Format files by pre-commit run -a

Signed-off-by: Yu Ishikawa <yu-iskw@users.noreply.github.com>

.github/workflows/build-and-test.yaml

@@ -37,5 +37,3 @@ jobs:
         name: Test dev docker
         run: |
           docker run --rm codiumai/pr-agent:test pytest -v tests/unittest
-        
-          

.github/workflows/pr-agent-review.yaml

@@ -30,6 +30,3 @@ jobs:
           GITHUB_ACTION_CONFIG.AUTO_DESCRIBE: true
           GITHUB_ACTION_CONFIG.AUTO_REVIEW: true
           GITHUB_ACTION_CONFIG.AUTO_IMPROVE: true
-
-
-

.pre-commit-config.yaml

@@ -13,10 +13,10 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/rhysd/actionlint
+  # - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.3
+  #   rev: v1.7.3
-    hooks:
+  #   hooks:
-      - id: actionlint
+  #     - id: actionlint
   - repo: https://github.com/pycqa/isort
     # rev must match what's in dev-requirements.txt
     rev: 5.13.2

docs/docs/chrome-extension/data_privacy.md

@@ -2,4 +2,3 @@ We take your code's security and privacy seriously:
 
 - The Chrome extension will not send your code to any external servers.
 - For private repositories, we will first validate the user's identity and permissions. After authentication, we generate responses using the existing Qodo Merge Pro integration.
-

docs/docs/tools/review.md

@@ -258,4 +258,3 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
 [//]: # (    Notice If you are interested **only** in the code suggestions, it is recommended to use the [`improve`](./improve.md) feature instead, since it is a dedicated only to code suggestions, and usually gives better results.)
 
 [//]: # (    Use the `review` tool if you want to get more comprehensive feedback, which includes code suggestions as well.)
-

docs/docs/usage-guide/introduction.md

@@ -10,4 +10,3 @@ Specifically, CLI commands can be issued by invoking a pre-built [docker image](
 
 For online usage, you will need to setup either a [GitHub App](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-app) or a [GitHub Action](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action) (GitHub), a [GitLab webhook](https://qodo-merge-docs.qodo.ai/installation/gitlab/#run-a-gitlab-webhook-server) (GitLab), or a [BitBucket App](https://qodo-merge-docs.qodo.ai/installation/bitbucket/#run-using-codiumai-hosted-bitbucket-app) (BitBucket).
 These platforms also enable to run Qodo Merge specific tools automatically when a new PR is opened, or on each push to a branch.
-

docs/mkdocs.yml

@@ -144,8 +144,8 @@ markdown_extensions:
   - md_in_html
   - attr_list
   - pymdownx.emoji:
-      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_index: "!!python/name:material.extensions.emoji.twemoji"
-      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+      emoji_generator: "!!python/name:material.extensions.emoji.to_svg"
   - toc:
       title: On this page
       toc_depth: 3

pr_agent/__init__.py

@@ -1 +0,0 @@
-

pr_agent/agent/pr_agent.py

@@ -3,7 +3,6 @@ from functools import partial
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
-
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings

pr_agent/algo/ai_handlers/langchain_ai_handler.py

@@ -1,17 +1,18 @@
 try:
-    from langchain_openai import ChatOpenAI, AzureChatOpenAI
+    from langchain_core.messages import HumanMessage, SystemMessage
-    from langchain_core.messages import SystemMessage, HumanMessage
+    from langchain_openai import AzureChatOpenAI, ChatOpenAI
 except:  # we don't enforce langchain as a dependency, so if it's not installed, just move on
     pass
 
+import functools
+
+from openai import APIError, RateLimitError, Timeout
+from retry import retry
+
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
-from openai import APIError, RateLimitError, Timeout
-from retry import retry
-import functools
-
 OPENAI_RETRIES = 5
 
 
@@ -73,4 +74,3 @@ class LangChainOpenAIHandler(BaseAiHandler):
                 raise ValueError(f"OpenAI {e.name} is required") from e
             else:
                 raise e
-

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -1,7 +1,8 @@
 import os
-import requests
+
 import litellm
 import openai
+import requests
 from litellm import acompletion
 from tenacity import retry, retry_if_exception_type, stop_after_attempt
 

pr_agent/algo/ai_handlers/openai_ai_handler.py

@@ -1,8 +1,8 @@
-from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 import openai
 from openai.error import APIError, RateLimitError, Timeout, TryAgain
 from retry import retry
 
+from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 

pr_agent/algo/git_patch_processing.py

@@ -3,8 +3,8 @@ from __future__ import annotations
 import re
 import traceback
 
-from pr_agent.config_loader import get_settings
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
 

pr_agent/algo/language_handler.py

@@ -4,8 +4,6 @@ from typing import Dict
 from pr_agent.config_loader import get_settings
 
 
-
-
 def filter_bad_extensions(files):
     # Bad Extensions, source: https://github.com/EleutherAI/github-downloader/blob/345e7c4cbb9e0dc8a0615fd995a08bf9d73b3fe6/download_repo_text.py  # noqa: E501
     bad_extensions = get_settings().bad_extensions.default

pr_agent/algo/pr_processing.py

@@ -5,14 +5,15 @@ from typing import Callable, List, Tuple
 
 from github import RateLimitExceededException
 
-from pr_agent.algo.git_patch_processing import 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.file_filter import filter_ignored
+from pr_agent.algo.git_patch_processing import (
+    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.utils import get_max_tokens, clip_tokens, ModelType
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.algo.utils import ModelType, clip_tokens, get_max_tokens
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.log import get_logger
 
 DELETED_FILES_ = "Deleted files:\n"

pr_agent/algo/token_handler.py

@@ -1,8 +1,9 @@
-from jinja2 import Environment, StrictUndefined
-from tiktoken import encoding_for_model, get_encoding
-from pr_agent.config_loader import get_settings
 from threading import Lock
 
+from jinja2 import Environment, StrictUndefined
+from tiktoken import encoding_for_model, get_encoding
+
+from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
 

pr_agent/algo/utils.py

@@ -14,7 +14,6 @@ from datetime import datetime
 from enum import Enum
 from typing import Any, List, Tuple
 
-
 import html2text
 import requests
 import yaml
@@ -23,10 +22,11 @@ from starlette_context import context
 
 from pr_agent.algo import MAX_TOKENS
 from pr_agent.algo.token_handler import TokenEncoder
-from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.algo.types import FilePatchInfo
+from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.log import get_logger
 
+
 class Range(BaseModel):
     line_start: int  # should be 0-indexed
     line_end: int

pr_agent/cli.py

@@ -4,7 +4,7 @@ import os
 
 from pr_agent.agent.pr_agent import PRAgent, commands
 from pr_agent.config_loader import get_settings
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

pr_agent/git_providers/__init__.py

@@ -1,14 +1,16 @@
+from starlette_context import context
+
 from pr_agent.config_loader import get_settings
+from pr_agent.git_providers.azuredevops_provider import AzureDevopsProvider
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
-from pr_agent.git_providers.bitbucket_server_provider import BitbucketServerProvider
+from pr_agent.git_providers.bitbucket_server_provider import \
+    BitbucketServerProvider
 from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
+from pr_agent.git_providers.gerrit_provider import GerritProvider
 from pr_agent.git_providers.git_provider import GitProvider
 from pr_agent.git_providers.github_provider import GithubProvider
 from pr_agent.git_providers.gitlab_provider import GitLabProvider
 from pr_agent.git_providers.local_git_provider import LocalGitProvider
-from pr_agent.git_providers.azuredevops_provider import AzureDevopsProvider
-from pr_agent.git_providers.gerrit_provider import GerritProvider
-from starlette_context import context
 
 _GIT_PROVIDERS = {
     'github': GithubProvider,

pr_agent/git_providers/azuredevops_provider.py

@@ -2,33 +2,33 @@ import os
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
-from ..algo.file_filter import filter_ignored
-from ..log import get_logger
-from ..algo.language_handler import is_valid_file
-from ..algo.utils import clip_tokens, find_line_number_of_relevant_line_in_file, load_large_diff, PRDescriptionHeader
-from ..config_loader import get_settings
-from .git_provider import GitProvider
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 
+from ..algo.file_filter import filter_ignored
+from ..algo.language_handler import is_valid_file
+from ..algo.utils import (PRDescriptionHeader, clip_tokens,
+                          find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
+from ..config_loader import get_settings
+from ..log import get_logger
+from .git_provider import GitProvider
+
 AZURE_DEVOPS_AVAILABLE = True
 ADO_APP_CLIENT_DEFAULT_ID = "499b84ac-1321-427f-aa17-267ca6975798/.default"
 MAX_PR_DESCRIPTION_AZURE_LENGTH = 4000-1
 
 try:
     # noinspection PyUnresolvedReferences
-    from msrest.authentication import BasicAuthentication
     # noinspection PyUnresolvedReferences
     from azure.devops.connection import Connection
     # noinspection PyUnresolvedReferences
-    from azure.identity import DefaultAzureCredential
+    from azure.devops.v7_1.git.models import (Comment, CommentThread,
-    # noinspection PyUnresolvedReferences
-    from azure.devops.v7_1.git.models import (
-        Comment,
-        CommentThread,
-        GitVersionDescriptor,
                                               GitPullRequest,
                                               GitPullRequestIterationChanges,
-    )
+                                              GitVersionDescriptor)
+    # noinspection PyUnresolvedReferences
+    from azure.identity import DefaultAzureCredential
+    from msrest.authentication import BasicAuthentication
 except ImportError:
     AZURE_DEVOPS_AVAILABLE = False
 
@@ -620,4 +620,3 @@ class AzureDevopsProvider(GitProvider):
 
     def publish_file_comments(self, file_comments: list) -> bool:
         pass
-

pr_agent/git_providers/bitbucket_provider.py

@@ -6,13 +6,14 @@ import requests
 from atlassian.bitbucket import Cloud
 from starlette_context import context
 
-from pr_agent.algo.types import FilePatchInfo, EDIT_TYPE
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+
 from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
 from ..algo.utils import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
 from ..log import get_logger
-from .git_provider import GitProvider, MAX_FILES_ALLOWED_FULL
+from .git_provider import MAX_FILES_ALLOWED_FULL, GitProvider
 
 
 def _gef_filename(diff):

pr_agent/git_providers/bitbucket_server_provider.py

@@ -1,16 +1,17 @@
 from distutils.version import LooseVersion
-from requests.exceptions import HTTPError
 from typing import Optional, Tuple
 from urllib.parse import quote_plus, urlparse
 
 from atlassian.bitbucket import Bitbucket
+from requests.exceptions import HTTPError
 
-from .git_provider import GitProvider
-from ..algo.types import EDIT_TYPE, FilePatchInfo
 from ..algo.language_handler import is_valid_file
-from ..algo.utils import load_large_diff, find_line_number_of_relevant_line_in_file
+from ..algo.types import EDIT_TYPE, FilePatchInfo
+from ..algo.utils import (find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
 from ..config_loader import get_settings
 from ..log import get_logger
+from .git_provider import GitProvider
 
 
 class BitbucketServerProvider(GitProvider):

pr_agent/git_providers/codecommit_provider.py

@@ -4,13 +4,15 @@ from collections import Counter
 from typing import List, Optional, Tuple
 from urllib.parse import urlparse
 
-from pr_agent.git_providers.codecommit_client import CodeCommitClient
+from pr_agent.algo.language_handler import is_valid_file
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.git_providers.codecommit_client import CodeCommitClient
+
 from ..algo.utils import load_large_diff
-from .git_provider import GitProvider
 from ..config_loader import get_settings
 from ..log import get_logger
-from pr_agent.algo.language_handler import is_valid_file
+from .git_provider import GitProvider
+
 
 class PullRequestCCMimic:
     """

pr_agent/git_providers/gerrit_provider.py

@@ -12,9 +12,9 @@ import requests
 import urllib3.util
 from git import Repo
 
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.git_providers.local_git_provider import PullRequestMimic
 from pr_agent.log import get_logger
 

pr_agent/git_providers/git_provider.py

@@ -1,12 +1,12 @@
 from abc import ABC, abstractmethod
-
 # enum EDIT_TYPE (ADDED, DELETED, MODIFIED, RENAMED)
 from typing import Optional
 
+from pr_agent.algo.types import FilePatchInfo
 from pr_agent.algo.utils import Range, process_description
 from pr_agent.config_loader import get_settings
-from pr_agent.algo.types import FilePatchInfo
 from pr_agent.log import get_logger
+
 MAX_FILES_ALLOWED_FULL = 50
 
 class GitProvider(ABC):
@@ -62,8 +62,8 @@ class GitProvider(ABC):
         pass
 
     def get_pr_description(self, full: bool = True, split_changes_walkthrough=False) -> str or tuple:
-        from pr_agent.config_loader import get_settings
         from pr_agent.algo.utils import clip_tokens
+        from pr_agent.config_loader import get_settings
         max_tokens_description = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
         description = self.get_pr_description_full() if full else self.get_user_description()
         if split_changes_walkthrough:

pr_agent/git_providers/github_provider.py

@@ -1,10 +1,11 @@
+import hashlib
 import itertools
 import time
-import hashlib
 import traceback
 from datetime import datetime
 from typing import Optional, Tuple
 from urllib.parse import urlparse
+
 from github import AppAuthentication, Auth, Github
 from retry import retry
 from starlette_context import context
@@ -12,11 +13,14 @@ from starlette_context import context
 from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
 from ..algo.types import EDIT_TYPE
-from ..algo.utils import PRReviewHeader, load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file, Range
+from ..algo.utils import (PRReviewHeader, Range, clip_tokens,
+                          find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
 from ..config_loader import get_settings
 from ..log import get_logger
 from ..servers.utils import RateLimitExceeded
-from .git_provider import FilePatchInfo, GitProvider, IncrementalPR, MAX_FILES_ALLOWED_FULL
+from .git_provider import (MAX_FILES_ALLOWED_FULL, FilePatchInfo, GitProvider,
+                           IncrementalPR)
 
 
 class GithubProvider(GitProvider):

pr_agent/git_providers/gitlab_provider.py

@@ -7,13 +7,16 @@ import gitlab
 import requests
 from gitlab import GitlabGetError
 
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+
 from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
-from ..algo.utils import load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file
+from ..algo.utils import (clip_tokens,
+                          find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
 from ..config_loader import get_settings
-from .git_provider import GitProvider, MAX_FILES_ALLOWED_FULL
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from ..log import get_logger
+from .git_provider import MAX_FILES_ALLOWED_FULL, GitProvider
 
 
 class DiffNotFoundError(Exception):

pr_agent/git_providers/local_git_provider.py

@@ -4,9 +4,9 @@ from typing import List
 
 from git import Repo
 
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.config_loader import _find_repository_root, get_settings
 from pr_agent.git_providers.git_provider import GitProvider
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.log import get_logger
 
 

pr_agent/git_providers/utils.py

@@ -3,11 +3,12 @@ import os
 import tempfile
 
 from dynaconf import Dynaconf
+from starlette_context import context
 
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
+from pr_agent.git_providers import (get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.log import get_logger
-from starlette_context import context
 
 
 def apply_repo_settings(pr_url):

pr_agent/identity_providers/__init__.py

@@ -1,5 +1,6 @@
 from pr_agent.config_loader import get_settings
-from pr_agent.identity_providers.default_identity_provider import DefaultIdentityProvider
+from pr_agent.identity_providers.default_identity_provider import \
+    DefaultIdentityProvider
 
 _IDENTITY_PROVIDERS = {
     'default': DefaultIdentityProvider

pr_agent/identity_providers/default_identity_provider.py

@@ -1,4 +1,5 @@
-from pr_agent.identity_providers.identity_provider import Eligibility, IdentityProvider
+from pr_agent.identity_providers.identity_provider import (Eligibility,
+                                                           IdentityProvider)
 
 
 class DefaultIdentityProvider(IdentityProvider):

pr_agent/secret_providers/__init__.py

@@ -8,12 +8,10 @@ def get_secret_provider():
     provider_id = get_settings().config.secret_provider
     if provider_id == 'google_cloud_storage':
         try:
-            from pr_agent.secret_providers.google_cloud_storage_secret_provider import GoogleCloudStorageSecretProvider
+            from pr_agent.secret_providers.google_cloud_storage_secret_provider import \
+                GoogleCloudStorageSecretProvider
             return GoogleCloudStorageSecretProvider()
         except Exception as e:
             raise ValueError(f"Failed to initialize google_cloud_storage secret provider {provider_id}") from e
     else:
         raise ValueError("Unknown SECRET_PROVIDER")
-
-
-

pr_agent/servers/azuredevops_server_webhook.py

@@ -9,9 +9,9 @@ import secrets
 from urllib.parse import unquote
 
 import uvicorn
-from fastapi import APIRouter, Depends, FastAPI, HTTPException
+from fastapi import APIRouter, Depends, FastAPI, HTTPException, Request
-from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from fastapi.encoders import jsonable_encoder
+from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from starlette import status
 from starlette.background import BackgroundTasks
 from starlette.middleware import Middleware
@@ -23,9 +23,6 @@ from pr_agent.agent.pr_agent import PRAgent, command2class
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
-from pr_agent.log import get_logger
-from fastapi import Request, Depends
-from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 
 setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")

pr_agent/servers/bitbucket_server_webhook.py

@@ -6,20 +6,20 @@ from typing import List
 import uvicorn
 from fastapi import APIRouter, FastAPI
 from fastapi.encoders import jsonable_encoder
+from fastapi.responses import RedirectResponse
 from starlette import status
 from starlette.background import BackgroundTasks
 from starlette.middleware import Middleware
 from starlette.requests import Request
 from starlette.responses import JSONResponse
 from starlette_context.middleware import RawContextMiddleware
+
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.servers.utils import verify_signature
-from fastapi.responses import RedirectResponse
-
 
 setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 router = APIRouter()

pr_agent/servers/github_app.py

@@ -15,7 +15,8 @@ from starlette_context.middleware import RawContextMiddleware
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
+from pr_agent.git_providers import (get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.git_providers.git_provider import IncrementalPR
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.identity_providers import get_identity_provider

pr_agent/servers/github_polling.py

@@ -1,11 +1,12 @@
 import asyncio
 import multiprocessing
-from collections import deque
-import traceback
-from datetime import datetime, timezone
 import time
-import requests
+import traceback
+from collections import deque
+from datetime import datetime, timezone
+
 import aiohttp
+import requests
 
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings

pr_agent/servers/gitlab_webhook.py

@@ -1,6 +1,6 @@
 import copy
-import re
 import json
+import re
 from datetime import datetime
 
 import uvicorn

pr_agent/servers/serverless.py

@@ -5,7 +5,6 @@ from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.servers.github_app import router
 
-
 middleware = [Middleware(RawContextMiddleware)]
 app = FastAPI(middleware=middleware)
 app.include_router(router)

pr_agent/servers/utils.py

@@ -2,7 +2,7 @@ import hashlib
 import hmac
 import time
 from collections import defaultdict
-from typing import Callable, Any
+from typing import Any, Callable
 
 from fastapi import HTTPException
 

pr_agent/tools/pr_code_suggestions.py

@@ -1,25 +1,29 @@
 import asyncio
 import copy
+import difflib
+import re
 import textwrap
 from functools import partial
 from typing import Dict, List
+
 from jinja2 import Environment, StrictUndefined
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
-from pr_agent.algo.pr_processing import get_pr_diff, get_pr_multi_diffs, retry_with_fallback_models, \
+from pr_agent.algo.pr_processing import (add_ai_metadata_to_diff_files,
-    add_ai_metadata_to_diff_files
+                                         get_pr_diff, get_pr_multi_diffs,
+                                         retry_with_fallback_models)
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import load_yaml, replace_code_tags, ModelType, show_relevant_configurations
+from pr_agent.algo.utils import (ModelType, load_yaml, replace_code_tags,
+                                 show_relevant_configurations)
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context, GithubProvider, GitLabProvider, \
+from pr_agent.git_providers import (AzureDevopsProvider, GithubProvider,
-    AzureDevopsProvider
+                                    GitLabProvider, get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.git_providers.git_provider import get_main_pr_language
 from pr_agent.log import get_logger
 from pr_agent.servers.help import HelpMessage
 from pr_agent.tools.pr_description import insert_br_after_x_chars
-import difflib
-import re
 
 
 class PRCodeSuggestions:
@@ -778,4 +782,3 @@ class PRCodeSuggestions:
             get_logger().info(f"Could not reflect on suggestions, error: {e}")
             return ""
         return response_reflect
-

pr_agent/tools/pr_description.py

@@ -9,19 +9,24 @@ from jinja2 import Environment, StrictUndefined
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
-from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models, get_pr_diff_multiple_patchs, \
+from pr_agent.algo.pr_processing import (OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD,
-    OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD
+                                         get_pr_diff,
+                                         get_pr_diff_multiple_patchs,
+                                         retry_with_fallback_models)
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import set_custom_labels, PRDescriptionHeader
+from pr_agent.algo.utils import (ModelType, PRDescriptionHeader, clip_tokens,
-from pr_agent.algo.utils import load_yaml, get_user_labels, ModelType, show_relevant_configurations, get_max_tokens, \
+                                 get_max_tokens, get_user_labels, load_yaml,
-    clip_tokens
+                                 set_custom_labels,
+                                 show_relevant_configurations)
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, GithubProvider, get_git_provider_with_context
+from pr_agent.git_providers import (GithubProvider, get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.git_providers.git_provider import get_main_pr_language
 from pr_agent.log import get_logger
 from pr_agent.servers.help import HelpMessage
-from pr_agent.tools.ticket_pr_compliance_check import extract_ticket_links_from_pr_description, extract_tickets, \
+from pr_agent.tools.ticket_pr_compliance_check import (
-    extract_and_cache_pr_tickets
+    extract_and_cache_pr_tickets, extract_ticket_links_from_pr_description,
+    extract_tickets)
 
 
 class PRDescription:

pr_agent/tools/pr_generate_labels.py

@@ -9,7 +9,7 @@ from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import load_yaml, set_custom_labels, get_user_labels
+from pr_agent.algo.utils import get_user_labels, load_yaml, set_custom_labels
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language

pr_agent/tools/pr_help_message.py

@@ -9,10 +9,10 @@ from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
 from pr_agent.algo.pr_processing import retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import ModelType, load_yaml, clip_tokens
+from pr_agent.algo.utils import ModelType, clip_tokens, load_yaml
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import GithubProvider, BitbucketServerProvider, \
+from pr_agent.git_providers import (BitbucketServerProvider, GithubProvider,
-    get_git_provider_with_context
+                                    get_git_provider_with_context)
 from pr_agent.log import get_logger
 
 

pr_agent/tools/pr_line_questions.py

@@ -6,8 +6,8 @@ from jinja2 import Environment, StrictUndefined
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
-from pr_agent.algo.git_patch_processing import convert_to_hunks_with_lines_numbers, \
+from pr_agent.algo.git_patch_processing import (
-    extract_hunk_lines_from_patch
+    convert_to_hunks_with_lines_numbers, extract_hunk_lines_from_patch)
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.algo.utils import ModelType

pr_agent/tools/pr_reviewer.py

@@ -4,19 +4,27 @@ import traceback
 from collections import OrderedDict
 from functools import partial
 from typing import List, Tuple
+
 from jinja2 import Environment, StrictUndefined
+
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
-from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models, add_ai_metadata_to_diff_files
+from pr_agent.algo.pr_processing import (add_ai_metadata_to_diff_files,
+                                         get_pr_diff,
+                                         retry_with_fallback_models)
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import github_action_output, load_yaml, ModelType, \
+from pr_agent.algo.utils import (ModelType, PRReviewHeader,
-    show_relevant_configurations, convert_to_markdown_v2, PRReviewHeader
+                                 convert_to_markdown_v2, github_action_output,
+                                 load_yaml, show_relevant_configurations)
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
+from pr_agent.git_providers import (get_git_provider,
-from pr_agent.git_providers.git_provider import IncrementalPR, get_main_pr_language
+                                    get_git_provider_with_context)
+from pr_agent.git_providers.git_provider import (IncrementalPR,
+                                                 get_main_pr_language)
 from pr_agent.log import get_logger
 from pr_agent.servers.help import HelpMessage
-from pr_agent.tools.ticket_pr_compliance_check import extract_tickets, extract_and_cache_pr_tickets
+from pr_agent.tools.ticket_pr_compliance_check import (
+    extract_and_cache_pr_tickets, extract_tickets)
 
 
 class PRReviewer:

pr_agent/tools/pr_similar_issue.py

@@ -34,9 +34,9 @@ class PRSimilarIssue:
 
         if get_settings().pr_similar_issue.vectordb == "pinecone":
             try:
+                import pandas as pd
                 import pinecone
                 from pinecone_datasets import Dataset, DatasetMetadata
-                import pandas as pd
             except:
                 raise Exception("Please install 'pinecone' and 'pinecone_datasets' to use pinecone as vectordb")
             # assuming pinecone api key and environment are set in secrets file

pr_agent/tools/pr_update_changelog.py

@@ -3,14 +3,16 @@ from datetime import date
 from functools import partial
 from time import sleep
 from typing import Tuple
+
 from jinja2 import Environment, StrictUndefined
+
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.algo.utils import ModelType, show_relevant_configurations
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, GithubProvider
+from pr_agent.git_providers import GithubProvider, get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
 from pr_agent.log import get_logger
 

pyproject.toml

@@ -40,17 +40,17 @@ license-files = ["LICENSE"]
 
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["pr_agent*"] # include pr_agent and any sub-packages it finds under it.
+include = [
+  "pr_agent*",
+] # include pr_agent and any sub-packages it finds under it.
 
 [project.scripts]
 pr-agent = "pr_agent.cli:run"
 
-
 [tool.ruff]
-
 line-length = 120
 
-select = [
+lint.select = [
   "E",    # Pyflakes
   "F",    # Pyflakes
   "B",    # flake8-bugbear
@@ -59,22 +59,24 @@ select = [
 ]
 
 # First commit - only fixing isort
-fixable = [
+lint.fixable = [
   "I001", # isort basic checks
 ]
 
-unfixable = [
+lint.unfixable = [
   "B", # Avoid trying to fix flake8-bugbear (`B`) violations.
 ]
 
-exclude = [
+lint.exclude = ["api/code_completions"]
-  "api/code_completions",
-]
 
-ignore = [
+lint.ignore = ["E999", "B008"]
-  "E999", "B008"
-]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402"]  # Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
+"__init__.py" = [
-# TODO: should decide if maybe not to ignore these.
+  "E402",
+] # Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B101"]
+tests = []

tests/e2e_tests/e2e_utils.py

@@ -32,4 +32,3 @@ def main():
 if __name__ == '__main__':
     main()
 """
-

tests/e2e_tests/test_bitbucket_app.py

@@ -5,16 +5,16 @@ import time
 from datetime import datetime
 
 import jwt
-from atlassian.bitbucket import Cloud
-
 import requests
+from atlassian.bitbucket import Cloud
 from requests.auth import HTTPBasicAuth
 
 from pr_agent.config_loader import get_settings
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
-from tests.e2e_tests.e2e_utils import NEW_FILE_CONTENT, FILE_PATH, PR_HEADER_START_WITH, REVIEW_START_WITH, \
+from tests.e2e_tests.e2e_utils import (FILE_PATH,
-    IMPROVE_START_WITH_REGEX_PATTERN, NUM_MINUTES
+                                       IMPROVE_START_WITH_REGEX_PATTERN,
-
+                                       NEW_FILE_CONTENT, NUM_MINUTES,
+                                       PR_HEADER_START_WITH, REVIEW_START_WITH)
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

tests/e2e_tests/test_github_app.py

@@ -5,9 +5,11 @@ from datetime import datetime
 
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
-from tests.e2e_tests.e2e_utils import NEW_FILE_CONTENT, FILE_PATH, PR_HEADER_START_WITH, REVIEW_START_WITH, \
+from tests.e2e_tests.e2e_utils import (FILE_PATH,
-    IMPROVE_START_WITH_REGEX_PATTERN, NUM_MINUTES
+                                       IMPROVE_START_WITH_REGEX_PATTERN,
+                                       NEW_FILE_CONTENT, NUM_MINUTES,
+                                       PR_HEADER_START_WITH, REVIEW_START_WITH)
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

tests/e2e_tests/test_gitlab_webhook.py

@@ -7,9 +7,11 @@ import gitlab
 
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
-from tests.e2e_tests.e2e_utils import NEW_FILE_CONTENT, FILE_PATH, PR_HEADER_START_WITH, REVIEW_START_WITH, \
+from tests.e2e_tests.e2e_utils import (FILE_PATH,
-    IMPROVE_START_WITH_REGEX_PATTERN, NUM_MINUTES
+                                       IMPROVE_START_WITH_REGEX_PATTERN,
+                                       NEW_FILE_CONTENT, NUM_MINUTES,
+                                       PR_HEADER_START_WITH, REVIEW_START_WITH)
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

tests/unittest/test_bitbucket_provider.py

@@ -1,8 +1,10 @@
+from unittest.mock import MagicMock
+
+from atlassian.bitbucket import Bitbucket
+
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.git_providers import BitbucketServerProvider
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
-from unittest.mock import MagicMock
-from atlassian.bitbucket import Bitbucket
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 
 
 class TestBitbucketProvider:

tests/unittest/test_codecommit_client.py

@@ -1,4 +1,5 @@
 from unittest.mock import MagicMock
+
 from pr_agent.git_providers.codecommit_client import CodeCommitClient
 
 

tests/unittest/test_codecommit_provider.py

@@ -1,9 +1,11 @@
-import pytest
 from unittest.mock import patch
-from pr_agent.git_providers.codecommit_provider import CodeCommitFile
+
-from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
+import pytest
-from pr_agent.git_providers.codecommit_provider import PullRequestCCMimic
+
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.git_providers.codecommit_provider import (CodeCommitFile,
+                                                        CodeCommitProvider,
+                                                        PullRequestCCMimic)
 
 
 class TestCodeCommitFile:

tests/unittest/test_extend_patch.py

@@ -1,4 +1,5 @@
 import pytest
+
 from pr_agent.algo.git_patch_processing import extend_patch
 from pr_agent.algo.pr_processing import pr_generate_extended_diff
 from pr_agent.algo.token_handler import TokenHandler

tests/unittest/test_file_filter.py

@@ -1,7 +1,9 @@
 import pytest
+
 from pr_agent.algo.file_filter import filter_ignored
 from pr_agent.config_loader import global_settings
 
+
 class TestIgnoreFilter:
     def test_no_ignores(self):
         """

tests/unittest/test_find_line_number_of_relevant_line_in_file.py

@@ -1,9 +1,10 @@
 
 # Generated by CodiumAI
+import pytest
+
 from pr_agent.algo.types import FilePatchInfo
 from pr_agent.algo.utils import find_line_number_of_relevant_line_in_file
 
-import pytest
 
 class TestFindLineNumberOfRelevantLineInFile:
     # Tests that the function returns the correct line number and absolute position when the relevant line is found in the patch

tests/unittest/test_github_action_output.py

@@ -1,7 +1,9 @@
-import os
 import json
+import os
+
 from pr_agent.algo.utils import get_settings, github_action_output
 
+
 class TestGitHubOutput:
     def test_github_action_output_enabled(self, monkeypatch, tmp_path):
         get_settings().set('GITHUB_ACTION_CONFIG.ENABLE_OUTPUT', True)

tests/unittest/test_load_yaml.py

@@ -47,7 +47,3 @@ PR Feedback:
 
         expected_output = [{'relevant file': 'src/app.py:\n', 'suggestion content': 'The print statement is outside inside the if __name__ ==:'}]
         assert load_yaml(yaml_str) == expected_output
-
-
-
-

tests/unittest/test_try_fix_yaml.py

@@ -1,10 +1,10 @@
 
 # Generated by CodiumAI
+import pytest
+
 from pr_agent.algo.utils import try_fix_yaml
 
 
-import pytest
-
 class TestTryFixYaml:
 
     # The function successfully parses a valid YAML string.