chore: adopt ruff as the linter, replace flake8

.pre-commit-config.yaml

@@ -17,30 +17,16 @@ repos:
   #   rev: v1.7.3
   #   hooks:
   #     - id: actionlint
-  - repo: https://github.com/pycqa/isort
-    # rev must match what's in dev-requirements.txt
-    rev: 5.13.2
+  # ruff handles linting and import sorting (config in pyproject.toml).
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.20
     hooks:
-      - id: isort
+      - id: ruff
+        args: [--fix]
   # - repo: https://github.com/PyCQA/bandit
   #   rev: 1.7.10
   #   hooks:
   #     - id: bandit
   #       args: [
   #         "-c", "pyproject.toml",
   #       ]
-  # - repo: https://github.com/astral-sh/ruff-pre-commit
-  #   rev: v0.7.1
-  #   hooks:
-  #     - id: ruff
-  #       args:
-  #         - --fix
-  #     - id: ruff-format
-  # -   repo: https://github.com/PyCQA/autoflake
-  #     rev: v2.3.1
-  #     hooks:
-  #     -   id: autoflake
-  #         args:
-  #           - --in-place
-  #           - --remove-all-unused-imports
-  #           - --remove-unused-variables

AGENTS.md

@@ -34,8 +34,8 @@ PR-Agent automates AI-assisted reviews for pull requests across multiple git pro
 ## Coding Style and Naming Conventions
 
 - Python sources follow the Ruff configuration in `pyproject.toml` (`line-length = 120`, Pyflakes plus `flake8-bugbear` checks, and isort ordering). Keep imports grouped as isort would produce and prefer double quotes for strings.
-- Pre-commit (`.pre-commit-config.yaml`) enforces trailing whitespace cleanup, final newlines, TOML/YAML validity, and optional `isort`; run `pre-commit run --all-files` before submitting patches if installed.
-- Before committing, run `flake8` and fix every issue it reports. Keep fixes mechanical (rename, reformat, remove unused imports, add missing newlines); do not alter program logic while cleaning up—if a lint fix would change behavior, surface it instead of applying it silently.
+- Pre-commit (`.pre-commit-config.yaml`) enforces trailing whitespace cleanup, final newlines, TOML/YAML validity, and `ruff` (lint + import sorting); run `pre-commit run --all-files` before submitting patches if installed.
+- Before committing, run `uv run ruff check --fix` and fix every issue it reports. Keep fixes mechanical (rename, reformat, remove unused imports, add missing newlines); do not alter program logic while cleaning up—if a lint fix would change behavior, surface it instead of applying it silently.
 - Match existing docstring and comment style—concise English comments using imperative phrasing only where necessary.
 - Configuration files in `pr_agent/settings/` are TOML; preserve formatting, section order, and comments when editing prompts or defaults.
 - Markdown in `docs/` uses MkDocs conventions (YAML front matter absent; rely on heading hierarchy already in place).

pr_agent/algo/ai_handlers/langchain_ai_handler.py

@@ -7,11 +7,10 @@
 except:  # we don't enforce langchain as a dependency, so if it's not installed, just move on
     pass
 
-import functools
 
 import openai
-from tenacity import retry, retry_if_exception_type, retry_if_not_exception_type, stop_after_attempt
 from langchain_core.runnables import Runnable
+from tenacity import retry, retry_if_exception_type, retry_if_not_exception_type, stop_after_attempt
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -7,18 +7,22 @@
 import openai
 import requests
 from litellm import acompletion
-from tenacity import (retry, retry_if_exception_type,
-                      retry_if_not_exception_type, stop_after_attempt)
-
-from pr_agent.algo import (CLAUDE_EXTENDED_THINKING_MODELS,
-                           NO_SUPPORT_TEMPERATURE_MODELS,
-                           STREAMING_REQUIRED_MODELS,
-                           SUPPORT_REASONING_EFFORT_MODELS,
-                           USER_MESSAGE_ONLY_MODELS)
+from tenacity import retry, retry_if_exception_type, retry_if_not_exception_type, stop_after_attempt
+
+from pr_agent.algo import (
+    CLAUDE_EXTENDED_THINKING_MODELS,
+    NO_SUPPORT_TEMPERATURE_MODELS,
+    STREAMING_REQUIRED_MODELS,
+    SUPPORT_REASONING_EFFORT_MODELS,
+    USER_MESSAGE_ONLY_MODELS,
+)
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_helpers import (
-    MockResponse, _get_azure_ad_token, _handle_streaming_response,
-    _process_litellm_extra_body)
+    MockResponse,
+    _get_azure_ad_token,
+    _handle_streaming_response,
+    _process_litellm_extra_body,
+)
 from pr_agent.algo.utils import ReasoningEffort, get_version
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
@@ -456,7 +460,7 @@ async def chat_completion(self, model: str, system: str, user: str, temperature:
                         # check if the image link is alive
                         r = requests.head(img_path, allow_redirects=True)
                         if r.status_code == 404:
-                            error_msg = f"The image link is not [alive](img_path).\nPlease repost the original image as a comment, and send the question again with 'quote reply' (see [instructions](https://pr-agent-docs.codium.ai/tools/ask/#ask-on-images-using-the-pr-code-as-context))."
+                            error_msg = "The image link is not [alive](img_path).\nPlease repost the original image as a comment, and send the question again with 'quote reply' (see [instructions](https://pr-agent-docs.codium.ai/tools/ask/#ask-on-images-using-the-pr-code-as-context))."
                             get_logger().error(error_msg)
                             return f"{error_msg}", "error"
                     except Exception as e:

pr_agent/algo/ai_handlers/openai_ai_handler.py

@@ -1,5 +1,5 @@
 from os import environ
-from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
+
 import openai
 from openai import AsyncOpenAI
 from tenacity import retry, retry_if_exception_type, retry_if_not_exception_type, stop_after_attempt

pr_agent/algo/cli_args.py

@@ -1,5 +1,5 @@
-from base64 import b64decode, encode, b64encode
-import hashlib
+from base64 import b64decode
+
 
 class CliArgs:
     @staticmethod

pr_agent/algo/git_patch_processing.py

@@ -3,7 +3,7 @@
 import re
 import traceback
 
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.algo.types import EDIT_TYPE
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 

pr_agent/algo/pr_processing.py

@@ -5,13 +5,14 @@
 
 from github import RateLimitExceededException
 
-from pr_agent.algo.file_filter import filter_ignored
 from pr_agent.algo.git_patch_processing import (
-    extend_patch, handle_patch_deletions,
-    decouple_and_convert_to_hunks_with_lines_numbers)
+    decouple_and_convert_to_hunks_with_lines_numbers,
+    extend_patch,
+    handle_patch_deletions,
+)
 from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.algo.types import EDIT_TYPE
 from pr_agent.algo.utils import ModelType, clip_tokens, get_max_tokens, get_model
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
@@ -506,7 +507,7 @@ def add_ai_metadata_to_diff_files(git_provider, pr_description_files):
     """
     try:
         if not pr_description_files:
-            get_logger().warning(f"PR description files are empty.")
+            get_logger().warning("PR description files are empty.")
             return
         available_files = {pr_file['full_file_name'].strip(): pr_file for pr_file in pr_description_files}
         diff_files = git_provider.get_diff_files()
@@ -517,7 +518,7 @@ def add_ai_metadata_to_diff_files(git_provider, pr_description_files):
                 file.ai_file_summary = available_files[filename]
                 found_any_match = True
         if not found_any_match:
-            get_logger().error(f"Failed to find any matching files between PR description and diff files.",
+            get_logger().error("Failed to find any matching files between PR description and diff files.",
                                artifact={"pr_description_files": pr_description_files})
     except Exception as e:
         get_logger().error(f"Failed to add AI metadata to diff files: {e}",

pr_agent/algo/token_handler.py

@@ -1,6 +1,6 @@
-from threading import Lock
-from math import ceil
 import re
+from math import ceil
+from threading import Lock
 
 from jinja2 import Environment, StrictUndefined
 from tiktoken import encoding_for_model, get_encoding
@@ -99,6 +99,7 @@ def _get_system_user_tokens(self, pr, encoder, vars: dict, system, user):
     def _calc_claude_tokens(self, patch: str) -> int:
         try:
             import anthropic
+
             from pr_agent.algo import MAX_TOKENS
 
             client = anthropic.Anthropic(api_key=get_settings(use_context=False).get('anthropic.key'))