Merge remote-tracking branch 'origin/main' into ok/settings_refactor

Adding Commit Messages Retrieval Functionality

.dockerignore

@@ -1,3 +1,5 @@
 venv/
 pr_agent/settings/.secrets.toml
 pics/
+pr_agent.egg-info/
+build/

.gitignore

@@ -4,3 +4,5 @@ pr_agent/settings/.secrets.toml
 __pycache__
 dist/
 *.egg-info/
+build/
+review.md

CHANGELOG.md

@@ -1,3 +1,24 @@
+## 2023-08-01
+
+### Enhanced
+- Introduced the ability to retrieve commit messages from pull requests across different git providers.
+- Implemented commit messages retrieval for GitHub and GitLab providers.
+- Updated the PR description template to include a section for commit messages if they exist.
+
+## 2023-07-30
+
+### Enhanced
+- Added the ability to modify any configuration parameter from 'configuration.toml' on-the-fly.
+- Updated the command line interface and bot commands to accept configuration changes as arguments.
+- Improved the PR agent to handle additional arguments for each action.
+
+## 2023-07-28
+
+### Improved
+- Enhanced error handling and logging in the GitLab provider.
+- Improved handling of inline comments and code suggestions in GitLab.
+- Fixed a bug where an additional unneeded line was added to code suggestions in GitLab.
+
 ## 2023-07-26
 
 ### Added

CONFIGURATION.md

@@ -1,19 +1,12 @@
 ## Configuration
 
-The different tools and sub-tools used by CodiumAI pr-agent are easily configurable via the configuration file: `/pr-agent/settings/configuration.toml`.
-##### Git Provider:
-You can select your git_provider with the flag `git_provider` in the `config` section
+The different tools and sub-tools used by CodiumAI pr-agent are adjustable via the configuration file: `/pr-agent/settings/configuration.toml`.
 
-##### PR Reviewer:
+To edit the configuration of any tool, just add `--config_path=<value>` to you command.
+For example if you want to edit online the `pr_reviewer` configurations, you can run:
+```
+/review --pr_reviewer.extra_instructions="focus on the file xyz" --pr_reviewer.require_score_review=false ...
+```
+
+Any configuration value in `configuration.toml` file can be similarly edited.
 
-You can enable/disable the different PR Reviewer abilities with the following flags (`pr_reviewer` section):
-```
-require_focused_review=true
-require_score_review=true
-require_tests_review=true
-require_security_review=true
-```
-You can contol the number of suggestions returned by the PR Reviewer with the following flag:
-```inline_code_comments=3```
-And enable/disable the inline code suggestions with the following flag:
-```inline_code_comments=true```

PR_COMPRESSION.md

@@ -31,7 +31,7 @@ We prioritize additions over deletions:
  - File patches are a list of hunks, remove all hunks of type deletion-only from the hunks in the file patch
 ####  Adaptive and token-aware file patch fitting
 We use [tiktoken](https://github.com/openai/tiktoken) to tokenize the patches after the modifications described above, and we use the following strategy to fit the patches into the prompt:
-1. Withing each language we sort the files by the number of tokens in the file (in descending order):
+1. Within each language we sort the files by the number of tokens in the file (in descending order):
    * ```[[file2.py, file.py],[file4.jsx, file3.js],[readme.md]]```
 2. Iterate through the patches in the order described above
 2. Add the patches to the prompt until the prompt reaches a certain buffer from the max token length

README.md

@@ -23,7 +23,9 @@ CodiumAI `PR-Agent` is an open-source tool aiming to help developers review pull
 \
 **Question Answering**: Answering free-text questions about the PR.
 \
-**Code Suggestion**: Committable code suggestions for improving the PR.
+**Code Suggestions**: Committable code suggestions for improving the PR.
+\
+**Update Changelog**: Automatically updating the CHANGELOG.md file with the PR changes.
 
 <h3>Example results:</h2>
 </div>
@@ -100,7 +102,7 @@ Examples for invoking the different tools via the CLI:
 - **Improve**:      python cli.py --pr-url=<pr_url>  improve
 - **Ask**:          python cli.py --pr-url=<pr_url>  ask "Write me a poem about this PR"
 - **Reflect**:      python cli.py --pr-url=<pr_url>  reflect
-- **Update changelog**:      python cli.py --pr-url=<pr_url>  update_changelog
+- **Update Changelog**:      python cli.py --pr-url=<pr_url>  update_changelog
 
 "<pr_url>" is the url of the relevant PR (for example: https://github.com/Codium-ai/pr-agent/pull/50).
 
@@ -135,13 +137,14 @@ There are several ways to use PR-Agent:
 
 ## Usage and Tools
 
-**PR-Agent** provides five types of interactions ("tools"): `"PR Reviewer"`, `"PR Q&A"`, `"PR Description"`, `"PR Code Sueggestions"` and `"PR Reflect and Review"`.
+**PR-Agent** provides six types of interactions ("tools"): `"PR Reviewer"`, `"PR Q&A"`, `"PR Description"`, `"PR Code Sueggestions"`, `"PR Reflect and Review"` and `"PR Update Changlog"`.
 
 - The "PR Reviewer" tool automatically analyzes PRs, and provides various types of feedback.
 - The "PR Q&A" tool answers free-text questions about the PR.
 - The "PR Description" tool automatically sets the PR Title and body.
 - The "PR Code Suggestion" tool provide inline code suggestions for the PR that can be applied and committed.
 - The "PR Reflect and Review" tool initiates a dialog with the user, asks them to reflect on the PR, and then provides a more focused review.
+- The "PR Update Changelog" tool automatically updates the CHANGELOG.md file with the PR changes.
 
 ## How it works
 
@@ -158,7 +161,7 @@ Here are some of the reasons why:
 - We emphasize **real-life practical usage**. Each tool (review, improve, ask, ...) has a single GPT-4 call, no more. We feel that this is critical for realistic team usage - obtaining an answer quickly (~30 seconds) and affordably.
 - Our [PR Compression strategy](./PR_COMPRESSION.md)  is a core ability that enables to effectively tackle both short and long PRs.
 - Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the configuration file. Adding additional categories is easy and accessible.
-- We support **multiple git providers** (GitHub, Gitlab, Bitbucket), and multiple ways to use the tool (CLI, GitHub Action, Docker, ...).
+- We support **multiple git providers** (GitHub, Gitlab, Bitbucket), and multiple ways to use the tool (CLI, GitHub Action, GitHub App, Docker, ...).
 - We are open-source, and welcome contributions from the community.
 
 

pr_agent/agent/pr_agent.py

@@ -1,6 +1,7 @@
-import re
+import shlex
 
-from pr_agent.config_loader import settings
+from pr_agent.algo.utils import update_settings_from_args
+from pr_agent.config_loader import get_settings
 from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
 from pr_agent.tools.pr_description import PRDescription
 from pr_agent.tools.pr_information_from_user import PRInformationFromUser
@@ -8,29 +9,40 @@ from pr_agent.tools.pr_questions import PRQuestions
 from pr_agent.tools.pr_reviewer import PRReviewer
 from pr_agent.tools.pr_update_changelog import PRUpdateChangelog
 
+command2class = {
+    "answer": PRReviewer,
+    "review": PRReviewer,
+    "review_pr": PRReviewer,
+    "reflect": PRInformationFromUser,
+    "reflect_and_review": PRInformationFromUser,
+    "describe": PRDescription,
+    "describe_pr": PRDescription,
+    "improve": PRCodeSuggestions,
+    "improve_code": PRCodeSuggestions,
+    "ask": PRQuestions,
+    "ask_question": PRQuestions,
+    "update_changelog": PRUpdateChangelog,
+}
+
+commands = list(command2class.keys())
 
 class PRAgent:
     def __init__(self):
         pass
 
     async def handle_request(self, pr_url, request) -> bool:
-        action, *args = request.strip().split()
-        if any(cmd == action for cmd in ["/answer"]):
-            await PRReviewer(pr_url, is_answer=True).review()
-        elif any(cmd == action for cmd in ["/review", "/review_pr", "/reflect_and_review"]):
-            if settings.pr_reviewer.ask_and_reflect or "/reflect_and_review" in request:
-                await PRInformationFromUser(pr_url).generate_questions()
-            else:
-                await PRReviewer(pr_url, args=args).review()
-        elif any(cmd == action for cmd in ["/describe", "/describe_pr"]):
-            await PRDescription(pr_url).describe()
-        elif any(cmd == action for cmd in ["/improve", "/improve_code"]):
-            await PRCodeSuggestions(pr_url).suggest()
-        elif any(cmd == action for cmd in ["/ask", "/ask_question"]):
-            await PRQuestions(pr_url, args=args).answer()
-        elif any(cmd == action for cmd in ["/update_changelog"]):
-            await PRUpdateChangelog(pr_url, args=args).update_changelog()
+        request = request.replace("'", "\\'")
+        lexer = shlex.shlex(request, posix=True)
+        lexer.whitespace_split = True
+        action, *args = list(lexer)
+        args = update_settings_from_args(args)
+        action = action.lstrip("/").lower()
+        if action == "reflect_and_review" and not get_settings().pr_reviewer.ask_and_reflect:
+            action = "review"
+        if action == "answer":
+            await PRReviewer(pr_url, is_answer=True, args=args).run()
+        elif action in command2class:
+            await command2class[action](pr_url, args=args).run()
         else:
             return False
-
         return True

pr_agent/algo/ai_handler.py

@@ -1,10 +1,10 @@
 import logging
 
 import openai
-from openai.error import APIError, Timeout, TryAgain, RateLimitError
+from openai.error import APIError, RateLimitError, Timeout, TryAgain
 from retry import retry
 
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 
 OPENAI_RETRIES=5
 
@@ -21,16 +21,16 @@ class AiHandler:
         Raises a ValueError if the OpenAI key is missing.
         """
         try:
-            openai.api_key = settings.openai.key
-            if settings.get("OPENAI.ORG", None):
-                openai.organization = settings.openai.org
-            self.deployment_id = settings.get("OPENAI.DEPLOYMENT_ID", None)
-            if settings.get("OPENAI.API_TYPE", None):
-                openai.api_type = settings.openai.api_type
-            if settings.get("OPENAI.API_VERSION", None):
-                openai.api_version = settings.openai.api_version
-            if settings.get("OPENAI.API_BASE", None):
-                openai.api_base = settings.openai.api_base
+            openai.api_key = get_settings().openai.key
+            if get_settings().get("OPENAI.ORG", None):
+                openai.organization = get_settings().openai.org
+            self.deployment_id = get_settings().get("OPENAI.DEPLOYMENT_ID", None)
+            if get_settings().get("OPENAI.API_TYPE", None):
+                openai.api_type = get_settings().openai.api_type
+            if get_settings().get("OPENAI.API_VERSION", None):
+                openai.api_version = get_settings().openai.api_version
+            if get_settings().get("OPENAI.API_BASE", None):
+                openai.api_base = get_settings().openai.api_base
         except AttributeError as e:
             raise ValueError("OpenAI key is required") from e
 

pr_agent/algo/git_patch_processing.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import logging
 import re
 
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 
 
 def extend_patch(original_file_str, patch_str, num_lines) -> str:
@@ -55,7 +55,7 @@ def extend_patch(original_file_str, patch_str, num_lines) -> str:
                     continue
             extended_patch_lines.append(line)
     except Exception as e:
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.error(f"Failed to extend patch: {e}")
         return patch_str
 
@@ -126,14 +126,14 @@ def handle_patch_deletions(patch: str, original_file_content_str: str,
     """
     if not new_file_content_str:
         # logic for handling deleted files - don't show patch, just show that the file was deleted
-        if settings.config.verbosity_level > 0:
+        if get_settings().config.verbosity_level > 0:
             logging.info(f"Processing file: {file_name}, minimizing deletion file")
         patch = None # file was deleted
     else:
         patch_lines = patch.splitlines()
         patch_new = omit_deletion_hunks(patch_lines)
         if patch != patch_new:
-            if settings.config.verbosity_level > 0:
+            if get_settings().config.verbosity_level > 0:
                 logging.info(f"Processing file: {file_name}, hunks were deleted")
             patch = patch_new
     return patch
@@ -141,7 +141,8 @@ def handle_patch_deletions(patch: str, original_file_content_str: str,
 
 def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
     """
-    Convert a given patch string into a string with line numbers for each hunk, indicating the new and old content of the file.
+    Convert a given patch string into a string with line numbers for each hunk, indicating the new and old content of
+    the file.
 
     Args:
         patch (str): The patch string to be converted.

pr_agent/algo/language_handler.py

@@ -1,15 +1,15 @@
 # Language Selection, source: https://github.com/bigcode-project/bigcode-dataset/blob/main/language_selection/programming-languages-to-file-extensions.json  # noqa E501
 from typing import Dict
 
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 
-language_extension_map_org = settings.language_extension_map_org
+language_extension_map_org = get_settings().language_extension_map_org
 language_extension_map = {k.lower(): v for k, v in language_extension_map_org.items()}
 
 # Bad Extensions, source: https://github.com/EleutherAI/github-downloader/blob/345e7c4cbb9e0dc8a0615fd995a08bf9d73b3fe6/download_repo_text.py  # noqa: E501
-bad_extensions = settings.bad_extensions.default
-if settings.config.use_extra_bad_extensions:
-    bad_extensions += settings.bad_extensions.extra
+bad_extensions = get_settings().bad_extensions.default
+if get_settings().config.use_extra_bad_extensions:
+    bad_extensions += get_settings().bad_extensions.extra
 
 
 def filter_bad_extensions(files):

pr_agent/algo/pr_processing.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import logging
-from typing import Tuple, Union, Callable, List
+from typing import Callable, Tuple
 
 from github import RateLimitExceededException
 
@@ -10,7 +10,7 @@ from pr_agent.algo.git_patch_processing import convert_to_hunks_with_lines_numbe
 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 load_large_diff
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
 
 DELETED_FILES_ = "Deleted files:\n"
@@ -27,11 +27,15 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: s
     Returns a string with the diff of the pull request, applying diff minimization techniques if needed.
 
     Args:
-        git_provider (GitProvider): An object of the GitProvider class representing the Git provider used for the pull request.
-        token_handler (TokenHandler): An object of the TokenHandler class used for handling tokens in the context of the pull request.
+        git_provider (GitProvider): An object of the GitProvider class representing the Git provider used for the pull
+        request.
+        token_handler (TokenHandler): An object of the TokenHandler class used for handling tokens in the context of the
+        pull request.
         model (str): The name of the model used for tokenization.
-        add_line_numbers_to_hunks (bool, optional): A boolean indicating whether to add line numbers to the hunks in the diff. Defaults to False.
-        disable_extra_lines (bool, optional): A boolean indicating whether to disable the extension of each patch with extra lines of context. Defaults to False.
+        add_line_numbers_to_hunks (bool, optional): A boolean indicating whether to add line numbers to the hunks in the
+        diff. Defaults to False.
+        disable_extra_lines (bool, optional): A boolean indicating whether to disable the extension of each patch with
+        extra lines of context. Defaults to False.
 
     Returns:
         str: A string with the diff of the pull request, applying diff minimization techniques if needed.
@@ -76,10 +80,12 @@ def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
                               add_line_numbers_to_hunks: bool) -> \
         Tuple[list, int]:
     """
-    Generate a standard diff string with patch extension, while counting the number of tokens used and applying diff minimization techniques if needed.
+    Generate a standard diff string with patch extension, while counting the number of tokens used and applying diff
+    minimization techniques if needed.
 
     Args:
-    - pr_languages: A list of dictionaries representing the languages used in the pull request and their corresponding files.
+    - pr_languages: A list of dictionaries representing the languages used in the pull request and their corresponding
+      files.
     - token_handler: An object of the TokenHandler class used for handling tokens in the context of the pull request.
     - add_line_numbers_to_hunks: A boolean indicating whether to add line numbers to the hunks in the diff.
 
@@ -119,10 +125,13 @@ def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
 def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, model: str,
                                 convert_hunks_to_line_numbers: bool) -> Tuple[list, list, list]:
     """
-    Generate a compressed diff string for a pull request, using diff minimization techniques to reduce the number of tokens used.
+    Generate a compressed diff string for a pull request, using diff minimization techniques to reduce the number of
+    tokens used.
     Args:
-        top_langs (list): A list of dictionaries representing the languages used in the pull request and their corresponding files.
-        token_handler (TokenHandler): An object of the TokenHandler class used for handling tokens in the context of the pull request.
+        top_langs (list): A list of dictionaries representing the languages used in the pull request and their
+        corresponding files.
+        token_handler (TokenHandler): An object of the TokenHandler class used for handling tokens in the context of the
+        pull request.
         model (str): The model used for tokenization.
         convert_hunks_to_line_numbers (bool): A boolean indicating whether to convert hunks to line numbers in the diff.
     Returns:
@@ -181,7 +190,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
             # Current logic is to skip the patch if it's too large
             # TODO: Option for alternative logic to remove hunks from the patch to reduce the number of tokens
             #  until we meet the requirements
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.warning(f"Patch too large, minimizing it, {file.filename}")
             if not modified_files_list:
                 total_tokens += token_handler.count_tokens(MORE_MODIFIED_FILES_)
@@ -196,15 +205,15 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
                 patch_final = patch
             patches.append(patch_final)
             total_tokens += token_handler.count_tokens(patch_final)
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.info(f"Tokens: {total_tokens}, last filename: {file.filename}")
 
     return patches, modified_files_list, deleted_files_list
 
 
 async def retry_with_fallback_models(f: Callable):
-    model = settings.config.model
-    fallback_models = settings.config.fallback_models
+    model = get_settings().config.model
+    fallback_models = get_settings().config.fallback_models
     if not isinstance(fallback_models, list):
         fallback_models = [fallback_models]
     all_models = [model] + fallback_models

pr_agent/algo/token_handler.py

@@ -1,8 +1,7 @@
 from jinja2 import Environment, StrictUndefined
 from tiktoken import encoding_for_model
 
-from pr_agent.algo import MAX_TOKENS
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 
 
 class TokenHandler:
@@ -10,9 +9,12 @@ class TokenHandler:
     A class for handling tokens in the context of a pull request.
 
     Attributes:
-    - encoder: An object of the encoding_for_model class from the tiktoken module. Used to encode strings and count the number of tokens in them.
-    - limit: The maximum number of tokens allowed for the given model, as defined in the MAX_TOKENS dictionary in the pr_agent.algo module.
-    - prompt_tokens: The number of tokens in the system and user strings, as calculated by the _get_system_user_tokens method.
+    - encoder: An object of the encoding_for_model class from the tiktoken module. Used to encode strings and count the
+      number of tokens in them.
+    - limit: The maximum number of tokens allowed for the given model, as defined in the MAX_TOKENS dictionary in the
+      pr_agent.algo module.
+    - prompt_tokens: The number of tokens in the system and user strings, as calculated by the _get_system_user_tokens
+      method.
     """
 
     def __init__(self, pr, vars: dict, system, user):
@@ -25,7 +27,7 @@ class TokenHandler:
         - system: The system string.
         - user: The user string.
         """
-        self.encoder = encoding_for_model(settings.config.model)
+        self.encoder = encoding_for_model(get_settings().config.model)
         self.prompt_tokens = self._get_system_user_tokens(pr, self.encoder, vars, system, user)
 
     def _get_system_user_tokens(self, pr, encoder, vars: dict, system, user):

pr_agent/algo/utils.py

@@ -1,14 +1,24 @@
 from __future__ import annotations
 
 import difflib
-from datetime import datetime
 import json
 import logging
 import re
 import textwrap
+from datetime import datetime
+from typing import Any, List
 
-from pr_agent.config_loader import settings
+from starlette_context import context
 
+from pr_agent.config_loader import get_settings, global_settings
+
+
+def get_setting(key: str) -> Any:
+    try:
+        key = key.upper()
+        return context.get("settings", global_settings).get(key, global_settings.get(key, None))
+    except Exception:
+        return global_settings.get(key, None)
 
 def convert_to_markdown(output_data: dict) -> str:
     """
@@ -96,12 +106,16 @@ def try_fix_json(review, max_iter=10, code_suggestions=False):
     - data: A dictionary containing the parsed JSON data.
 
     The function attempts to fix broken or incomplete JSON messages by parsing until the last valid code suggestion.
-    If the JSON message ends with a closing bracket, the function calls the fix_json_escape_char function to fix the message.
-    If code_suggestions is True and the JSON message contains code suggestions, the function tries to fix the JSON message by parsing until the last valid code suggestion.
-    The function uses regular expressions to find the last occurrence of "}," with any number of whitespaces or newlines.
+    If the JSON message ends with a closing bracket, the function calls the fix_json_escape_char function to fix the
+    message.
+    If code_suggestions is True and the JSON message contains code suggestions, the function tries to fix the JSON
+    message by parsing until the last valid code suggestion.
+    The function uses regular expressions to find the last occurrence of "}," with any number of whitespaces or
+    newlines.
     It tries to parse the JSON message with the closing bracket and checks if it is valid.
     If the JSON message is valid, the parsed JSON data is returned.
-    If the JSON message is not valid, the last code suggestion is removed and the process is repeated until a valid JSON message is obtained or the maximum number of iterations is reached.
+    If the JSON message is not valid, the last code suggestion is removed and the process is repeated until a valid JSON
+    message is obtained or the maximum number of iterations is reached.
     If a valid JSON message is not obtained, an error is logged and an empty dictionary is returned.
     """
 
@@ -183,7 +197,8 @@ def convert_str_to_datetime(date_str):
 
 def load_large_diff(file, new_file_content_str: str, original_file_content_str: str, patch: str) -> str:
     """
-    Generate a patch for a modified file by comparing the original content of the file with the new content provided as input.
+    Generate a patch for a modified file by comparing the original content of the file with the new content provided as
+    input.
 
     Args:
         file: The file object for which the patch needs to be generated.
@@ -198,16 +213,55 @@ def load_large_diff(file, new_file_content_str: str, original_file_content_str:
         None.
 
     Additional Information:
-        - If 'patch' is not provided as input, the function generates a patch using the 'difflib' library and returns it as output.
-        - If the 'settings.config.verbosity_level' is greater than or equal to 2, a warning message is logged indicating that the file was modified but no patch was found, and a patch is manually created.
+        - If 'patch' is not provided as input, the function generates a patch using the 'difflib' library and returns it
+          as output.
+        - If the 'settings.config.verbosity_level' is greater than or equal to 2, a warning message is logged indicating
+          that the file was modified but no patch was found, and a patch is manually created.
     """
     if not patch:  # to Do - also add condition for file extension
         try:
             diff = difflib.unified_diff(original_file_content_str.splitlines(keepends=True),
                                         new_file_content_str.splitlines(keepends=True))
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.warning(f"File was modified, but no patch was found. Manually creating patch: {file.filename}.")
             patch = ''.join(diff)
         except Exception:
             pass
     return patch
+
+
+def update_settings_from_args(args: List[str]) -> List[str]:
+    """
+    Update the settings of the Dynaconf object based on the arguments passed to the function.
+
+    Args:
+        args: A list of arguments passed to the function.
+        Example args: ['--pr_code_suggestions.extra_instructions="be funny',
+                  '--pr_code_suggestions.num_code_suggestions=3']
+
+    Returns:
+        None
+
+    Raises:
+        ValueError: If the argument is not in the correct format.
+
+    """
+    other_args = []
+    if args:
+        for arg in args:
+            arg = arg.strip()
+            if arg.startswith('--'):
+                arg = arg.strip('-').strip()
+                vals = arg.split('=')
+                if len(vals) != 2:
+                    logging.error(f'Invalid argument format: {arg}')
+                    other_args.append(arg)
+                    continue
+                key, value = vals
+                key = key.strip().upper()
+                value = value.strip()
+                get_settings().set(key, value)
+                logging.info(f'Updated setting {key} to: "{value}"')
+            else:
+                other_args.append(arg)
+    return other_args

pr_agent/cli.py

@@ -3,15 +3,11 @@ import asyncio
 import logging
 import os
 
-from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
-from pr_agent.tools.pr_description import PRDescription
-from pr_agent.tools.pr_information_from_user import PRInformationFromUser
-from pr_agent.tools.pr_questions import PRQuestions
-from pr_agent.tools.pr_reviewer import PRReviewer
-from pr_agent.tools.pr_update_changelog import PRUpdateChangelog
+from pr_agent.agent.pr_agent import PRAgent, commands
+from pr_agent.config_loader import get_settings
 
 
-def run(args=None):
+def run(inargs=None):
     parser = argparse.ArgumentParser(description='AI based pull request analyzer', usage=
 """\
 Usage: cli.py --pr-url <URL on supported git hosting service> <command> [<args>].
@@ -29,81 +25,21 @@ describe / describe_pr - Modify the PR title and description based on the PR's c
 improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
 reflect - Ask the PR author questions about the PR.
 update_changelog - Update the changelog based on the PR's contents.
+
+To edit any configuration parameter from 'configuration.toml', just add -config_path=<value>.
+For example: '- cli.py --pr-url=... review --pr_reviewer.extra_instructions="focus on the file: ..."'
 """)
     parser.add_argument('--pr_url', type=str, help='The URL of the PR to review', required=True)
-    parser.add_argument('command', type=str, help='The', choices=['review', 'review_pr',
-                                                                  'ask', 'ask_question',
-                                                                  'describe', 'describe_pr',
-                                                                  'improve', 'improve_code',
-                                                                  'reflect', 'review_after_reflect',
-                                                                   'update_changelog'],
-                                                                   default='review')
+    parser.add_argument('command', type=str, help='The', choices=commands, default='review')
     parser.add_argument('rest', nargs=argparse.REMAINDER, default=[])
-    args = parser.parse_args(args)
+    args = parser.parse_args(inargs)
     logging.basicConfig(level=os.environ.get("LOGLEVEL", "INFO"))
     command = args.command.lower()
-    commands = {
-        'ask': _handle_ask_command,
-        'ask_question': _handle_ask_command,
-        'describe': _handle_describe_command,
-        'describe_pr': _handle_describe_command,
-        'improve': _handle_improve_command,
-        'improve_code': _handle_improve_command,
-        'review': _handle_review_command,
-        'review_pr': _handle_review_command,
-        'reflect': _handle_reflect_command,
-        'review_after_reflect': _handle_review_after_reflect_command,
-        'update_changelog': _handle_update_changelog,
-    }
-    if command in commands:
-        commands[command](args.pr_url, args.rest)
-    else:
-        print(f"Unknown command: {command}")
+    get_settings().set("CONFIG.CLI_MODE", True)
+    result = asyncio.run(PRAgent().handle_request(args.pr_url, command + " " + " ".join(args.rest)))
+    if not result:
         parser.print_help()
 
 
-def _handle_ask_command(pr_url: str, rest: list):
-    if len(rest) == 0:
-        print("Please specify a question")
-        return
-    print(f"Question: {' '.join(rest)} about PR {pr_url}")
-    reviewer = PRQuestions(pr_url, rest)
-    asyncio.run(reviewer.answer())
-
-
-def _handle_describe_command(pr_url: str, rest: list):
-    print(f"PR description: {pr_url}")
-    reviewer = PRDescription(pr_url)
-    asyncio.run(reviewer.describe())
-
-
-def _handle_improve_command(pr_url: str, rest: list):
-    print(f"PR code suggestions: {pr_url}")
-    reviewer = PRCodeSuggestions(pr_url)
-    asyncio.run(reviewer.suggest())
-
-
-def _handle_review_command(pr_url: str, rest: list):
-    print(f"Reviewing PR: {pr_url}")
-    reviewer = PRReviewer(pr_url, cli_mode=True, args=rest)
-    asyncio.run(reviewer.review())
-
-
-def _handle_reflect_command(pr_url: str, rest: list):
-    print(f"Asking the PR author questions: {pr_url}")
-    reviewer = PRInformationFromUser(pr_url)
-    asyncio.run(reviewer.generate_questions())
-
-
-def _handle_review_after_reflect_command(pr_url: str, rest: list):
-    print(f"Processing author's answers and sending review: {pr_url}")
-    reviewer = PRReviewer(pr_url, cli_mode=True, is_answer=True)
-    asyncio.run(reviewer.review())
-
-def _handle_update_changelog(pr_url: str, rest: list):
-    print(f"Updating changlog for: {pr_url}")
-    reviewer = PRUpdateChangelog(pr_url, cli_mode=True, args=rest)
-    asyncio.run(reviewer.update_changelog())
-
 if __name__ == '__main__':
     run()

pr_agent/config_loader.py

@@ -3,28 +3,36 @@ from pathlib import Path
 from typing import Optional
 
 from dynaconf import Dynaconf
+from starlette_context import context
 
 PR_AGENT_TOML_KEY = 'pr-agent'
 
 current_dir = dirname(abspath(__file__))
-settings = Dynaconf(
+global_settings = Dynaconf(
     envvar_prefix=False,
     merge_enabled=True,
     settings_files=[join(current_dir, f) for f in [
-         "settings/.secrets.toml",
-         "settings/configuration.toml",
-         "settings/language_extensions.toml",
-         "settings/pr_reviewer_prompts.toml",
-         "settings/pr_questions_prompts.toml",
-         "settings/pr_description_prompts.toml",
-         "settings/pr_code_suggestions_prompts.toml",
-         "settings/pr_information_from_user_prompts.toml",
-         "settings/pr_update_changelog.toml",
-         "settings_prod/.secrets.toml"
-        ]]
+        "settings/.secrets.toml",
+        "settings/configuration.toml",
+        "settings/language_extensions.toml",
+        "settings/pr_reviewer_prompts.toml",
+        "settings/pr_questions_prompts.toml",
+        "settings/pr_description_prompts.toml",
+        "settings/pr_code_suggestions_prompts.toml",
+        "settings/pr_information_from_user_prompts.toml",
+        "settings/pr_update_changelog_prompts.toml",
+        "settings_prod/.secrets.toml"
+    ]]
 )
 
 
+def get_settings():
+    try:
+        return context["settings"]
+    except Exception:
+        return global_settings
+
+
 # Add local configuration from pyproject.toml of the project being reviewed
 def _find_repository_root() -> Path:
     """
@@ -39,6 +47,7 @@ def _find_repository_root() -> Path:
         cwd = cwd.parent
     return None
 
+
 def _find_pyproject() -> Optional[Path]:
     """
     Search for file pyproject.toml in the repository root.
@@ -49,6 +58,7 @@ def _find_pyproject() -> Optional[Path]:
         return pyproject if pyproject.is_file() else None
     return None
 
+
 pyproject_path = _find_pyproject()
 if pyproject_path is not None:
-    settings.load_file(pyproject_path, env=f'tool.{PR_AGENT_TOML_KEY}')
+    get_settings().load_file(pyproject_path, env=f'tool.{PR_AGENT_TOML_KEY}')

pr_agent/git_providers/__init__.py

@@ -1,4 +1,4 @@
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
 from pr_agent.git_providers.github_provider import GithubProvider
 from pr_agent.git_providers.gitlab_provider import GitLabProvider
@@ -13,7 +13,7 @@ _GIT_PROVIDERS = {
 
 def get_git_provider():
     try:
-        provider_id = settings.config.git_provider
+        provider_id = get_settings().config.git_provider
     except AttributeError as e:
         raise ValueError("git_provider is a required attribute in the configuration file") from e
     if provider_id not in _GIT_PROVIDERS:

pr_agent/git_providers/bitbucket_provider.py

@@ -5,15 +5,14 @@ from urllib.parse import urlparse
 import requests
 from atlassian.bitbucket import Cloud
 
-from pr_agent.config_loader import settings
-
+from ..config_loader import get_settings
 from .git_provider import FilePatchInfo
 
 
 class BitbucketProvider:
     def __init__(self, pr_url: Optional[str] = None, incremental: Optional[bool] = False):
         s = requests.Session()
-        s.headers['Authorization'] = f'Bearer {settings.get("BITBUCKET.BEARER_TOKEN", None)}'
+        s.headers['Authorization'] = f'Bearer {get_settings().get("BITBUCKET.BEARER_TOKEN", None)}'
         self.bitbucket_client = Cloud(session=s)
 
         self.workspace_slug = None
@@ -121,3 +120,6 @@ class BitbucketProvider:
 
     def _get_pr_file_content(self, remote_link: str):
         return ""
+
+    def get_commit_messages(self):
+        return ""  # not implemented yet

pr_agent/git_providers/github_provider.py

@@ -5,19 +5,22 @@ from urllib.parse import urlparse
 
 from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
-
-from pr_agent.config_loader import settings
+from starlette_context import context
 
 from ..algo.language_handler import is_valid_file
 from ..algo.utils import load_large_diff
-from .git_provider import FilePatchInfo, GitProvider, IncrementalPR
+from ..config_loader import get_settings
 from ..servers.utils import RateLimitExceeded
+from .git_provider import FilePatchInfo, GitProvider, IncrementalPR
 
 
 class GithubProvider(GitProvider):
     def __init__(self, pr_url: Optional[str] = None, incremental=IncrementalPR(False)):
         self.repo_obj = None
-        self.installation_id = settings.get("GITHUB.INSTALLATION_ID")
+        try:
+            self.installation_id = context.get("installation_id", None)
+        except Exception:
+            self.installation_id = None
         self.github_client = self._get_github_client()
         self.repo = None
         self.pr_num = None
@@ -81,7 +84,7 @@ class GithubProvider(GitProvider):
         return self.pr.get_files()
 
     @retry(exceptions=RateLimitExceeded,
-           tries=settings.github.ratelimit_retries, delay=2, backoff=2, jitter=(1, 3))
+           tries=get_settings().github.ratelimit_retries, delay=2, backoff=2, jitter=(1, 3))
     def get_diff_files(self) -> list[FilePatchInfo]:
         try:
             files = self.get_files()
@@ -114,7 +117,7 @@ class GithubProvider(GitProvider):
         # self.pr.create_issue_comment(pr_comment)
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
-        if is_temporary and not settings.config.publish_output_progress:
+        if is_temporary and not get_settings().config.publish_output_progress:
             logging.debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
             return
         response = self.pr.create_issue_comment(pr_comment)
@@ -145,7 +148,7 @@ class GithubProvider(GitProvider):
                         position = i
                         break
         if position == -1:
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
             subject_type = "FILE"
         else:
@@ -170,13 +173,13 @@ class GithubProvider(GitProvider):
             relevant_lines_end = suggestion['relevant_lines_end']
 
             if not relevant_lines_start or relevant_lines_start == -1:
-                if settings.config.verbosity_level >= 2:
+                if get_settings().config.verbosity_level >= 2:
                     logging.exception(
                         f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}")
                 continue
 
             if relevant_lines_end < relevant_lines_start:
-                if settings.config.verbosity_level >= 2:
+                if get_settings().config.verbosity_level >= 2:
                     logging.exception(f"Failed to publish code suggestion, "
                                       f"relevant_lines_end is {relevant_lines_end} and "
                                       f"relevant_lines_start is {relevant_lines_start}")
@@ -203,7 +206,7 @@ class GithubProvider(GitProvider):
             self.pr.create_review(commit=self.last_commit_id, comments=post_parameters_list)
             return True
         except Exception as e:
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.error(f"Failed to publish code suggestion, error: {e}")
             return False
 
@@ -237,7 +240,7 @@ class GithubProvider(GitProvider):
         return self.github_user_id
 
     def get_notifications(self, since: datetime):
-        deployment_type = settings.get("GITHUB.DEPLOYMENT_TYPE", "user")
+        deployment_type = get_settings().get("GITHUB.DEPLOYMENT_TYPE", "user")
 
         if deployment_type != 'user':
             raise ValueError("Deployment mode must be set to 'user' to get notifications")
@@ -278,12 +281,12 @@ class GithubProvider(GitProvider):
         return repo_name, pr_number
 
     def _get_github_client(self):
-        deployment_type = settings.get("GITHUB.DEPLOYMENT_TYPE", "user")
+        deployment_type = get_settings().get("GITHUB.DEPLOYMENT_TYPE", "user")
 
         if deployment_type == 'app':
             try:
-                private_key = settings.github.private_key
-                app_id = settings.github.app_id
+                private_key = get_settings().github.private_key
+                app_id = get_settings().github.app_id
             except AttributeError as e:
                 raise ValueError("GitHub app ID and private key are required when using GitHub app deployment") from e
             if not self.installation_id:
@@ -294,7 +297,7 @@ class GithubProvider(GitProvider):
 
         if deployment_type == 'user':
             try:
-                token = settings.github.user_token
+                token = get_settings().github.user_token
             except AttributeError as e:
                 raise ValueError(
                     "GitHub token is required when using user deployment. See: "
@@ -323,7 +326,9 @@ class GithubProvider(GitProvider):
 
     def publish_labels(self, pr_types):
         try:
-            label_color_map = {"Bug fix": "1d76db", "Tests": "e99695", "Bug fix with tests": "c5def5", "Refactoring": "bfdadc", "Enhancement": "bfd4f2", "Documentation": "d4c5f9", "Other": "d1bcf9"}
+            label_color_map = {"Bug fix": "1d76db", "Tests": "e99695", "Bug fix with tests": "c5def5",
+                               "Refactoring": "bfdadc", "Enhancement": "bfd4f2", "Documentation": "d4c5f9",
+                               "Other": "d1bcf9"}
             post_parameters = []
             for p in pr_types:
                 color = label_color_map.get(p, "d1bcf9")  # default to "Other" color
@@ -340,3 +345,18 @@ class GithubProvider(GitProvider):
         except Exception as e:
             logging.exception(f"Failed to get labels, error: {e}")
             return []
+
+    def get_commit_messages(self) -> str:
+        """
+        Retrieves the commit messages of a pull request.
+
+        Returns:
+            str: A string containing the commit messages of the pull request.
+        """
+        try:
+            commit_list = self.pr.get_commits()
+            commit_messages = [commit.commit.message for commit in commit_list]
+            commit_messages_str = "\n".join([f"{i + 1}. {message}" for i, message in enumerate(commit_messages)])
+        except:
+            commit_messages_str = ""
+        return commit_messages_str

pr_agent/git_providers/gitlab_provider.py

@@ -6,19 +6,20 @@ from urllib.parse import urlparse
 import gitlab
 from gitlab import GitlabGetError
 
-from pr_agent.config_loader import settings
-
 from ..algo.language_handler import is_valid_file
+from ..config_loader import get_settings
 from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
 
+logger = logging.getLogger()
+
 
 class GitLabProvider(GitProvider):
 
     def __init__(self, merge_request_url: Optional[str] = None, incremental: Optional[bool] = False):
-        gitlab_url = settings.get("GITLAB.URL", None)
+        gitlab_url = get_settings().get("GITLAB.URL", None)
         if not gitlab_url:
             raise ValueError("GitLab URL is not set in the config file")
-        gitlab_access_token = settings.get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
+        gitlab_access_token = get_settings().get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
         if not gitlab_access_token:
             raise ValueError("GitLab personal access token is not set in the config file")
         self.gl = gitlab.Gitlab(
@@ -48,7 +49,12 @@ class GitLabProvider(GitProvider):
     def _set_merge_request(self, merge_request_url: str):
         self.id_project, self.id_mr = self._parse_merge_request_url(merge_request_url)
         self.mr = self._get_merge_request()
-        self.last_diff = self.mr.diffs.list()[-1]
+        try:
+            self.last_diff = self.mr.diffs.list(get_all=True)[-1]
+        except IndexError as e:
+            logger.error(f"Could not get diff for merge request {self.id_mr}")
+            raise ValueError(f"Could not get diff for merge request {self.id_mr}") from e
+
 
     def _get_pr_file_content(self, file_path: str, branch: str) -> str:
         try:
@@ -133,32 +139,42 @@ class GitLabProvider(GitProvider):
             else:
                 pos_obj['new_line'] = target_line_no - 1
                 pos_obj['old_line'] = source_line_no - 1
+            logging.debug(f"Creating comment in {self.id_mr} with body {body} and position {pos_obj}")
             self.mr.discussions.create({'body': body,
                                         'position': pos_obj})
 
     def publish_code_suggestions(self, code_suggestions: list):
         for suggestion in code_suggestions:
-            body = suggestion['body']
-            relevant_file = suggestion['relevant_file']
-            relevant_lines_start = suggestion['relevant_lines_start']
-            relevant_lines_end = suggestion['relevant_lines_end']
+            try:
+                body = suggestion['body']
+                relevant_file = suggestion['relevant_file']
+                relevant_lines_start = suggestion['relevant_lines_start']
+                relevant_lines_end = suggestion['relevant_lines_end']
 
-            self.diff_files = self.diff_files if self.diff_files else self.get_diff_files()
-            target_file = None
-            for file in self.diff_files:
-                if file.filename == relevant_file:
+                self.diff_files = self.diff_files if self.diff_files else self.get_diff_files()
+                target_file = None
+                for file in self.diff_files:
                     if file.filename == relevant_file:
-                        target_file = file
-                        break
-            range = relevant_lines_end - relevant_lines_start + 1
-            body = body.replace('```suggestion', f'```suggestion:-0+{range}')
+                        if file.filename == relevant_file:
+                            target_file = file
+                            break
+                range = relevant_lines_end - relevant_lines_start # no need to add 1
+                body = body.replace('```suggestion', f'```suggestion:-0+{range}')
+                lines = target_file.head_file.splitlines()
+                relevant_line_in_file = lines[relevant_lines_start - 1]
 
-            lines = target_file.head_file.splitlines()
-            relevant_line_in_file = lines[relevant_lines_start - 1]
-            edit_type, found, source_line_no, target_file, target_line_no = self.find_in_file(target_file,
-                                                                                              relevant_line_in_file)
-            self.send_inline_comment(body, edit_type, found, relevant_file, relevant_line_in_file, source_line_no,
-                                     target_file, target_line_no)
+                # edit_type, found, source_line_no, target_file, target_line_no = self.find_in_file(target_file,
+                #                                                                            relevant_line_in_file)
+                # for code suggestions, we want to edit the new code
+                source_line_no = None
+                target_line_no = relevant_lines_start + 1
+                found = True
+                edit_type = 'addition'
+
+                self.send_inline_comment(body, edit_type, found, relevant_file, relevant_line_in_file, source_line_no,
+                                         target_file, target_line_no)
+            except Exception as e:
+                logging.exception(f"Could not publish code suggestion:\nsuggestion: {suggestion}\nerror: {e}")
 
     def search_line(self, relevant_file, relevant_line_in_file):
         target_file = None
@@ -281,3 +297,17 @@ class GitLabProvider(GitProvider):
 
     def get_labels(self):
         return self.mr.labels
+
+    def get_commit_messages(self) -> str:
+        """
+        Retrieves the commit messages of a pull request.
+
+        Returns:
+            str: A string containing the commit messages of the pull request.
+        """
+        try:
+            commit_messages_list = [commit['message'] for commit in self.mr.commits()._list]
+            commit_messages_str = "\n".join([f"{i + 1}. {message}" for i, message in enumerate(commit_messages_list)])
+        except:
+            commit_messages_str = ""
+        return commit_messages_str

pr_agent/git_providers/local_git_provider.py

@@ -5,7 +5,7 @@ from typing import List
 
 from git import Repo
 
-from pr_agent.config_loader import _find_repository_root, settings
+from pr_agent.config_loader import _find_repository_root, get_settings
 from pr_agent.git_providers.git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
 
 
@@ -38,12 +38,12 @@ class LocalGitProvider(GitProvider):
         self._prepare_repo()
         self.diff_files = None
         self.pr = PullRequestMimic(self.get_pr_title(), self.get_diff_files())
-        self.description_path = settings.get('local.description_path') \
-            if settings.get('local.description_path') is not None else self.repo_path / 'description.md'
-        self.review_path = settings.get('local.review_path') \
-            if settings.get('local.review_path') is not None else self.repo_path / 'review.md'
+        self.description_path = get_settings().get('local.description_path') \
+            if get_settings().get('local.description_path') is not None else self.repo_path / 'description.md'
+        self.review_path = get_settings().get('local.review_path') \
+            if get_settings().get('local.review_path') is not None else self.repo_path / 'review.md'
         # inline code comments are not supported for local git repositories
-        settings.pr_reviewer.inline_code_comments = False
+        get_settings().pr_reviewer.inline_code_comments = False
 
     def _prepare_repo(self):
         """

pr_agent/servers/github_action_runner.py

@@ -3,7 +3,7 @@ import json
 import os
 
 from pr_agent.agent.pr_agent import PRAgent
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 from pr_agent.tools.pr_reviewer import PRReviewer
 
 
@@ -30,11 +30,11 @@ async def run_action():
         return
 
     # Set the environment variables in the settings
-    settings.set("OPENAI.KEY", OPENAI_KEY)
+    get_settings().set("OPENAI.KEY", OPENAI_KEY)
     if OPENAI_ORG:
-        settings.set("OPENAI.ORG", OPENAI_ORG)
-    settings.set("GITHUB.USER_TOKEN", GITHUB_TOKEN)
-    settings.set("GITHUB.DEPLOYMENT_TYPE", "user")
+        get_settings().set("OPENAI.ORG", OPENAI_ORG)
+    get_settings().set("GITHUB.USER_TOKEN", GITHUB_TOKEN)
+    get_settings().set("GITHUB.DEPLOYMENT_TYPE", "user")
 
     # Load the event payload
     try:
@@ -50,7 +50,7 @@ async def run_action():
         if action in ["opened", "reopened"]:
             pr_url = event_payload.get("pull_request", {}).get("url")
             if pr_url:
-                await PRReviewer(pr_url).review()
+                await PRReviewer(pr_url).run()
 
     # Handle issue comment event
     elif GITHUB_EVENT_NAME == "issue_comment":

pr_agent/servers/github_app.py

@@ -1,12 +1,16 @@
-from typing import Dict, Any
+import copy
 import logging
 import sys
+from typing import Any, Dict
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, HTTPException, Request, Response
+from starlette.middleware import Middleware
+from starlette_context import context
+from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.servers.utils import verify_signature
 
 logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
@@ -17,27 +21,40 @@ router = APIRouter()
 async def handle_github_webhooks(request: Request, response: Response):
     """
     Receives and processes incoming GitHub webhook requests.
-    Verifies the request signature, parses the request body, and passes it to the handle_request function for further processing.
+    Verifies the request signature, parses the request body, and passes it to the handle_request function for further
+    processing.
     """
     logging.debug("Received a GitHub webhook")
 
+    body = await get_body(request)
+
+    logging.debug(f'Request body:\n{body}')
+    installation_id = body.get("installation", {}).get("id")
+    context["installation_id"] = installation_id
+    context["settings"] = copy.deepcopy(global_settings)
+
+    return await handle_request(body)
+
+
+@router.post("/api/v1/marketplace_webhooks")
+async def handle_marketplace_webhooks(request: Request, response: Response):
+    body = await get_body(request)
+    logging.info(f'Request body:\n{body}')
+
+async def get_body(request):
     try:
         body = await request.json()
     except Exception as e:
         logging.error("Error parsing request body", e)
         raise HTTPException(status_code=400, detail="Error parsing request body") from e
-    
     body_bytes = await request.body()
     signature_header = request.headers.get('x-hub-signature-256', None)
-    
-    webhook_secret = getattr(settings.github, 'webhook_secret', None)
-    
+    webhook_secret = getattr(get_settings().github, 'webhook_secret', None)
     if webhook_secret:
         verify_signature(body_bytes, webhook_secret, signature_header)
+    return body
 
-    logging.debug(f'Request body:\n{body}')
 
-    return await handle_request(body)
 
 
 async def handle_request(body: Dict[str, Any]):
@@ -48,8 +65,8 @@ async def handle_request(body: Dict[str, Any]):
         body: The request body.
     """
     action = body.get("action")
-    installation_id = body.get("installation", {}).get("id")
-    settings.set("GITHUB.INSTALLATION_ID", installation_id)
+    if not action:
+        return {}
     agent = PRAgent()
 
     if action == 'created':
@@ -65,7 +82,7 @@ async def handle_request(body: Dict[str, Any]):
         api_url = pull_request.get("url")
         await agent.handle_request(api_url, comment_body)
 
-    elif action in ["opened"] or 'reopened' in action:
+    elif action == "opened" or 'reopened' in action:
         pull_request = body.get("pull_request")
         if not pull_request:
             return {}
@@ -84,8 +101,9 @@ async def root():
 
 def start():
     # Override the deployment type to app
-    settings.set("GITHUB.DEPLOYMENT_TYPE", "app")
-    app = FastAPI()
+    get_settings().set("GITHUB.DEPLOYMENT_TYPE", "app")
+    middleware = [Middleware(RawContextMiddleware)]
+    app = FastAPI(middleware=middleware)
     app.include_router(router)
 
     uvicorn.run(app, host="0.0.0.0", port=3000)

pr_agent/servers/github_polling.py

@@ -6,7 +6,7 @@ from datetime import datetime, timezone
 import aiohttp
 
 from pr_agent.agent.pr_agent import PRAgent
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.servers.help import bot_help_text
 
@@ -38,8 +38,8 @@ async def polling_loop():
     agent = PRAgent()
 
     try:
-        deployment_type = settings.github.deployment_type
-        token = settings.github.user_token
+        deployment_type = get_settings().github.deployment_type
+        token = get_settings().github.user_token
     except AttributeError:
         deployment_type = 'none'
         token = None

pr_agent/servers/gitlab_webhook.py

@@ -7,7 +7,7 @@ from fastapi.responses import JSONResponse
 from starlette.background import BackgroundTasks
 
 from pr_agent.agent.pr_agent import PRAgent
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 
 app = FastAPI()
 router = APIRouter()
@@ -29,13 +29,13 @@ async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
     return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
 def start():
-    gitlab_url = settings.get("GITLAB.URL", None)
+    gitlab_url = get_settings().get("GITLAB.URL", None)
     if not gitlab_url:
         raise ValueError("GITLAB.URL is not set")
-    gitlab_token = settings.get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
+    gitlab_token = get_settings().get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
     if not gitlab_token:
         raise ValueError("GITLAB.PERSONAL_ACCESS_TOKEN is not set")
-    settings.config.git_provider = "gitlab"
+    get_settings().config.git_provider = "gitlab"
 
     app = FastAPI()
     app.include_router(router)

pr_agent/servers/help.py

@@ -1,9 +1,10 @@
 commands_text = "> **/review [-i]**: Request a review of your Pull Request. For an incremental review, which only " \
                 "considers changes since the last review, include the '-i' option.\n" \
                 "> **/describe**: Modify the PR title and description based on the contents of the PR.\n" \
-                "> **/improve**: Suggest improvements to the code in the PR. " \
-                "These will be provided as pull request comments, ready to commit.\n" \
-                "> **/ask \\<QUESTION\\>**: Pose a question about the PR.\n"
+                "> **/improve**: Suggest improvements to the code in the PR. \n" \
+                "> **/ask \\<QUESTION\\>**: Pose a question about the PR.\n\n" \
+                ">To edit any configuration parameter from 'configuration.toml', add --config_path=new_value\n" \
+                ">For example: /review --pr_reviewer.extra_instructions=\"focus on the file: ...\" " \
 
 
 def bot_help_text(user: str):

pr_agent/settings/configuration.toml

@@ -7,7 +7,7 @@ publish_output_progress=true
 verbosity_level=0 # 0,1,2
 use_extra_bad_extensions=false
 
-[pr_reviewer]
+[pr_reviewer] # /review #
 require_focused_review=true
 require_score_review=false
 require_tests_review=true
@@ -15,17 +15,21 @@ require_security_review=true
 num_code_suggestions=0
 inline_code_comments = true
 ask_and_reflect=false
+extra_instructions = ""
 
-[pr_description]
+[pr_description] # /describe #
 publish_description_as_comment=false
+extra_instructions = ""
 
-[pr_questions]
+[pr_questions] # /ask #
 
-[pr_code_suggestions]
+[pr_code_suggestions] # /improve #
 num_code_suggestions=4
+extra_instructions = ""
 
-[pr_update_changelog]
+[pr_update_changelog] # /update_changelog #
 push_changelog_changes=false
+extra_instructions = ""
 
 [github]
 # The type of deployment to create. Valid values are 'app' or 'user'.

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -9,6 +9,12 @@ Your task is to provide meaningfull non-trivial code suggestions to improve the
 - Make sure not to provide suggestions repeating modifications already implemented in the new PR code (the '+' lines).
 - Don't output line numbers in the 'improved code' snippets.
 
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+{{ extra_instructions }}
+{% endif %}
+
 You must use the following JSON schema to format your answer:
 ```json
 {

pr_agent/settings/pr_description_prompts.toml

@@ -3,6 +3,12 @@ system="""You are CodiumAI-PR-Reviewer, a language model designed to review git
 Your task is to provide full description of the PR content.
 - Make sure not to focus the new PR code (the '+' lines).
 
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+{{ extra_instructions }}
+{% endif %}
+
 You must use the following JSON schema to format your answer:
 ```json
 {
@@ -30,8 +36,14 @@ Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'desc
 user="""PR Info:
 Branch: '{{branch}}'
 {%- if language %}
+
 Main language: {{language}}
 {%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
 
 
 The PR Git Diff:

pr_agent/settings/pr_reviewer_prompts.toml

@@ -8,6 +8,12 @@ Your task is to provide constructive and concise feedback for the PR, and also p
 - Make sure not to provide suggestions repeating modifications already implemented in the new PR code (the '+' lines).
 {%- endif %}
 
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+{{ extra_instructions }}
+{% endif %}
+
 You must use the following JSON schema to format your answer:
 ```json
 {

pr_agent/settings/pr_update_changelog_prompts.toml

@@ -4,6 +4,12 @@ Your task is to update the CHANGELOG.md file of the project, to shortly summariz
 - The output should match the existing CHANGELOG.md format, style and conventions, so it will look like a natural part of the file. For example, if previous changes were summarized in a single line, you should do the same.
 - Don't repeat previous changes. Generate only new content, that is not already in the CHANGELOG.md file.
 - Be general, and avoid specific details, files, etc. The output should be minimal, no more than 3-4 short lines. Ignore non-relevant subsections.
+
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+{{ extra_instructions }}
+{%- endif %}
 """
 
 user="""PR Info:

pr_agent/tools/pr_code_suggestions.py

@@ -9,18 +9,19 @@ from pr_agent.algo.ai_handler import AiHandler
 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 try_fix_json
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import BitbucketProvider, get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
 
 
 class PRCodeSuggestions:
-    def __init__(self, pr_url: str, cli_mode=False):
+    def __init__(self, pr_url: str, cli_mode=False, args: list = None):
 
         self.git_provider = get_git_provider()(pr_url)
         self.main_language = get_main_pr_language(
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
+
         self.ai_handler = AiHandler()
         self.patches_diff = None
         self.prediction = None
@@ -31,23 +32,24 @@ class PRCodeSuggestions:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_language,
             "diff": "",  # empty diff for initial calculation
-            'num_code_suggestions': settings.pr_code_suggestions.num_code_suggestions,
+            "num_code_suggestions": get_settings().pr_code_suggestions.num_code_suggestions,
+            "extra_instructions": get_settings().pr_code_suggestions.extra_instructions,
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,
-                                          settings.pr_code_suggestions_prompt.system,
-                                          settings.pr_code_suggestions_prompt.user)
+                                          get_settings().pr_code_suggestions_prompt.system,
+                                          get_settings().pr_code_suggestions_prompt.user)
 
-    async def suggest(self):
+    async def run(self):
         assert type(self.git_provider) != BitbucketProvider, "Bitbucket is not supported for now"
 
         logging.info('Generating code suggestions for PR...')
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing review...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
         logging.info('Preparing PR review...')
         data = self._prepare_pr_code_suggestions()
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             logging.info('Pushing PR review...')
             self.git_provider.remove_initial_comment()
             logging.info('Pushing inline code comments...')
@@ -68,9 +70,9 @@ class PRCodeSuggestions:
         variables = copy.deepcopy(self.vars)
         variables["diff"] = self.patches_diff  # update diff
         environment = Environment(undefined=StrictUndefined)
-        system_prompt = environment.from_string(settings.pr_code_suggestions_prompt.system).render(variables)
-        user_prompt = environment.from_string(settings.pr_code_suggestions_prompt.user).render(variables)
-        if settings.config.verbosity_level >= 2:
+        system_prompt = environment.from_string(get_settings().pr_code_suggestions_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_code_suggestions_prompt.user).render(variables)
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"\nSystem prompt:\n{system_prompt}")
             logging.info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
@@ -83,7 +85,7 @@ class PRCodeSuggestions:
         try:
             data = json.loads(review)
         except json.decoder.JSONDecodeError:
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.info(f"Could not parse json response: {review}")
             data = try_fix_json(review, code_suggestions=True)
         return data
@@ -91,22 +93,28 @@ class PRCodeSuggestions:
     def push_inline_code_suggestions(self, data):
         code_suggestions = []
         for d in data['Code suggestions']:
-            if settings.config.verbosity_level >= 2:
-                logging.info(f"suggestion: {d}")
-            relevant_file = d['relevant file'].strip()
-            relevant_lines_str = d['relevant lines'].strip()
-            relevant_lines_start = int(relevant_lines_str.split('-')[0])  # absolute position
-            relevant_lines_end = int(relevant_lines_str.split('-')[-1])
-            content = d['suggestion content']
-            new_code_snippet = d['improved code']
+            try:
+                if get_settings().config.verbosity_level >= 2:
+                    logging.info(f"suggestion: {d}")
+                relevant_file = d['relevant file'].strip()
+                relevant_lines_str = d['relevant lines'].strip()
+                if ',' in relevant_lines_str:  # handling 'relevant lines': '181, 190' or '178-184, 188-194'
+                    relevant_lines_str = relevant_lines_str.split(',')[0]
+                relevant_lines_start = int(relevant_lines_str.split('-')[0])  # absolute position
+                relevant_lines_end = int(relevant_lines_str.split('-')[-1])
+                content = d['suggestion content']
+                new_code_snippet = d['improved code']
 
-            if new_code_snippet:
-                new_code_snippet = self.dedent_code(relevant_file, relevant_lines_start, new_code_snippet)
+                if new_code_snippet:
+                    new_code_snippet = self.dedent_code(relevant_file, relevant_lines_start, new_code_snippet)
 
-            body = f"**Suggestion:** {content}\n```suggestion\n" + new_code_snippet + "\n```"
-            code_suggestions.append({'body': body,'relevant_file': relevant_file,
-                                     'relevant_lines_start': relevant_lines_start,
-                                     'relevant_lines_end': relevant_lines_end})
+                body = f"**Suggestion:** {content}\n```suggestion\n" + new_code_snippet + "\n```"
+                code_suggestions.append({'body': body, 'relevant_file': relevant_file,
+                                         'relevant_lines_start': relevant_lines_start,
+                                         'relevant_lines_end': relevant_lines_end})
+            except Exception:
+                if get_settings().config.verbosity_level >= 2:
+                    logging.info(f"Could not parse suggestion: {d}")
 
         self.git_provider.publish_code_suggestions(code_suggestions)
 
@@ -127,7 +135,8 @@ class PRCodeSuggestions:
                 if delta_spaces > 0:
                     new_code_snippet = textwrap.indent(new_code_snippet, delta_spaces * " ").rstrip('\n')
         except Exception as e:
-            if settings.config.verbosity_level >= 2:
+            if get_settings().config.verbosity_level >= 2:
                 logging.info(f"Could not dedent code snippet for file {relevant_file}, error: {e}")
 
         return new_code_snippet
+

pr_agent/tools/pr_description.py

@@ -1,31 +1,33 @@
 import copy
 import json
 import logging
-from typing import Tuple, List
+from typing import List, Tuple
 
 from jinja2 import Environment, StrictUndefined
 
 from pr_agent.algo.ai_handler import AiHandler
 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.config_loader import settings
+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
 
 
 class PRDescription:
-    def __init__(self, pr_url: str):
+    def __init__(self, pr_url: str, args: list = None):
         """
-        Initialize the PRDescription object with the necessary attributes and objects for generating a PR description using an AI model.
+        Initialize the PRDescription object with the necessary attributes and objects for generating a PR description
+        using an AI model.
         Args:
             pr_url (str): The URL of the pull request.
+            args (list, optional): List of arguments passed to the PRDescription class. Defaults to None.
         """
-        
         # Initialize the git provider and main PR language
         self.git_provider = get_git_provider()(pr_url)
         self.main_pr_language = get_main_pr_language(
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
+        commit_messages_str = self.git_provider.get_commit_messages()
 
         # Initialize the AI handler
         self.ai_handler = AiHandler()
@@ -37,26 +39,28 @@ class PRDescription:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_pr_language,
             "diff": "",  # empty diff for initial calculation
+            "extra_instructions": get_settings().pr_description.extra_instructions,
+            "commit_messages_str": commit_messages_str
         }
     
         # Initialize the token handler
         self.token_handler = TokenHandler(
             self.git_provider.pr,
             self.vars,
-            settings.pr_description_prompt.system,
-            settings.pr_description_prompt.user,
+            get_settings().pr_description_prompt.system,
+            get_settings().pr_description_prompt.user,
         )
     
         # Initialize patches_diff and prediction attributes
         self.patches_diff = None
         self.prediction = None
 
-    async def describe(self):
+    async def run(self):
         """
         Generates a PR description using an AI model and publishes it to the PR.
         """
         logging.info('Generating a PR description...')
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing pr description...", is_temporary=True)
         
         await retry_with_fallback_models(self._prepare_prediction)
@@ -64,9 +68,9 @@ class PRDescription:
         logging.info('Preparing answer...')
         pr_title, pr_body, pr_types, markdown_text = self._prepare_pr_answer()
         
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             logging.info('Pushing answer...')
-            if settings.pr_description.publish_description_as_comment:
+            if get_settings().pr_description.publish_description_as_comment:
                 self.git_provider.publish_comment(markdown_text)
             else:
                 self.git_provider.publish_description(pr_title, pr_body)
@@ -112,10 +116,10 @@ class PRDescription:
         variables["diff"] = self.patches_diff  # update diff
 
         environment = Environment(undefined=StrictUndefined)
-        system_prompt = environment.from_string(settings.pr_description_prompt.system).render(variables)
-        user_prompt = environment.from_string(settings.pr_description_prompt.user).render(variables)
+        system_prompt = environment.from_string(get_settings().pr_description_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_description_prompt.user).render(variables)
 
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"\nSystem prompt:\n{system_prompt}")
             logging.info(f"\nUser prompt:\n{user_prompt}")
 
@@ -160,13 +164,13 @@ class PRDescription:
         # Iterate over the remaining dictionary items and append the key and value to 'pr_body' in a markdown format,
         # except for the items containing the word 'walkthrough'
         for key, value in data.items():
-            pr_body += f"{key}:\n"
+            pr_body += f"## {key}:\n"
             if 'walkthrough' in key.lower():
                 pr_body += f"{value}\n"
             else:
-                pr_body += f"**{value}**\n\n___\n"
+                pr_body += f"{value}\n\n___\n"
 
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"title:\n{title}\n{pr_body}")
 
         return title, pr_body, pr_types, markdown_text

pr_agent/tools/pr_information_from_user.py

@@ -6,15 +6,13 @@ from jinja2 import Environment, StrictUndefined
 from pr_agent.algo.ai_handler import AiHandler
 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.config_loader import settings
+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
 
 
-
-
 class PRInformationFromUser:
-    def __init__(self, pr_url: str):
+    def __init__(self, pr_url: str, args: list = None):
         self.git_provider = get_git_provider()(pr_url)
         self.main_pr_language = get_main_pr_language(
             self.git_provider.get_languages(), self.git_provider.get_files()
@@ -29,19 +27,19 @@ class PRInformationFromUser:
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,
-                                          settings.pr_information_from_user_prompt.system,
-                                          settings.pr_information_from_user_prompt.user)
+                                          get_settings().pr_information_from_user_prompt.system,
+                                          get_settings().pr_information_from_user_prompt.user)
         self.patches_diff = None
         self.prediction = None
 
-    async def generate_questions(self):
+    async def run(self):
         logging.info('Generating question to the user...')
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing questions...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
         logging.info('Preparing questions...')
         pr_comment = self._prepare_pr_answer()
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             logging.info('Pushing questions...')
             self.git_provider.publish_comment(pr_comment)
             self.git_provider.remove_initial_comment()
@@ -57,9 +55,9 @@ class PRInformationFromUser:
         variables = copy.deepcopy(self.vars)
         variables["diff"] = self.patches_diff  # update diff
         environment = Environment(undefined=StrictUndefined)
-        system_prompt = environment.from_string(settings.pr_information_from_user_prompt.system).render(variables)
-        user_prompt = environment.from_string(settings.pr_information_from_user_prompt.user).render(variables)
-        if settings.config.verbosity_level >= 2:
+        system_prompt = environment.from_string(get_settings().pr_information_from_user_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_information_from_user_prompt.user).render(variables)
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"\nSystem prompt:\n{system_prompt}")
             logging.info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
@@ -68,7 +66,7 @@ class PRInformationFromUser:
 
     def _prepare_pr_answer(self) -> str:
         model_output = self.prediction.strip()
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"answer_str:\n{model_output}")
         answer_str = f"{model_output}\n\n Please respond to the questions above in the following format:\n\n" +\
                      "\n>/answer\n>1) ...\n>2) ...\n>...\n"

pr_agent/tools/pr_questions.py

@@ -6,7 +6,7 @@ from jinja2 import Environment, StrictUndefined
 from pr_agent.algo.ai_handler import AiHandler
 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.config_loader import settings
+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
 
@@ -30,8 +30,8 @@ class PRQuestions:
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,
-                                          settings.pr_questions_prompt.system,
-                                          settings.pr_questions_prompt.user)
+                                          get_settings().pr_questions_prompt.system,
+                                          get_settings().pr_questions_prompt.user)
         self.patches_diff = None
         self.prediction = None
 
@@ -42,14 +42,14 @@ class PRQuestions:
             question_str = ""
         return question_str
 
-    async def answer(self):
+    async def run(self):
         logging.info('Answering a PR question...')
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing answer...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
         logging.info('Preparing answer...')
         pr_comment = self._prepare_pr_answer()
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             logging.info('Pushing answer...')
             self.git_provider.publish_comment(pr_comment)
             self.git_provider.remove_initial_comment()
@@ -65,9 +65,9 @@ class PRQuestions:
         variables = copy.deepcopy(self.vars)
         variables["diff"] = self.patches_diff  # update diff
         environment = Environment(undefined=StrictUndefined)
-        system_prompt = environment.from_string(settings.pr_questions_prompt.system).render(variables)
-        user_prompt = environment.from_string(settings.pr_questions_prompt.user).render(variables)
-        if settings.config.verbosity_level >= 2:
+        system_prompt = environment.from_string(get_settings().pr_questions_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_questions_prompt.user).render(variables)
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"\nSystem prompt:\n{system_prompt}")
             logging.info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
@@ -77,6 +77,6 @@ class PRQuestions:
     def _prepare_pr_answer(self) -> str:
         answer_str = f"Question: {self.question_str}\n\n"
         answer_str += f"Answer:\n{self.prediction.strip()}\n\n"
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"answer_str:\n{answer_str}")
         return answer_str

pr_agent/tools/pr_reviewer.py

@@ -2,7 +2,7 @@ import copy
 import json
 import logging
 from collections import OrderedDict
-from typing import Tuple, List
+from typing import List, Tuple
 
 from jinja2 import Environment, StrictUndefined
 
@@ -10,9 +10,9 @@ from pr_agent.algo.ai_handler import AiHandler
 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 convert_to_markdown, try_fix_json
-from pr_agent.config_loader import settings
+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, IncrementalPR
+from pr_agent.git_providers.git_provider import IncrementalPR, get_main_pr_language
 from pr_agent.servers.help import actions_help_text, bot_help_text
 
 
@@ -20,17 +20,16 @@ class PRReviewer:
     """
     The PRReviewer class is responsible for reviewing a pull request and generating feedback using an AI model.
     """
-    def __init__(self, pr_url: str, cli_mode: bool = False, is_answer: bool = False, args: list = None):
+    def __init__(self, pr_url: str, is_answer: bool = False, args: list = None):
         """
         Initialize the PRReviewer object with the necessary attributes and objects to review a pull request.
 
         Args:
             pr_url (str): The URL of the pull request to be reviewed.
-            cli_mode (bool, optional): Indicates whether the review is being done in command-line interface mode. Defaults to False.
             is_answer (bool, optional): Indicates whether the review is being done in answer mode. Defaults to False.
             args (list, optional): List of arguments passed to the PRReviewer class. Defaults to None.
         """
-        self.parse_args(args)
+        self.parse_args(args) # -i command
 
         self.git_provider = get_git_provider()(pr_url, incremental=self.incremental)
         self.main_language = get_main_pr_language(
@@ -40,11 +39,10 @@ class PRReviewer:
         self.is_answer = is_answer
 
         if self.is_answer and not self.git_provider.is_supported("get_issue_comments"):
-            raise Exception(f"Answer mode is not supported for {settings.config.git_provider} for now")
+            raise Exception(f"Answer mode is not supported for {get_settings().config.git_provider} for now")
         self.ai_handler = AiHandler()
         self.patches_diff = None
         self.prediction = None
-        self.cli_mode = cli_mode
 
         answer_str, question_str = self._get_user_answers()
         self.vars = {
@@ -53,20 +51,21 @@ class PRReviewer:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_language,
             "diff": "",  # empty diff for initial calculation
-            "require_score": settings.pr_reviewer.require_score_review,
-            "require_tests": settings.pr_reviewer.require_tests_review,
-            "require_security": settings.pr_reviewer.require_security_review,
-            "require_focused": settings.pr_reviewer.require_focused_review,
-            'num_code_suggestions': settings.pr_reviewer.num_code_suggestions,
+            "require_score": get_settings().pr_reviewer.require_score_review,
+            "require_tests": get_settings().pr_reviewer.require_tests_review,
+            "require_security": get_settings().pr_reviewer.require_security_review,
+            "require_focused": get_settings().pr_reviewer.require_focused_review,
+            'num_code_suggestions': get_settings().pr_reviewer.num_code_suggestions,
             'question_str': question_str,
             'answer_str': answer_str,
+            "extra_instructions": get_settings().pr_reviewer.extra_instructions,
         }
 
         self.token_handler = TokenHandler(
             self.git_provider.pr,
             self.vars,
-            settings.pr_review_prompt.system,
-            settings.pr_review_prompt.user
+            get_settings().pr_review_prompt.system,
+            get_settings().pr_review_prompt.user
         )
 
     def parse_args(self, args: List[str]) -> None:
@@ -86,13 +85,13 @@ class PRReviewer:
                 is_incremental = True
         self.incremental = IncrementalPR(is_incremental)
 
-    async def review(self) -> None:
+    async def run(self) -> None:
         """
         Review the pull request and generate feedback.
         """
         logging.info('Reviewing PR...')
     
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing review...", is_temporary=True)
     
         await retry_with_fallback_models(self._prepare_prediction)
@@ -100,12 +99,12 @@ class PRReviewer:
         logging.info('Preparing PR review...')
         pr_comment = self._prepare_pr_review()
     
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             logging.info('Pushing PR review...')
             self.git_provider.publish_comment(pr_comment)
             self.git_provider.remove_initial_comment()
         
-            if settings.pr_reviewer.inline_code_comments:
+            if get_settings().pr_reviewer.inline_code_comments:
                 logging.info('Pushing inline code comments...')
                 self._publish_inline_code_comments()
 
@@ -138,10 +137,10 @@ class PRReviewer:
         variables["diff"] = self.patches_diff  # update diff
 
         environment = Environment(undefined=StrictUndefined)
-        system_prompt = environment.from_string(settings.pr_review_prompt.system).render(variables)
-        user_prompt = environment.from_string(settings.pr_review_prompt.user).render(variables)
+        system_prompt = environment.from_string(get_settings().pr_review_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_review_prompt.user).render(variables)
 
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"\nSystem prompt:\n{system_prompt}")
             logging.info(f"\nUser prompt:\n{user_prompt}")
 
@@ -156,7 +155,8 @@ class PRReviewer:
 
     def _prepare_pr_review(self) -> str:
         """
-        Prepare the PR review by processing the AI prediction and generating a markdown-formatted text that summarizes the feedback.
+        Prepare the PR review by processing the AI prediction and generating a markdown-formatted text that summarizes
+        the feedback.
         """
         review = self.prediction.strip()
     
@@ -172,7 +172,8 @@ class PRReviewer:
             data['PR Analysis']['Security concerns'] = val
 
         # Filter out code suggestions that can be submitted as inline comments
-        if settings.config.git_provider != 'bitbucket' and settings.pr_reviewer.inline_code_comments and 'Code suggestions' in data['PR Feedback']:
+        if get_settings().config.git_provider != 'bitbucket' and get_settings().pr_reviewer.inline_code_comments \
+                and 'Code suggestions' in data['PR Feedback']:
             data['PR Feedback']['Code suggestions'] = [
                 d for d in data['PR Feedback']['Code suggestions']
                 if any(key not in d for key in ('relevant file', 'relevant line in file', 'suggestion content'))
@@ -182,7 +183,8 @@ class PRReviewer:
 
         # Add incremental review section
         if self.incremental.is_incremental:
-            last_commit_url = f"{self.git_provider.get_pr_url()}/commits/{self.git_provider.incremental.first_new_commit_sha}"
+            last_commit_url = f"{self.git_provider.get_pr_url()}/commits/" \
+                              f"{self.git_provider.incremental.first_new_commit_sha}"
             data = OrderedDict(data)
             data.update({'Incremental PR Review': {
                 "⏮️ Review for commits since previous PR-Agent review": f"Starting from commit {last_commit_url}"}})
@@ -192,7 +194,7 @@ class PRReviewer:
         user = self.git_provider.get_user_id()
 
         # Add help text if not in CLI mode
-        if not self.cli_mode:
+        if not get_settings().get("CONFIG.CLI_MODE", False):
             markdown_text += "\n### How to use\n"
             if user and '[bot]' not in user:
                 markdown_text += bot_help_text(user)
@@ -200,7 +202,7 @@ class PRReviewer:
                 markdown_text += actions_help_text
 
         # Log markdown response if verbosity level is high
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"Markdown response:\n{markdown_text}")
     
         return markdown_text
@@ -209,7 +211,7 @@ class PRReviewer:
         """
         Publishes inline comments on a pull request with code suggestions generated by the AI model.
         """
-        if settings.pr_reviewer.num_code_suggestions == 0:
+        if get_settings().pr_reviewer.num_code_suggestions == 0:
             return
 
         review = self.prediction.strip()
@@ -250,7 +252,7 @@ class PRReviewer:
         if self.is_answer:
             discussion_messages = self.git_provider.get_issue_comments()
 
-            for message in reversed(discussion_messages):
+            for message in discussion_messages.reversed:
                 if "Questions to better understand the PR:" in message.body:
                     question_str = message.body
                 elif '/answer' in message.body:

pr_agent/tools/pr_update_changelog.py

@@ -9,8 +9,8 @@ from jinja2 import Environment, StrictUndefined
 from pr_agent.algo.ai_handler import AiHandler
 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.config_loader import settings
-from pr_agent.git_providers import get_git_provider, GithubProvider
+from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import GithubProvider, get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
 
 CHANGELOG_LINES = 50
@@ -23,7 +23,7 @@ class PRUpdateChangelog:
         self.main_language = get_main_pr_language(
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
-        self.commit_changelog = self._parse_args(args, settings)
+        self.commit_changelog = get_settings().pr_update_changelog.push_changelog_changes
         self._get_changlog_file()  # self.changelog_file_str
         self.ai_handler = AiHandler()
         self.patches_diff = None
@@ -37,22 +37,23 @@ class PRUpdateChangelog:
             "diff": "",  # empty diff for initial calculation
             "changelog_file_str": self.changelog_file_str,
             "today": date.today(),
+            "extra_instructions": get_settings().pr_update_changelog.extra_instructions,
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,
-                                          settings.pr_update_changelog_prompt.system,
-                                          settings.pr_update_changelog_prompt.user)
+                                          get_settings().pr_update_changelog_prompt.system,
+                                          get_settings().pr_update_changelog_prompt.user)
 
-    async def update_changelog(self):
+    async def run(self):
         assert type(self.git_provider) == GithubProvider, "Currently only Github is supported"
 
         logging.info('Updating the changelog...')
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing changelog updates...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
         logging.info('Preparing PR changelog updates...')
         new_file_content, answer = self._prepare_changelog_update()
-        if settings.config.publish_output:
+        if get_settings().config.publish_output:
             self.git_provider.remove_initial_comment()
             logging.info('Publishing changelog updates...')
             if self.commit_changelog:
@@ -72,9 +73,9 @@ class PRUpdateChangelog:
         variables = copy.deepcopy(self.vars)
         variables["diff"] = self.patches_diff  # update diff
         environment = Environment(undefined=StrictUndefined)
-        system_prompt = environment.from_string(settings.pr_update_changelog_prompt.system).render(variables)
-        user_prompt = environment.from_string(settings.pr_update_changelog_prompt.user).render(variables)
-        if settings.config.verbosity_level >= 2:
+        system_prompt = environment.from_string(get_settings().pr_update_changelog_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_update_changelog_prompt.user).render(variables)
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"\nSystem prompt:\n{system_prompt}")
             logging.info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
@@ -83,7 +84,7 @@ class PRUpdateChangelog:
         return response
 
     def _prepare_changelog_update(self) -> Tuple[str, str]:
-        answer = self.prediction.strip().strip("```").strip()
+        answer = self.prediction.strip().strip("```").strip()  # noqa B005
         if hasattr(self, "changelog_file"):
             existing_content = self.changelog_file.decoded_content.decode()
         else:
@@ -95,9 +96,9 @@ class PRUpdateChangelog:
 
         if not self.commit_changelog:
             answer += "\n\n\n>to commit the new content to the CHANGELOG.md file, please type:" \
-                      "\n>'/update_changelog -commit'\n"
+                      "\n>'/update_changelog --pr_update_changelog.push_changelog_changes=true'\n"
 
-        if settings.config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2:
             logging.info(f"answer:\n{answer}")
 
         return new_file_content, answer
@@ -117,7 +118,7 @@ class PRUpdateChangelog:
         last_commit_id = list(self.git_provider.pr.get_commits())[-1]
         try:
             self.git_provider.pr.create_review(commit=last_commit_id, comments=[d])
-        except:
+        except Exception:
             # we can't create a review for some reason, let's just publish a comment
             self.git_provider.publish_comment(f"**Changelog updates:**\n\n{answer}")
 
@@ -137,19 +138,6 @@ Example:
 """
         return example_changelog
 
-    def _parse_args(self, args, setting):
-        commit_changelog = False
-        if args and len(args) >= 1:
-            try:
-                if args[0] == "-commit":
-                    commit_changelog = True
-            except:
-                pass
-        else:
-            commit_changelog = setting.pr_update_changelog.push_changelog_changes
-
-        return commit_changelog
-
     def _get_changlog_file(self):
         try:
             self.changelog_file = self.git_provider.repo_obj.get_contents("CHANGELOG.md",
@@ -157,7 +145,7 @@ Example:
             changelog_file_lines = self.changelog_file.decoded_content.decode().splitlines()
             changelog_file_lines = changelog_file_lines[:CHANGELOG_LINES]
             self.changelog_file_str = "\n".join(changelog_file_lines)
-        except:
+        except Exception:
             self.changelog_file_str = ""
             if self.commit_changelog:
                 logging.info("No CHANGELOG.md file found in the repository. Creating one...")

pyproject.toml

@@ -41,6 +41,7 @@ dependencies = [
   "aiohttp~=3.8.4",
   "atlassian-python-api==3.39.0",
   "GitPython~=3.1.32",
+  "starlette-context==0.3.6"
 ]
 
 [project.urls]

tests/unittest/test_handle_patch_deletions.py

@@ -2,7 +2,7 @@
 import logging
 
 from pr_agent.algo.git_patch_processing import handle_patch_deletions
-from pr_agent.config_loader import settings
+from pr_agent.config_loader import get_settings
 
 """
 Code Analysis
@@ -49,7 +49,7 @@ class TestHandlePatchDeletions:
         original_file_content_str = 'foo\nbar\n'
         new_file_content_str = ''
         file_name = 'file.py'
-        settings.config.verbosity_level = 1
+        get_settings().config.verbosity_level = 1
 
         with caplog.at_level(logging.INFO):
             handle_patch_deletions(patch, original_file_content_str, new_file_content_str, file_name)