: Optional[str] = None) -> bool:
             if self.verbose >= 1:
                 self.logger.info("No credentials file found")
             return False
-        
+
         try:
-            with open(creds_path, 'r') as f:
+            with open(creds_path, "r") as f:
                 self.credentials = json.load(f)
-            
+
             if self.verbose >= 1:
                 self.logger.info(f"Loaded credentials from {creds_path}")
             return True
         except Exception as e:
             self.logger.error(f"Error loading credentials: {str(e)}")
             return False
-    
-    def get_token(self, service: str, token_command: Optional[str] = None) -> Optional[str]:
+
+    def get_token(
+        self, service: str, token_command: Optional[str] = None
+    ) -> Optional[str]:
         """
         Get authentication token for a service.
-        
+
         Tries multiple sources in this order:
         1. Command provided token command
         2. Environment variable
         3. Credentials file
-        
+
         Args:
             service: Service name ('github' or 'gitlab')
             token_command: Optional command to retrieve token from password manager
-            
+
         Returns:
             Authentication token or None if not found
         """
         # Standardize service name
         service = service.lower()
-        
+
         # 1. Try token command if provided
         if token_command:
             try:
                 if self.verbose >= 2:
                     self.logger.debug(f"Running token command: {token_command}")
                 result = subprocess.run(
-                    token_command, 
-                    shell=True, 
+                    token_command,
+                    shell=True,
                     check=True,
                     capture_output=True,
-                    text=True
+                    text=True,
                 )
                 token = result.stdout.strip()
                 if token:
@@ -102,63 +105,63 @@ def get_token(self, service: str, token_command: Optional[str] = None) -> Option
                     return token
             except Exception as e:
                 self.logger.error(f"Failed to get token from command: {str(e)}")
-        
+
         # 2. Try environment variable
         env_var = f"{service.upper()}_TOKEN"
         token = os.environ.get(env_var)
         if token:
             if self.verbose >= 1:
                 self.logger.info(f"Using {service} token from environment variable")
             return token
-        
+
         # 3. Try credentials file
         if service in self.credentials and "token" in self.credentials[service]:
             if self.verbose >= 1:
                 self.logger.info(f"Using {service} token from credentials file")
             return self.credentials[service]["token"]
-        
+
         # Token not found
         self.logger.warning(f"No {service} token found")
         return None
-    
+
     def get_organization(self, service: str) -> Optional[str]:
         """
         Get organization or group for a service.
-        
+
         Args:
             service: Service name ('github' or 'gitlab')
-            
+
         Returns:
             Organization/group name or None if not specified
         """
         # Standardize service name
         service = service.lower()
-        
+
         # Try environment variable first
         env_var = f"{service.upper()}_ORGANIZATION"
         if service == "gitlab":
             env_var = "GITLAB_GROUP"  # GitLab uses "group" terminology
-        
+
         org = os.environ.get(env_var)
         if org:
             return org
-        
+
         # Try credentials file
         if service in self.credentials:
             if service == "github" and "organization" in self.credentials[service]:
                 return self.credentials[service]["organization"]
             elif service == "gitlab" and "group" in self.credentials[service]:
                 return self.credentials[service]["group"]
-        
+
         return None
-    
+
     def get_api_url(self, service: str) -> str:
         """
         Get API URL for a service.
-        
+
         Args:
             service: Service name ('github' or 'gitlab')
-            
+
         Returns:
             API URL for the service
         """
@@ -168,69 +171,73 @@ def get_api_url(self, service: str) -> str:
             return os.environ.get("GITLAB_API_URL", "https://gitlab.com/api/v4")
         else:
             return ""
-    
-    def store_credentials(self, service: str, token: str, 
-                        organization: Optional[str] = None,
-                        file_path: Optional[str] = None) -> bool:
+
+    def store_credentials(
+        self,
+        service: str,
+        token: str,
+        organization: Optional[str] = None,
+        file_path: Optional[str] = None,
+    ) -> bool:
         """
         Store credentials in the credentials file.
-        
+
         Args:
             service: Service name ('github' or 'gitlab')
             token: Authentication token
             organization: Organization or group name (optional)
             file_path: Path to credentials file (or None to use default)
-            
+
         Returns:
             True if stored successfully, False otherwise
         """
         # Standardize service name
         service = service.lower()
-        
+
         # Load existing credentials if file exists
         if file_path:
             creds_path = Path(file_path)
         else:
             creds_path = self.default_creds_path
             # Ensure directory exists
             creds_path.parent.mkdir(parents=True, exist_ok=True)
-        
+
         # Load existing credentials if file exists
         existing_creds = {}
         if creds_path.exists():
             try:
-                with open(creds_path, 'r') as f:
+                with open(creds_path, "r") as f:
                     existing_creds = json.load(f)
             except Exception as e:
                 self.logger.error(f"Error loading existing credentials: {str(e)}")
                 # Continue with empty credentials
-        
+
         # Update credentials
         service_creds = existing_creds.get(service, {})
         service_creds["token"] = token
-        
+
         if organization:
             if service == "github":
                 service_creds["organization"] = organization
             elif service == "gitlab":
                 service_creds["group"] = organization
-        
+
         existing_creds[service] = service_creds
-        
+
         # Save credentials
         try:
-            with open(creds_path, 'w') as f:
+            with open(creds_path, "w") as f:
                 json.dump(existing_creds, f, indent=2)
-            
+
             # Set restrictive permissions
             os.chmod(creds_path, 0o600)
-            
+
             if self.verbose >= 1:
                 self.logger.info(f"Stored {service} credentials in {creds_path}")
-            
+
             # Update in-memory credentials
             self.credentials = existing_creds
-            
+
             return True
         except Exception as e:
             self.logger.error(f"Error storing credentials: {str(e)}")