refactor: replace print statements with logger.warning calls

Co-Authored-By: Patched <[email protected]>

patchwork/steps/FixIssue/FixIssue.py

@@ -4,6 +4,7 @@
 from typing import Any, Optional
 
 from git import Repo, InvalidGitRepositoryError
+from patchwork.logger import logger
 from openai.types.chat import ChatCompletionMessageParam
 
 from patchwork.common.client.llm.aio import AioLlmClient
@@ -177,10 +178,10 @@ def run(self):
                                         modified_file["diff"] = diff
                                 except Exception as e:
                                     # Git-specific errors (untracked files, etc) - keep empty diff
-                                    print(f"Note: Could not get git diff for {file}: {str(e)}")
+                                    logger.warning(f"Could not get git diff for {file}: {str(e)}")
                         except Exception as e:
                             # General file processing errors
-                            print(f"Warning: Failed to process file {file}: {str(e)}")
+                            logger.warning(f"Failed to process file {file}: {str(e)}")
 
                     modified_files_with_diffs.append(modified_file)
 

patchwork/steps/ModifyCode/ModifyCode.py

@@ -3,6 +3,7 @@
 import difflib
 from pathlib import Path
 
+from patchwork.logger import logger
 from patchwork.step import Step, StepStatus
 
 
@@ -128,7 +129,7 @@ def run(self) -> dict:
                 if not diff and new_code:  # If no diff but we have new code (new file)
                     diff = f"+++ {file_path}\n{new_code}"
             except (OSError, IOError) as e:
-                print(f"Warning: Failed to generate diff for {file_path}: {str(e)}")
+                logger.warning(f"Failed to generate diff for {file_path}: {str(e)}")
                 # Still proceed with the modification even if diff generation fails
                 replace_code_in_file(file_path, start_line, end_line, new_code)
                 diff = f"+++ {file_path}\n{new_code}"  # Use new code as diff on error