Default timeout for AI is now 180s, configurable

Update README and CONFIGURATION Documentation

CHANGELOG.md

@@ -1,9 +1,27 @@
+## 2023-08-03
+
+### Optimized
+- Optimized PR diff processing by introducing caching for diff files, reducing the number of API calls.
+- Refactored `load_large_diff` function to generate a patch only when necessary.
+- Fixed a bug in the GitLab provider where the new file was not retrieved correctly.
+
+## 2023-08-02
+
+### Enhanced
+- Updated several tools in the `pr_agent` package to use commit messages in their functionality.
+- Commit messages are now retrieved and stored in the `vars` dictionary for each tool.
+- Added a section to display the commit messages in the prompts of various tools.
+
 ## 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.
+- Added support for repository-specific configuration files (.pr_agent.yaml) for the PR Agent.
+- Implemented this feature for both GitHub and GitLab providers.
+- Added a new configuration option 'use_repo_settings_file' to enable or disable the use of a repo-specific settings file.
+
 
 ## 2023-07-30
 
@@ -24,4 +42,4 @@
 ### Added
 - New feature for updating the CHANGELOG.md based on the contents of a PR.
 - Added support for this feature for the Github provider.
-- New configuration settings and prompts for the changelog update feature.
+- New configuration settings and prompts for the changelog update feature.

CONFIGURATION.md

@@ -1,12 +1,57 @@
 ## Configuration
 
-The different tools and sub-tools used by CodiumAI pr-agent are adjustable via the configuration file: `/pr-agent/settings/configuration.toml`.
+The different tools and sub-tools used by CodiumAI PR-Agent are adjustable via the **[configuration file](pr_agent/settings/configuration.toml)**
+
+### Working from CLI
+When running from source (CLI), your local configuration file will be initially used.
+
+Example for invoking the 'review' tools via the CLI: 
 
-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 ...
+python cli.py --pr-url=<pr_url>  review
+```
+In addition to general configurations, the 'review' tool will use parameters from the `[pr_reviewer]` section (every tool has a dedicated section in the configuration file).
+
+Note that you can print results locally, without publishing them, by setting in `configuration.toml`:
+
+```
+[config]
+publish_output=true
+verbosity_level=2
+```
+This is useful for debugging or experimenting with the different tools.
+
+### Working from pre-built repo (GitHub Action/GitHub App/Docker)
+When running PR-Agent from a pre-built repo, the default configuration file will be loaded.
+
+To edit the configuration, you have two options: 
+1. Place a local configuration file in the root of your local repo. The local file will be used instead of the default one.
+2. For online usage, just add `--config_path=<value>` to you command, to edit a specific configuration value.
+For example if you want to edit `pr_reviewer` configurations, you can run:
+```
+/review --pr_reviewer.extra_instructions="..." --pr_reviewer.require_score_review=false ...
 ```
 
 Any configuration value in `configuration.toml` file can be similarly edited.
 
+### General configuration parameters
+
+#### Changing a model
+See [here](pr_agent/algo/__init__.py) for the list of available models.
+
+To use Llama2 model, for example, set:
+```
+[config]
+model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
+[replicate]
+key = ...
+```
+(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
+
+Also review the [AiHandler](pr_agent/algo/ai_handler.py) file for instruction how to set keys for other models.
+
+#### Extra instructions
+All PR-Agent tools have a parameter called `extra_instructions`, that enables to add free-text extra instructions. Example usage:
+```
+/update_changelog --pr_update_changelog.extra_instructions="Make sure to update also the version ..."
+```

README.md

@@ -65,7 +65,6 @@ CodiumAI `PR-Agent` is an open-source tool aiming to help developers review pull
 - [Overview](#overview)
 - [Try it now](#try-it-now)
 - [Installation](#installation)
-- [Usage and tools](#usage-and-tools)
 - [Configuration](./CONFIGURATION.md)
 - [How it works](#how-it-works)
 - [Why use PR-Agent](#why-use-pr-agent)
@@ -94,6 +93,7 @@ CodiumAI `PR-Agent` is an open-source tool aiming to help developers review pull
 | CORE  | PR compression                              |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |
 |       | Repo language prioritization                |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |
 |       | Adaptive and token-aware<br />file patch fitting |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |
+|       | Multiple models support |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |
 |       | Incremental PR Review |   :white_check_mark:    |      |         |
 
 Examples for invoking the different tools via the CLI:
@@ -135,19 +135,11 @@ There are several ways to use PR-Agent:
 - [Method 5: Run as a GitHub App](INSTALL.md#method-5-run-as-a-github-app)
   - Allowing you to automate the review process on your private or public repositories
 
-## Usage and Tools
-
-**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
 
+The following diagram illustrates PR-Agent tools and their flow:
+
 ![PR-Agent Tools](https://www.codium.ai/wp-content/uploads/2023/07/codiumai-diagram-v4.jpg)
 
 Check out the [PR Compression strategy](./PR_COMPRESSION.md) page for more details on how we convert a code diff to a manageable LLM prompt
@@ -156,29 +148,28 @@ Check out the [PR Compression strategy](./PR_COMPRESSION.md) page for more detai
 
 A reasonable question that can be asked is: `"Why use PR-Agent? What make it stand out from existing tools?"`
 
-Here are some of the reasons why:
+Here are some advantages of PR-Agent:
 
 - 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, GitHub App, Docker, ...).
+- Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the [configuration](./CONFIGURATION.md) file. Adding additional categories is easy and accessible.
+- We support **multiple git providers** (GitHub, Gitlab, Bitbucket), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT-4, GPT-3.5, Anthropic, Cohere, Llama2).
 - We are open-source, and welcome contributions from the community.
 
 
 ## Roadmap
 
-- [ ] Support open-source models, as a replacement for OpenAI models. (Note - a minimal requirement for each open-source model is to have 8k+ context, and good support for generating JSON as an output)
-- [x] Support other Git providers, such as Gitlab and Bitbucket.
-- [ ] Develop additional logic for handling large PRs, and compressing git patches
+- [x] Support additional models, as a replacement for OpenAI (see [here](https://github.com/Codium-ai/pr-agent/pull/172))
+- [ ] Develop additional logic for handling large PRs
 - [ ] Add additional context to the prompt. For example, repo (or relevant files) summarization, with tools such a [ctags](https://github.com/universal-ctags/ctags)
 - [ ] Adding more tools. Possible directions:
   - [x] PR description
   - [x] Inline code suggestions
   - [x] Reflect and review
+  - [x] Rank the PR (see [here](https://github.com/Codium-ai/pr-agent/pull/89))   
   - [ ] Enforcing CONTRIBUTING.md guidelines
   - [ ] Performance (are there any performance issues)
   - [ ] Documentation (is the PR properly documented)
-  - [ ] Rank the PR importance
   - [ ] ...
 
 ## Similar Projects

pr_agent/agent/pr_agent.py

@@ -1,13 +1,18 @@
+import logging
+import os
 import shlex
+import tempfile
 
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import get_git_provider
 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.tools.pr_config import PRConfig
 
 command2class = {
     "answer": PRReviewer,
@@ -22,6 +27,8 @@ command2class = {
     "ask": PRQuestions,
     "ask_question": PRQuestions,
     "update_changelog": PRUpdateChangelog,
+    "config": PRConfig,
+    "settings": PRConfig,
 }
 
 commands = list(command2class.keys())
@@ -31,11 +38,31 @@ class PRAgent:
         pass
 
     async def handle_request(self, pr_url, request) -> bool:
+        # First, apply repo specific settings if exists
+        if get_settings().config.use_repo_settings_file:
+            repo_settings_file = None
+            try:
+                git_provider = get_git_provider()(pr_url)
+                repo_settings = git_provider.get_repo_settings()
+                if repo_settings:
+                    repo_settings_file = None
+                    fd, repo_settings_file = tempfile.mkstemp(suffix='.toml')
+                    os.write(fd, repo_settings)
+                    get_settings().load_file(repo_settings_file)
+            finally:
+                if repo_settings_file:
+                    try:
+                        os.remove(repo_settings_file)
+                    except Exception as e:
+                        logging.error(f"Failed to remove temporary settings file {repo_settings_file}", e)
+
+        # Then, apply user specific settings if exists
         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"

pr_agent/algo/__init__.py

@@ -7,4 +7,8 @@ MAX_TOKENS = {
     'gpt-4': 8000,
     'gpt-4-0613': 8000,
     'gpt-4-32k': 32000,
+    'claude-instant-1': 100000,
+    'claude-2': 100000,
+    'command-nightly': 4096,
+    'replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1': 4096,
 }

pr_agent/algo/ai_handler.py

@@ -1,12 +1,15 @@
 import logging
 
+import litellm
 import openai
+from litellm import acompletion
 from openai.error import APIError, RateLimitError, Timeout, TryAgain
 from retry import retry
 
 from pr_agent.config_loader import get_settings
 
-OPENAI_RETRIES=5
+OPENAI_RETRIES = 5
+
 
 class AiHandler:
     """
@@ -22,15 +25,25 @@ class AiHandler:
         """
         try:
             openai.api_key = get_settings().openai.key
+            litellm.openai_key = get_settings().openai.key
+            self.azure = False
             if get_settings().get("OPENAI.ORG", None):
-                openai.organization = get_settings().openai.org
+                litellm.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().openai.api_type == "azure":
+                    self.azure = True
+                    litellm.azure_key = get_settings().openai.key
             if get_settings().get("OPENAI.API_VERSION", None):
-                openai.api_version = get_settings().openai.api_version
+                litellm.api_version = get_settings().openai.api_version
             if get_settings().get("OPENAI.API_BASE", None):
-                openai.api_base = get_settings().openai.api_base
+                litellm.api_base = get_settings().openai.api_base
+            if get_settings().get("ANTHROPIC.KEY", None):
+                litellm.anthropic_key = get_settings().anthropic.key
+            if get_settings().get("COHERE.KEY", None):
+                litellm.cohere_key = get_settings().cohere.key
+            if get_settings().get("REPLICATE.KEY", None):
+                litellm.replicate_key = get_settings().replicate.key
         except AttributeError as e:
             raise ValueError("OpenAI key is required") from e
 
@@ -57,15 +70,17 @@ class AiHandler:
             TryAgain: If there is an attribute error during OpenAI inference.
         """
         try:
-            response = await openai.ChatCompletion.acreate(
-                            model=model,
-                            deployment_id=self.deployment_id,
-                            messages=[
-                                {"role": "system", "content": system},
-                                {"role": "user", "content": user}
-                            ],
-                            temperature=temperature,
-                        )
+            response = await acompletion(
+                model=model,
+                deployment_id=self.deployment_id,
+                messages=[
+                    {"role": "system", "content": system},
+                    {"role": "user", "content": user}
+                ],
+                temperature=temperature,
+                azure=self.azure,
+                force_timeout=get_settings().config.ai_timeout
+            )
         except (APIError, Timeout, TryAgain) as e:
             logging.error("Error during OpenAI inference: ", e)
             raise
@@ -75,8 +90,9 @@ class AiHandler:
         except (Exception) as e:
             logging.error("Unknown error during OpenAI inference: ", e)
             raise TryAgain from e
-        if response is None or len(response.choices) == 0:
+        if response is None or len(response["choices"]) == 0:
             raise TryAgain
-        resp = response.choices[0]['message']['content']
-        finish_reason = response.choices[0].finish_reason
-        return resp, finish_reason
+        resp = response["choices"][0]['message']['content']
+        finish_reason = response["choices"][0]["finish_reason"]
+        print(resp, finish_reason)
+        return resp, finish_reason

pr_agent/algo/git_patch_processing.py

@@ -41,7 +41,11 @@ def extend_patch(original_file_str, patch_str, num_lines) -> str:
                         extended_patch_lines.extend(
                             original_lines[start1 + size1 - 1:start1 + size1 - 1 + num_lines])
 
-                    start1, size1, start2, size2 = map(int, match.groups()[:4])
+                    try:
+                        start1, size1, start2, size2 = map(int, match.groups()[:4])
+                    except:  # '@@ -0,0 +1 @@' case
+                        start1, size1, size2 = map(int, match.groups()[:3])
+                        start2 = 0
                     section_header = match.groups()[4]
                     extended_start1 = max(1, start1 - num_lines)
                     extended_size1 = size1 + (start1 - extended_start1) + num_lines
@@ -198,7 +202,12 @@ def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
                         patch_with_lines_str += f"{line_old}\n"
                 new_content_lines = []
                 old_content_lines = []
-            start1, size1, start2, size2 = map(int, match.groups()[:4])
+            try:
+                start1, size1, start2, size2 = map(int, match.groups()[:4])
+            except: # '@@ -0,0 +1 @@' case
+                start1, size1, size2 = map(int, match.groups()[:3])
+                start2 = 0
+
         elif line.startswith('+'):
             new_content_lines.append(line)
         elif line.startswith('-'):

pr_agent/algo/pr_processing.py

@@ -1,7 +1,10 @@
 from __future__ import annotations
 
+import difflib
 import logging
-from typing import Callable, Tuple
+import re
+import traceback
+from typing import Any, Callable, List, Tuple
 
 from github import RateLimitExceededException
 
@@ -9,9 +12,8 @@ from pr_agent.algo import MAX_TOKENS
 from pr_agent.algo.git_patch_processing import convert_to_hunks_with_lines_numbers, extend_patch, handle_patch_deletions
 from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import load_large_diff
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers.git_provider import GitProvider
+from pr_agent.git_providers.git_provider import FilePatchInfo, GitProvider
 
 DELETED_FILES_ = "Deleted files:\n"
 
@@ -46,7 +48,7 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: s
         PATCH_EXTRA_LINES = 0
 
     try:
-        diff_files = list(git_provider.get_diff_files())
+        diff_files = git_provider.get_diff_files()
     except RateLimitExceededException as e:
         logging.error(f"Rate limit exceeded for git provider API. original message {e}")
         raise
@@ -98,12 +100,7 @@ def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
     for lang in pr_languages:
         for file in lang['files']:
             original_file_content_str = file.base_file
-            new_file_content_str = file.head_file
             patch = file.patch
-
-            # handle the case of large patch, that initially was not loaded
-            patch = load_large_diff(file, new_file_content_str, original_file_content_str, patch)
-
             if not patch:
                 continue
 
@@ -161,7 +158,6 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
         original_file_content_str = file.base_file
         new_file_content_str = file.head_file
         patch = file.patch
-        patch = load_large_diff(file, new_file_content_str, original_file_content_str, patch)
         if not patch:
             continue
 
@@ -221,6 +217,70 @@ async def retry_with_fallback_models(f: Callable):
         try:
             return await f(model)
         except Exception as e:
-            logging.warning(f"Failed to generate prediction with {model}: {e}")
+            logging.warning(f"Failed to generate prediction with {model}: {traceback.format_exc()}")
             if i == len(all_models) - 1:  # If it's the last iteration
                 raise  # Re-raise the last exception
+
+
+def find_line_number_of_relevant_line_in_file(diff_files: List[FilePatchInfo],
+                                              relevant_file: str,
+                                              relevant_line_in_file: str) -> Tuple[int, int]:
+    """
+    Find the line number and absolute position of a relevant line in a file.
+
+    Args:
+        diff_files (List[FilePatchInfo]): A list of FilePatchInfo objects representing the patches of files.
+        relevant_file (str): The name of the file where the relevant line is located.
+        relevant_line_in_file (str): The content of the relevant line.
+
+    Returns:
+        Tuple[int, int]: A tuple containing the line number and absolute position of the relevant line in the file.
+    """
+    position = -1
+    absolute_position = -1
+    re_hunk_header = re.compile(
+        r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
+
+    for file in diff_files:
+        if file.filename.strip() == relevant_file:
+            patch = file.patch
+            patch_lines = patch.splitlines()
+
+            # try to find the line in the patch using difflib, with some margin of error
+            matches_difflib: list[str | Any] = difflib.get_close_matches(relevant_line_in_file,
+                                                                         patch_lines, n=3, cutoff=0.93)
+            if len(matches_difflib) == 1 and matches_difflib[0].startswith('+'):
+                relevant_line_in_file = matches_difflib[0]
+
+            delta = 0
+            start1, size1, start2, size2 = 0, 0, 0, 0
+            for i, line in enumerate(patch_lines):
+                if line.startswith('@@'):
+                    delta = 0
+                    match = re_hunk_header.match(line)
+                    start1, size1, start2, size2 = map(int, match.groups()[:4])
+                elif not line.startswith('-'):
+                    delta += 1
+
+                if relevant_line_in_file in line and line[0] != '-':
+                    position = i
+                    absolute_position = start2 + delta - 1
+                    break
+
+            if position == -1 and relevant_line_in_file[0] == '+':
+                no_plus_line = relevant_line_in_file[1:].lstrip()
+                for i, line in enumerate(patch_lines):
+                    if line.startswith('@@'):
+                        delta = 0
+                        match = re_hunk_header.match(line)
+                        start1, size1, start2, size2 = map(int, match.groups()[:4])
+                    elif not line.startswith('-'):
+                        delta += 1
+
+                    if no_plus_line in line and line[0] != '-':
+                        # The model might add a '+' to the beginning of the relevant_line_in_file even if originally
+                        # it's a context line
+                        position = i
+                        absolute_position = start2 + delta - 1
+                        break
+    return position, absolute_position

pr_agent/algo/token_handler.py

@@ -1,5 +1,5 @@
 from jinja2 import Environment, StrictUndefined
-from tiktoken import encoding_for_model
+from tiktoken import encoding_for_model, get_encoding
 
 from pr_agent.config_loader import get_settings
 
@@ -27,7 +27,7 @@ class TokenHandler:
         - system: The system string.
         - user: The user string.
         """
-        self.encoder = encoding_for_model(get_settings().config.model)
+        self.encoder = encoding_for_model(get_settings().config.model) if "gpt" in get_settings().config.model else get_encoding("cl100k_base")
         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):
@@ -47,7 +47,6 @@ class TokenHandler:
         environment = Environment(undefined=StrictUndefined)
         system_prompt = environment.from_string(system).render(vars)
         user_prompt = environment.from_string(user).render(vars)
-
         system_prompt_tokens = len(encoder.encode(system_prompt))
         user_prompt_tokens = len(encoder.encode(user_prompt))
         return system_prompt_tokens + user_prompt_tokens

pr_agent/algo/utils.py

@@ -40,7 +40,7 @@ def convert_to_markdown(output_data: dict) -> str:
         "Security concerns": "🔒",
         "General PR suggestions": "💡",
         "Insights from user's answers": "📝",
-        "Code suggestions": "🤖",
+        "Code feedback": "🤖",
     }
 
     for key, value in output_data.items():
@@ -50,12 +50,12 @@ def convert_to_markdown(output_data: dict) -> str:
             markdown_text += f"## {key}\n\n"
             markdown_text += convert_to_markdown(value)
         elif isinstance(value, list):
-            if key.lower() == 'code suggestions':
+            if key.lower() == 'code feedback':
                 markdown_text += "\n"  # just looks nicer with additional line breaks
             emoji = emojis.get(key, "")
             markdown_text += f"- {emoji} **{key}:**\n\n"
             for item in value:
-                if isinstance(item, dict) and key.lower() == 'code suggestions':
+                if isinstance(item, dict) and key.lower() == 'code feedback':
                     markdown_text += parse_code_suggestion(item)
                 elif item:
                     markdown_text += f"  - {item}\n"
@@ -100,7 +100,7 @@ def try_fix_json(review, max_iter=10, code_suggestions=False):
     Args:
     - review: A string containing the JSON message to be fixed.
     - max_iter: An integer representing the maximum number of iterations to try and fix the JSON message.
-    - code_suggestions: A boolean indicating whether to try and fix JSON messages with code suggestions.
+    - code_suggestions: A boolean indicating whether to try and fix JSON messages with code feedback.
 
     Returns:
     - data: A dictionary containing the parsed JSON data.
@@ -108,7 +108,7 @@ def try_fix_json(review, max_iter=10, code_suggestions=False):
     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
+    If code_suggestions is True and the JSON message contains code feedback, 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.
@@ -128,7 +128,8 @@ def try_fix_json(review, max_iter=10, code_suggestions=False):
     else:
         closing_bracket = "]}}"
 
-    if review.rfind("'Code suggestions': [") > 0 or review.rfind('"Code suggestions": [') > 0:
+    if (review.rfind("'Code feedback': [") > 0 or review.rfind('"Code feedback": [') > 0) or \
+            (review.rfind("'Code suggestions': [") > 0 or review.rfind('"Code suggestions": [') > 0) :
         last_code_suggestion_ind = [m.end() for m in re.finditer(r"\}\s*,", review)][-1] - 1
         valid_json = False
         iter_count = 0
@@ -195,38 +196,30 @@ def convert_str_to_datetime(date_str):
     return datetime.strptime(date_str, datetime_format)
 
 
-def load_large_diff(file, new_file_content_str: str, original_file_content_str: str, patch: str) -> str:
+def load_large_diff(filename, new_file_content_str: str, original_file_content_str: str) -> str:
     """
     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.
         new_file_content_str: The new content of the file as a string.
         original_file_content_str: The original content of the file as a string.
-        patch: An optional patch string that can be provided as input.
 
     Returns:
         The generated or provided patch string.
 
     Raises:
         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 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 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
+    patch = ""
+    try:
+        diff = difflib.unified_diff(original_file_content_str.splitlines(keepends=True),
+                                    new_file_content_str.splitlines(keepends=True))
+        if get_settings().config.verbosity_level >= 2:
+            logging.warning(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
+        patch = ''.join(diff)
+    except Exception:
+        pass
     return patch
 
 

pr_agent/git_providers/github_provider.py

@@ -1,4 +1,6 @@
 import logging
+import hashlib
+
 from datetime import datetime
 from typing import Optional, Tuple
 from urllib.parse import urlparse
@@ -7,11 +9,12 @@ from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
 from starlette_context import context
 
+from .git_provider import FilePatchInfo, GitProvider, IncrementalPR
 from ..algo.language_handler import is_valid_file
 from ..algo.utils import load_large_diff
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
 from ..servers.utils import RateLimitExceeded
-from .git_provider import FilePatchInfo, GitProvider, IncrementalPR
 
 
 class GithubProvider(GitProvider):
@@ -27,6 +30,7 @@ class GithubProvider(GitProvider):
         self.pr = None
         self.github_user_id = None
         self.diff_files = None
+        self.git_files = None
         self.incremental = incremental
         if pr_url:
             self.set_pr(pr_url)
@@ -81,40 +85,56 @@ class GithubProvider(GitProvider):
     def get_files(self):
         if self.incremental.is_incremental and self.file_set:
             return self.file_set.values()
-        return self.pr.get_files()
+        if not self.git_files:
+            # bring files from GitHub only once
+            self.git_files = self.pr.get_files()
+        return self.git_files
 
     @retry(exceptions=RateLimitExceeded,
            tries=get_settings().github.ratelimit_retries, delay=2, backoff=2, jitter=(1, 3))
     def get_diff_files(self) -> list[FilePatchInfo]:
+        """
+        Retrieves the list of files that have been modified, added, deleted, or renamed in a pull request in GitHub,
+        along with their content and patch information.
+
+        Returns:
+            diff_files (List[FilePatchInfo]): List of FilePatchInfo objects representing the modified, added, deleted,
+            or renamed files in the merge request.
+        """
         try:
+            if self.diff_files:
+                return self.diff_files
+
             files = self.get_files()
             diff_files = []
-            for file in files:
-                if is_valid_file(file.filename):
-                    new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)
-                    patch = file.patch
-                    if self.incremental.is_incremental and self.file_set:
-                        original_file_content_str = self._get_pr_file_content(file,
-                                                                              self.incremental.last_seen_commit_sha)
-                        patch = load_large_diff(file,
-                                                new_file_content_str,
-                                                original_file_content_str,
-                                                None)
-                        self.file_set[file.filename] = patch
-                    else:
-                        original_file_content_str = self._get_pr_file_content(file, self.pr.base.sha)
 
-                    diff_files.append(
-                        FilePatchInfo(original_file_content_str, new_file_content_str, patch, file.filename))
+            for file in files:
+                if not is_valid_file(file.filename):
+                    continue
+
+                new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)  # communication with GitHub
+                patch = file.patch
+
+                if self.incremental.is_incremental and self.file_set:
+                    original_file_content_str = self._get_pr_file_content(file, self.incremental.last_seen_commit_sha)
+                    patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
+                    self.file_set[file.filename] = patch
+                else:
+                    original_file_content_str = self._get_pr_file_content(file, self.pr.base.sha)
+                    if not patch:
+                        patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
+
+                diff_files.append(FilePatchInfo(original_file_content_str, new_file_content_str, patch, file.filename))
+
             self.diff_files = diff_files
             return diff_files
+
         except GithubException.RateLimitExceededException as e:
             logging.error(f"Rate limit exceeded for GitHub API. Original message: {e}")
             raise RateLimitExceeded("Rate limit exceeded for GitHub API.") from e
 
     def publish_description(self, pr_title: str, pr_body: str):
         self.pr.edit(title=pr_title, body=pr_body)
-        # self.pr.create_issue_comment(pr_comment)
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         if is_temporary and not get_settings().config.publish_output_progress:
@@ -131,22 +151,9 @@ class GithubProvider(GitProvider):
     def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
         self.publish_inline_comments([self.create_inline_comment(body, relevant_file, relevant_line_in_file)])
 
+
     def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
-        self.diff_files = self.diff_files if self.diff_files else self.get_diff_files()
-        position = -1
-        for file in self.diff_files:
-            if file.filename.strip() == relevant_file:
-                patch = file.patch
-                patch_lines = patch.splitlines()
-                for i, line in enumerate(patch_lines):
-                    if relevant_line_in_file in line:
-                        position = i
-                        break
-                    elif relevant_line_in_file[0] == '+' and relevant_line_in_file[1:].lstrip() in line:
-                        # The model often adds a '+' to the beginning of the relevant_line_in_file even if originally
-                        # it's a context line
-                        position = i
-                        break
+        position = find_line_number_of_relevant_line_in_file(self.diff_files, relevant_file.strip('`'), relevant_line_in_file)
         if position == -1:
             if get_settings().config.verbosity_level >= 2:
                 logging.info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
@@ -154,8 +161,6 @@ class GithubProvider(GitProvider):
         else:
             subject_type = "LINE"
         path = relevant_file.strip()
-        # placeholder for future API support (already supported in single inline comment)
-        # return dict(body=body, path=path, position=position, subject_type=subject_type)
         return dict(body=body, path=path, position=position) if subject_type == "LINE" else {}
 
     def publish_inline_comments(self, comments: list[dict]):
@@ -251,6 +256,13 @@ class GithubProvider(GitProvider):
     def get_issue_comments(self):
         return self.pr.get_issue_comments()
 
+    def get_repo_settings(self):
+        try:
+            contents = self.repo_obj.get_contents(".pr_agent.toml", ref=self.pr.head.sha).decoded_content
+            return contents
+        except Exception:
+            return ""
+
     @staticmethod
     def _parse_pr_url(pr_url: str) -> Tuple[str, int]:
         parsed_url = urlparse(pr_url)
@@ -360,3 +372,25 @@ class GithubProvider(GitProvider):
         except:
             commit_messages_str = ""
         return commit_messages_str
+
+    def generate_link_to_relevant_line_number(self, suggestion) -> str:
+        try:
+            relevant_file = suggestion['relevant file']
+            relevant_line_str = suggestion['relevant line']
+            position, absolute_position = find_line_number_of_relevant_line_in_file \
+                (self.diff_files, relevant_file.strip('`'), relevant_line_str)
+
+            if absolute_position != -1:
+                # # link to right file only
+                # link = f"https://github.com/{self.repo}/blob/{self.pr.head.sha}/{relevant_file}" \
+                #        + "#" + f"L{absolute_position}"
+
+                # link to diff
+                sha_file = hashlib.sha256(relevant_file.encode('utf-8')).hexdigest()
+                link = f"https://github.com/{self.repo}/pull/{self.pr_num}/files#diff-{sha_file}R{absolute_position}"
+                return link
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                logging.info(f"Failed adding line link, error: {e}")
+
+        return ""

pr_agent/git_providers/gitlab_provider.py

@@ -7,6 +7,7 @@ import gitlab
 from gitlab import GitlabGetError
 
 from ..algo.language_handler import is_valid_file
+from ..algo.utils import load_large_diff
 from ..config_loader import get_settings
 from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
 
@@ -30,6 +31,7 @@ class GitLabProvider(GitProvider):
         self.id_mr = None
         self.mr = None
         self.diff_files = None
+        self.git_files = None
         self.temp_comments = []
         self._set_merge_request(merge_request_url)
         self.RE_HUNK_HEADER = re.compile(
@@ -65,19 +67,27 @@ class GitLabProvider(GitProvider):
             return ''
 
     def get_diff_files(self) -> list[FilePatchInfo]:
+        """
+        Retrieves the list of files that have been modified, added, deleted, or renamed in a pull request in GitLab,
+        along with their content and patch information.
+
+        Returns:
+            diff_files (List[FilePatchInfo]): List of FilePatchInfo objects representing the modified, added, deleted,
+            or renamed files in the merge request.
+        """
+
+        if self.diff_files:
+            return self.diff_files
+
         diffs = self.mr.changes()['changes']
         diff_files = []
         for diff in diffs:
             if is_valid_file(diff['new_path']):
-                original_file_content_str = self._get_pr_file_content(diff['old_path'], self.mr.target_branch)
-                new_file_content_str = self._get_pr_file_content(diff['new_path'], self.mr.source_branch)
-                edit_type = EDIT_TYPE.MODIFIED
-                if diff['new_file']:
-                    edit_type = EDIT_TYPE.ADDED
-                elif diff['deleted_file']:
-                    edit_type = EDIT_TYPE.DELETED
-                elif diff['renamed_file']:
-                    edit_type = EDIT_TYPE.RENAMED
+                # original_file_content_str = self._get_pr_file_content(diff['old_path'], self.mr.target_branch)
+                # new_file_content_str = self._get_pr_file_content(diff['new_path'], self.mr.source_branch)
+                original_file_content_str = self._get_pr_file_content(diff['old_path'], self.mr.diff_refs['base_sha'])
+                new_file_content_str = self._get_pr_file_content(diff['new_path'], self.mr.diff_refs['head_sha'])
+
                 try:
                     if isinstance(original_file_content_str, bytes):
                         original_file_content_str = bytes.decode(original_file_content_str, 'utf-8')
@@ -86,15 +96,33 @@ class GitLabProvider(GitProvider):
                 except UnicodeDecodeError:
                     logging.warning(
                         f"Cannot decode file {diff['old_path']} or {diff['new_path']} in merge request {self.id_mr}")
+
+                edit_type = EDIT_TYPE.MODIFIED
+                if diff['new_file']:
+                    edit_type = EDIT_TYPE.ADDED
+                elif diff['deleted_file']:
+                    edit_type = EDIT_TYPE.DELETED
+                elif diff['renamed_file']:
+                    edit_type = EDIT_TYPE.RENAMED
+
+                filename = diff['new_path']
+                patch = diff['diff']
+                if not patch:
+                    patch = load_large_diff(filename, new_file_content_str, original_file_content_str)
+
                 diff_files.append(
-                    FilePatchInfo(original_file_content_str, new_file_content_str, diff['diff'], diff['new_path'],
+                    FilePatchInfo(original_file_content_str, new_file_content_str,
+                                  patch=patch,
+                                  filename=filename,
                                   edit_type=edit_type,
                                   old_filename=None if diff['old_path'] == diff['new_path'] else diff['old_path']))
         self.diff_files = diff_files
         return diff_files
 
     def get_files(self):
-        return [change['new_path'] for change in self.mr.changes()['changes']]
+        if not self.git_files:
+            self.git_files = [change['new_path'] for change in self.mr.changes()['changes']]
+        return self.git_files
 
     def publish_description(self, pr_title: str, pr_body: str):
         try:
@@ -110,7 +138,6 @@ class GitLabProvider(GitProvider):
             self.temp_comments.append(comment)
 
     def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
-        self.diff_files = self.diff_files if self.diff_files else self.get_diff_files()
         edit_type, found, source_line_no, target_file, target_line_no = self.search_line(relevant_file,
                                                                                          relevant_line_in_file)
         self.send_inline_comment(body, edit_type, found, relevant_file, relevant_line_in_file, source_line_no,
@@ -151,9 +178,9 @@ class GitLabProvider(GitProvider):
                 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()
+                diff_files = self.get_diff_files()
                 target_file = None
-                for file in self.diff_files:
+                for file in diff_files:
                     if file.filename == relevant_file:
                         if file.filename == relevant_file:
                             target_file = file
@@ -180,7 +207,7 @@ class GitLabProvider(GitProvider):
         target_file = None
 
         edit_type = self.get_edit_type(relevant_line_in_file)
-        for file in self.diff_files:
+        for file in self.get_diff_files():
             if file.filename == relevant_file:
                 edit_type, found, source_line_no, target_file, target_line_no = self.find_in_file(file,
                                                                                                   relevant_line_in_file)
@@ -253,6 +280,13 @@ class GitLabProvider(GitProvider):
     def get_issue_comments(self):
         raise NotImplementedError("GitLab provider does not support issue comments yet")
 
+    def get_repo_settings(self):
+        try:
+            contents = self.gl.projects.get(self.id_project).files.get(file_path='.pr_agent.toml', ref=self.mr.source_branch)
+            return contents
+        except Exception:
+            return ""
+
     def _parse_merge_request_url(self, merge_request_url: str) -> Tuple[str, int]:
         parsed_url = urlparse(merge_request_url)
 
@@ -310,4 +344,4 @@ class GitLabProvider(GitProvider):
             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
+        return commit_messages_str

pr_agent/servers/help.py

@@ -4,7 +4,8 @@ commands_text = "> **/review [-i]**: Request a review of your Pull Request. For
                 "> **/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: ...\" " \
+                ">For example: /review --pr_reviewer.extra_instructions=\"focus on the file: ...\" \n" \
+                ">To list the possible configuration parameters, use the **/config** command.\n" \
 
 
 def bot_help_text(user: str):

pr_agent/settings/.secrets_template.toml

@@ -7,17 +7,26 @@
 # See README for details about GitHub App deployment.
 
 [openai]
-key = "<API_KEY>"  # Acquire through https://platform.openai.com
-org = "<ORGANIZATION>"  # Optional, may be commented out.
+key = ""  # Acquire through https://platform.openai.com
+#org = "<ORGANIZATION>"  # Optional, may be commented out.
 # Uncomment the following for Azure OpenAI
 #api_type = "azure"
 #api_version = '2023-05-15'  # Check Azure documentation for the current API version
-#api_base = "<API_BASE>"  # The base URL for your Azure OpenAI resource. e.g. "https://<your resource name>.openai.azure.com"
-#deployment_id = "<DEPLOYMENT_ID>"  # The deployment name you chose when you deployed the engine
+#api_base = ""  # The base URL for your Azure OpenAI resource. e.g. "https://<your resource name>.openai.azure.com"
+#deployment_id = ""  # The deployment name you chose when you deployed the engine
 
+[anthropic]
+key = "" # Optional, uncomment if you want to use Anthropic. Acquire through https://www.anthropic.com/
+
+[cohere]
+key = "" # Optional, uncomment if you want to use Cohere. Acquire through https://dashboard.cohere.ai/
+
+[replicate]
+key = "" # Optional, uncomment if you want to use Replicate. Acquire through https://replicate.com/
 [github]
 # ---- Set the following only for deployment type == "user"
-user_token = "<TOKEN>"  # A GitHub personal access token with 'repo' scope.
+user_token = ""  # A GitHub personal access token with 'repo' scope.
+deployment_type = "user" #set to user by default 
 
 # ---- Set the following only for deployment type == "app", see README for details.
 private_key = """\

pr_agent/settings/configuration.toml

@@ -6,14 +6,16 @@ publish_output=true
 publish_output_progress=true
 verbosity_level=0 # 0,1,2
 use_extra_bad_extensions=false
+use_repo_settings_file=true
+ai_timeout=180
 
 [pr_reviewer] # /review #
 require_focused_review=true
 require_score_review=false
 require_tests_review=true
 require_security_review=true
-num_code_suggestions=0
-inline_code_comments = true
+num_code_suggestions=3
+inline_code_comments = false
 ask_and_reflect=false
 extra_instructions = ""
 
@@ -31,6 +33,8 @@ extra_instructions = ""
 push_changelog_changes=false
 extra_instructions = ""
 
+[pr_config] # /config #
+
 [github]
 # The type of deployment to create. Valid values are 'app' or 'user'.
 deployment_type = "user"

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -73,6 +73,11 @@ Description: '{{description}}'
 {%- if language %}
 Main language: {{language}}
 {%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
 
 
 The PR Diff:

pr_agent/settings/pr_information_from_user_prompts.toml

@@ -21,6 +21,11 @@ Description: '{{description}}'
 {%- if language %}
 Main language: {{language}}
 {%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
 
 
 The PR Git Diff:

pr_agent/settings/pr_questions_prompts.toml

@@ -13,6 +13,11 @@ Description: '{{description}}'
 {%- 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

@@ -1,9 +1,9 @@
 [pr_review_prompt]
 system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
 Your task is to provide constructive and concise feedback for the PR, and also provide meaningfull code suggestions to improve the new PR code (the '+' lines).
-- Provide up to {{ num_code_suggestions }} code suggestions.
 {%- if num_code_suggestions > 0 %}
-- Try to focus on important suggestions like fixing code problems, issues and bugs. As a second priority, provide suggestions for meaningfull code improvements, like performance, vulnerability, modularity, and best practices.
+- Provide up to {{ num_code_suggestions }} code suggestions.
+- Try to focus on the most important suggestions, like fixing code problems, issues and bugs. As a second priority, provide suggestions for meaningfull code improvements, like performance, vulnerability, modularity, and best practices.
 - Suggestions should focus on improving the new added code lines.
 - Make sure not to provide suggestions repeating modifications already implemented in the new PR code (the '+' lines).
 {%- endif %}
@@ -24,7 +24,7 @@ You must use the following JSON schema to format your answer:
     },
     "Type of PR": {
       "type": "string",
-      "enum": ["Bug fix", "Tests", "Bug fix with tests", "Refactoring", "Enhancement", "Documentation", "Other"]
+      "enum": ["Bug fix", "Tests", "Refactoring", "Enhancement", "Documentation", "Other"]
     },
 {%- if require_score %}
     "Score": {
@@ -47,17 +47,17 @@ You must use the following JSON schema to format your answer:
 {%- if require_focused %}
     "Focused PR": {
       "type": "string",
-      "description": "Is this a focused PR, in the sense that it has a clear and coherent title and description, and all PR code diff changes are properly derived from the title and description? Explain your response."
+      "description": "Is this a focused PR, in the sense that all the PR code diff changes are united under a single focused theme ? If the theme is too broad, or the PR code diff changes are too scattered, then the PR is not focused. Explain your answer shortly."
     }
   },
 {%- endif %}
   "PR Feedback": {
-    "General PR suggestions": {
+    "General suggestions": {
       "type": "string",
-      "description": "General suggestions and feedback for the contributors and maintainers of this PR. May include important suggestions for the overall structure, primary purpose, best practices, critical bugs, and other aspects of the PR. Explain your suggestions."
+      "description": "General suggestions and feedback for the contributors and maintainers of this PR. May include important suggestions for the overall structure, primary purpose, best practices, critical bugs, and other aspects of the PR. Don't address PR title and description, or lack of tests. Explain your suggestions."
     },
 {%- if num_code_suggestions > 0 %}
-    "Code suggestions": {
+    "Code feedback": {
       "type": "array",
       "maxItems": {{ num_code_suggestions }},
       "uniqueItems": true,
@@ -66,13 +66,13 @@ You must use the following JSON schema to format your answer:
           "type": "string",
           "description": "the relevant file full path"
         },
-        "suggestion content": {
+        "suggestion": {
           "type": "string",
           "description": "a concrete suggestion for meaningfully improving the new PR code. Also describe how, specifically, the suggestion can be applied to new PR code. Add tags with importance measure that matches each suggestion ('important' or 'medium'). Do not make suggestions for updating or adding docstrings, renaming PR title and description, or linter like.
         },
-        "relevant line in file": {
+        "relevant line": {
           "type": "string",
-          "description": "an authentic single code line from the PR git diff section, to which the suggestion applies."
+          "description": "a single code line taken from the relevant file, to which the suggestion applies. The line should be a '+' line. Make sure to output the line exactly as it appears in the relevant file"
         }
       }
     },
@@ -80,8 +80,8 @@ You must use the following JSON schema to format your answer:
 {%- if require_security %}
     "Security concerns": {
       "type": "string",
-      "description": "yes\\no question: does this PR code introduce possible security concerns or issues, like SQL injection, XSS, CSRF, and others ? explain your answer"
-       ? explain your answer"
+      "description": "yes\\no question: does this PR code introduce possible security concerns or issues, like SQL injection, XSS, CSRF, and others ? If answered 'yes', explain your answer shortly"
+       ? explain your answer shortly"
     }
 {%- endif %}
   }
@@ -109,11 +109,11 @@ Example output:
     {
         "General PR suggestions": "..., `xxx`...",
 {%- if num_code_suggestions > 0 %}
-        "Code suggestions": [
+        "Code feedback": [
             {
                 "relevant file": "directory/xxx.py",
-                "suggestion content": "xxx [important]",
-                "relevant line in file": "xxx",
+                "suggestion": "xxx [important]",
+                "relevant line": "xxx",
             },
             ...
         ]
@@ -135,6 +135,11 @@ Description: '{{description}}'
 {%- if language %}
 Main language: {{language}}
 {%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
 
 {%- if question_str %}
 ######

pr_agent/settings/pr_update_changelog_prompts.toml

@@ -19,6 +19,11 @@ Description: '{{description}}'
 {%- if language %}
 Main language: {{language}}
 {%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
 
 
 The PR Diff:

pr_agent/tools/pr_code_suggestions.py

@@ -34,6 +34,7 @@ class PRCodeSuggestions:
             "diff": "",  # empty diff for initial calculation
             "num_code_suggestions": get_settings().pr_code_suggestions.num_code_suggestions,
             "extra_instructions": get_settings().pr_code_suggestions.extra_instructions,
+            "commit_messages_str": self.git_provider.get_commit_messages(),
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,
@@ -57,12 +58,12 @@ class PRCodeSuggestions:
 
     async def _prepare_prediction(self, model: str):
         logging.info('Getting PR diff...')
-        # we are using extended hunk with line numbers for code suggestions
         self.patches_diff = get_pr_diff(self.git_provider,
                                         self.token_handler,
                                         model,
                                         add_line_numbers_to_hunks=True,
                                         disable_extra_lines=True)
+
         logging.info('Getting AI prediction...')
         self.prediction = await self._get_prediction(model)
 

pr_agent/tools/pr_config.py

@@ -0,0 +1,48 @@
+import logging
+
+from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import get_git_provider
+
+
+class PRConfig:
+    """
+    The PRConfig class is responsible for listing all configuration options available for the user.
+    """
+    def __init__(self, pr_url: str, args=None):
+        """
+        Initialize the PRConfig object with the necessary attributes and objects to comment on a pull request.
+
+        Args:
+            pr_url (str): The URL of the pull request to be reviewed.
+            args (list, optional): List of arguments passed to the PRReviewer class. Defaults to None.
+        """
+        self.git_provider = get_git_provider()(pr_url)
+
+    async def run(self):
+        logging.info('Getting configuration settings...')
+        logging.info('Preparing configs...')
+        pr_comment = self._prepare_pr_configs()
+        if get_settings().config.publish_output:
+            logging.info('Pushing configs...')
+            self.git_provider.publish_comment(pr_comment)
+            self.git_provider.remove_initial_comment()
+        return ""
+
+    def _prepare_pr_configs(self) -> str:
+        import tomli
+        with open(get_settings().find_file("configuration.toml"), "rb") as conf_file:
+            configuration_headers = [header.lower() for header in tomli.load(conf_file).keys()]
+        relevant_configs = {
+            header: configs for header, configs in get_settings().to_dict().items()
+            if header.lower().startswith("pr_") and header.lower() in configuration_headers
+        }
+        comment_str = "Possible Configurations:"
+        for header, configs in relevant_configs.items():
+            if configs:
+                comment_str += "\n"
+            for key, value in configs.items():
+                comment_str += f"\n{header.lower()}.{key.lower()} = {repr(value) if isinstance(value, str) else value}"
+                comment_str += "  "
+        if get_settings().config.verbosity_level >= 2:
+            logging.info(f"comment_str:\n{comment_str}")
+        return comment_str

pr_agent/tools/pr_description.py

@@ -27,7 +27,6 @@ class PRDescription:
         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()
@@ -40,7 +39,7 @@ class PRDescription:
             "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
+            "commit_messages_str": self.git_provider.get_commit_messages()
         }
     
         # Initialize the token handler

pr_agent/tools/pr_information_from_user.py

@@ -24,6 +24,7 @@ class PRInformationFromUser:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_pr_language,
             "diff": "",  # empty diff for initial calculation
+            "commit_messages_str": self.git_provider.get_commit_messages(),
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,

pr_agent/tools/pr_questions.py

@@ -27,6 +27,7 @@ class PRQuestions:
             "language": self.main_pr_language,
             "diff": "",  # empty diff for initial calculation
             "questions": self.question_str,
+            "commit_messages_str": self.git_provider.get_commit_messages(),
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,

pr_agent/tools/pr_reviewer.py

@@ -7,7 +7,8 @@ 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.pr_processing import get_pr_diff, retry_with_fallback_models, \
+    find_line_number_of_relevant_line_in_file
 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 get_settings
@@ -59,6 +60,7 @@ class PRReviewer:
             'question_str': question_str,
             'answer_str': answer_str,
             "extra_instructions": get_settings().pr_reviewer.extra_instructions,
+            "commit_messages_str": self.git_provider.get_commit_messages(),
         }
 
         self.token_handler = TokenHandler(
@@ -159,27 +161,38 @@ class PRReviewer:
         the feedback.
         """
         review = self.prediction.strip()
-    
+
         try:
             data = json.loads(review)
         except json.decoder.JSONDecodeError:
             data = try_fix_json(review)
 
         # Move 'Security concerns' key to 'PR Analysis' section for better display
-        if 'PR Feedback' in data and 'Security concerns' in data['PR Feedback']:
-            val = data['PR Feedback']['Security concerns']
-            del data['PR Feedback']['Security concerns']
-            data['PR Analysis']['Security concerns'] = val
+        pr_feedback = data.get('PR Feedback', {})
+        security_concerns = pr_feedback.get('Security concerns')
+        if security_concerns:
+            del pr_feedback['Security concerns']
+            data.setdefault('PR Analysis', {})['Security concerns'] = security_concerns
 
-        # Filter out code suggestions that can be submitted as inline comments
-        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'))
-            ]
-            if not data['PR Feedback']['Code suggestions']:
-                del data['PR Feedback']['Code suggestions']
+        #
+        if 'Code feedback' in pr_feedback:
+            code_feedback = pr_feedback['Code feedback']
+
+            # Filter out code suggestions that can be submitted as inline comments
+            if get_settings().pr_reviewer.inline_code_comments:
+                del pr_feedback['Code feedback']
+            else:
+                for suggestion in code_feedback:
+                    relevant_line_str = suggestion['relevant line'].split('\n')[0]
+
+                    # removing '+'
+                    suggestion['relevant line'] = relevant_line_str.lstrip('+').strip()
+
+                    # try to add line numbers link to code suggestions
+                    if hasattr(self.git_provider, 'generate_link_to_relevant_line_number'):
+                        link = self.git_provider.generate_link_to_relevant_line_number(suggestion)
+                        if link:
+                            suggestion['relevant line'] = f"[{suggestion['relevant line']}]({link})"
 
         # Add incremental review section
         if self.incremental.is_incremental:
@@ -204,7 +217,10 @@ class PRReviewer:
         # Log markdown response if verbosity level is high
         if get_settings().config.verbosity_level >= 2:
             logging.info(f"Markdown response:\n{markdown_text}")
-    
+
+        if markdown_text == None or len(markdown_text) == 0:
+            markdown_text = review
+
         return markdown_text
 
     def _publish_inline_code_comments(self) -> None:
@@ -221,10 +237,10 @@ class PRReviewer:
             data = try_fix_json(review)
 
         comments: List[str] = []
-        for suggestion in data.get('PR Feedback', {}).get('Code suggestions', []):
+        for suggestion in data.get('PR Feedback', {}).get('Code feedback', []):
             relevant_file = suggestion.get('relevant file', '').strip()
-            relevant_line_in_file = suggestion.get('relevant line in file', '').strip()
-            content = suggestion.get('suggestion content', '')
+            relevant_line_in_file = suggestion.get('relevant line', '').strip()
+            content = suggestion.get('suggestion', '')
             if not relevant_file or not relevant_line_in_file or not content:
                 logging.info("Skipping inline comment with missing file/line/content")
                 continue

pr_agent/tools/pr_update_changelog.py

@@ -38,6 +38,7 @@ class PRUpdateChangelog:
             "changelog_file_str": self.changelog_file_str,
             "today": date.today(),
             "extra_instructions": get_settings().pr_update_changelog.extra_instructions,
+            "commit_messages_str": self.git_provider.get_commit_messages(),
         }
         self.token_handler = TokenHandler(self.git_provider.pr,
                                           self.vars,

pyproject.toml

@@ -41,7 +41,8 @@ dependencies = [
   "aiohttp~=3.8.4",
   "atlassian-python-api==3.39.0",
   "GitPython~=3.1.32",
-  "starlette-context==0.3.6"
+  "starlette-context==0.3.6",
+  "litellm~=0.1.351"
 ]
 
 [project.urls]

requirements.txt

@@ -1 +1,14 @@
--e .
+dynaconf==3.1.12
+fastapi==0.99.0
+PyGithub==1.59.*
+retry==0.9.2
+openai==0.27.8
+Jinja2==3.1.2
+tiktoken==0.4.0
+uvicorn==0.22.0
+python-gitlab==3.15.0
+pytest~=7.4.0
+aiohttp~=3.8.4
+atlassian-python-api==3.39.0
+GitPython~=3.1.32
+litellm~=0.1.351

tests/unittest/test_convert_to_markdown.py

@@ -51,7 +51,7 @@ class TestConvertToMarkdown:
             'Unrelated changes': 'n/a',  # won't be included in the output
             'Focused PR': 'Yes',
             'General PR suggestions': 'general suggestion...',
-            'Code suggestions': [
+            'Code feedback': [
                 {
                     'Code example': {
                         'Before': 'Code before',
@@ -73,7 +73,7 @@ class TestConvertToMarkdown:
 - ✨ **Focused PR:** Yes
 - 💡 **General PR suggestions:** general suggestion...
 
-- 🤖 **Code suggestions:**
+- 🤖 **Code feedback:**
 
   - **Code example:**
     - **Before:**

tests/unittest/test_find_line_number_of_relevant_line_in_file.py

@@ -0,0 +1,68 @@
+
+# Generated by CodiumAI
+from pr_agent.git_providers.git_provider import FilePatchInfo
+from pr_agent.algo.pr_processing import find_line_number_of_relevant_line_in_file
+
+
+import pytest
+
+class TestFindLineNumberOfRelevantLineInFile:
+    # Tests that the function returns the correct line number and absolute position when the relevant line is found in the patch
+    def test_relevant_line_found_in_patch(self):
+        diff_files = [
+            FilePatchInfo(base_file='file1', head_file='file1', patch='@@ -1,1 +1,2 @@\n-line1\n+line2\n+relevant_line\n', filename='file1')
+        ]
+        relevant_file = 'file1'
+        relevant_line_in_file = 'relevant_line'
+        expected = (3, 2) # (position in patch, absolute_position in new file)
+        assert find_line_number_of_relevant_line_in_file(diff_files, relevant_file, relevant_line_in_file) == expected
+
+    # Tests that the function returns the correct line number and absolute position when a similar line is found using difflib
+    def test_similar_line_found_using_difflib(self):
+        diff_files = [
+            FilePatchInfo(base_file='file1', head_file='file1', patch='@@ -1,1 +1,2 @@\n-line1\n+relevant_line in file similar match\n', filename='file1')
+        ]
+        relevant_file = 'file1'
+        relevant_line_in_file = '+relevant_line in file similar match ' # note the space at the end. This is to simulate a similar line found using difflib
+        expected = (2, 1)
+        assert find_line_number_of_relevant_line_in_file(diff_files, relevant_file, relevant_line_in_file) == expected
+
+    # Tests that the function returns (-1, -1) when the relevant line is not found in the patch and no similar line is found using difflib
+    def test_relevant_line_not_found(self):
+        diff_files = [
+            FilePatchInfo(base_file='file1', head_file='file1', patch='@@ -1,1 +1,2 @@\n-line1\n+relevant_line\n', filename='file1')
+        ]
+        relevant_file = 'file1'
+        relevant_line_in_file = 'not_found'
+        expected = (-1, -1)
+        assert find_line_number_of_relevant_line_in_file(diff_files, relevant_file, relevant_line_in_file) == expected
+
+    # Tests that the function returns (-1, -1) when the relevant file is not found in any of the patches
+    def test_relevant_file_not_found(self):
+        diff_files = [
+            FilePatchInfo(base_file='file1', head_file='file1', patch='@@ -1,1 +1,2 @@\n-line1\n+relevant_line\n', filename='file2')
+        ]
+        relevant_file = 'file1'
+        relevant_line_in_file = 'relevant_line'
+        expected = (-1, -1)
+        assert find_line_number_of_relevant_line_in_file(diff_files, relevant_file, relevant_line_in_file) == expected
+
+    # Tests that the function returns (-1, -1) when the relevant_line_in_file is an empty string
+    def test_empty_relevant_line(self):
+        diff_files = [
+            FilePatchInfo(base_file='file1', head_file='file1', patch='@@ -1,1 +1,2 @@\n-line1\n+relevant_line\n', filename='file1')
+        ]
+        relevant_file = 'file1'
+        relevant_line_in_file = ''
+        expected = (0, 0)
+        assert find_line_number_of_relevant_line_in_file(diff_files, relevant_file, relevant_line_in_file) == expected
+
+    # Tests that the function returns (-1, -1) when the relevant_line_in_file is found in the patch but it is a deleted line
+    def test_relevant_line_found_but_deleted(self):
+        diff_files = [
+            FilePatchInfo(base_file='file1', head_file='file1', patch='@@ -1,2 +1,1 @@\n-line1\n-relevant_line\n', filename='file1')
+        ]
+        relevant_file = 'file1'
+        relevant_line_in_file = 'relevant_line'
+        expected = (-1, -1)
+        assert find_line_number_of_relevant_line_in_file(diff_files, relevant_file, relevant_line_in_file) == expected