199 add ability to read markdown text and pdf files

[abuzarmahmood]

• feat: add functions to read and search markdown, text, and PDF files
• refactor: replace read_pdf_file with search functions for file types
• feat: define estimate_tokens function to resolve undefined name errors

[abuzarmahmood]

Generated edit command:

Summary of User's Issues and Requests

The user has requested the addition of functionality to read markdown, text, and PDF files within the repository abuzarmahmood/blech_github_bot. The last comment [ develop_issue ] suggests a focus on developing this feature. The user has also provided feedback to update the code to allow searching for these file types using glob instead of loops.

Overview of Plan to Address the Issues

1. Implement File Reading Functions:

   • Add functions to read markdown, text, and PDF files in bot_tools.py.

2. Implement File Searching Functions Using glob:

   • Add functions to search for markdown, text, and PDF files using glob in bot_tools.py.

3. Integrate Functions into Agents:

   • Register the new file reading and searching functions with the agents in agents.py.

4. Update GitHub Interaction Logic:

   • Modify git_utils.py to utilize the new file reading and searching capabilities.

Specific Details of Changes to be Made

1. Add File Reading Functions:

   • File: src/bot_tools.py
   • Description: Add utility functions to read markdown, text, and PDF files.
   • Code Snippet:

     import markdown
     from PyPDF2 import PdfReader
     
     def read_markdown_file(filepath: str) -> str:
         """Read a markdown file and return its content as HTML."""
         with open(filepath, 'r') as file:
             text = file.read()
         html = markdown.markdown(text)
         return html
     
     def read_text_file(filepath: str) -> str:
         """Read a text file and return its content."""
         with open(filepath, 'r') as file:
             return file.read()
     
     def read_pdf_file(filepath: str) -> str:
         """Read a PDF file and return its content."""
         reader = PdfReader(filepath)
         text = ''
         for page in reader.pages:
             text += page.extract_text()
         return text

2. Add File Searching Functions Using glob:

   • File: src/bot_tools.py
   • Description: Add utility functions to search for markdown, text, and PDF files using glob.
   • Code Snippet:

     import glob
     import os
     
     def search_for_markdown_files(directory: str) -> list:
         """Search for markdown files in a directory."""
         return glob.glob(os.path.join(directory, '**', '*.md'), recursive=True)
     
     def search_for_text_files(directory: str) -> list:
         """Search for text files in a directory."""
         return glob.glob(os.path.join(directory, '**', '*.txt'), recursive=True)
     
     def search_for_pdf_files(directory: str) -> list:
         """Search for PDF files in a directory."""
         return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)

3. Integrate Functions into Agents:

   • File: src/agents.py
   • Line: 76-98 (within register_functions)
   • Description: Register the new file reading and searching functions with the agents.
   • Code Snippet:

     # Add new functions to tool_funcs
     tool_funcs.extend([
         bot_tools.read_markdown_file,
         bot_tools.read_text_file,
         bot_tools.read_pdf_file,
         bot_tools.search_for_markdown_files,
         bot_tools.search_for_text_files,
         bot_tools.search_for_pdf_files
     ])

4. Update GitHub Interaction Logic:

   • File: src/git_utils.py
   • Description: Update functions that interact with GitHub to utilize the new file reading and searching capabilities.
   • Code Snippet:

     # Example: Modify a function to read and search for file types
     def process_file_content(filepath: str, file_type: str) -> str:
         if file_type == 'markdown':
             return bot_tools.read_markdown_file(filepath)
         elif file_type == 'text':
             return bot_tools.read_text_file(filepath)
         elif file_type == 'pdf':
             return bot_tools.read_pdf_file(filepath)
         else:
             raise ValueError("Unsupported file type")
     
     def find_files_of_type(directory: str, file_type: str) -> list:
         if file_type == 'markdown':
             return bot_tools.search_for_markdown_files(directory)
         elif file_type == 'text':
             return bot_tools.search_for_text_files(directory)
         elif file_type == 'pdf':
             return bot_tools.search_for_pdf_files(directory)
         else:
             raise ValueError("Unsupported file type")

These changes aim to enhance the bot's ability to handle and search for markdown, text, and PDF files in GitHub issues and pull requests efficiently.

---

This response was automatically generated by blech_bot using model gpt-4o

Aider output:

View Aider Output

Aider v0.86.1
Main model: gpt-4o with diff edit format
Weak model: gpt-4o-mini
Git repo: .git with 19 files
Repo-map: using 4096 tokens, auto refresh


src/agents.py

src/bot_tools.py

src/git_utils.py
Here are the changes to implement the requested functionality:                                                                                       

 1 Add File Reading Functions in src/bot_tools.py:                                                                                                   

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
import os                                                                                                                                            
import sys                                                                                                                                           
=======                                                                                                                                              
import os                                                                                                                                            
import sys                                                                                                                                           
import markdown                                                                                                                                      
from PyPDF2 import PdfReader                                                                                                                         
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def estimate_tokens(text: str) -> int:                                                                                                               
=======                                                                                                                                              
def read_markdown_file(filepath: str) -> str:                                                                                                        
    """Read a markdown file and return its content as HTML."""                                                                                       
    with open(filepath, 'r') as file:                                                                                                                
        text = file.read()                                                                                                                           
    html = markdown.markdown(text)                                                                                                                   
    return html                                                                                                                                      
                                                                                                                                                     
def read_text_file(filepath: str) -> str:                                                                                                            
    """Read a text file and return its content."""                                                                                                   
    with open(filepath, 'r') as file:                                                                                                                
        return file.read()                                                                                                                           
                                                                                                                                                     
def read_pdf_file(filepath: str) -> str:                                                                                                             
    """Read a PDF file and return its content."""                                                                                                    
    reader = PdfReader(filepath)                                                                                                                     
    text = ''                                                                                                                                        
    for page in reader.pages:                                                                                                                        
        text += page.extract_text()                                                                                                                  
    return text                                                                                                                                      
                                                                                                                                                     
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 2 Add File Searching Functions Using glob in src/bot_tools.py:                                                                                      

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def estimate_tokens(text: str) -> int:                                                                                                               
=======                                                                                                                                              
import glob                                                                                                                                          
                                                                                                                                                     
def search_for_markdown_files(directory: str) -> list:                                                                                               
    """Search for markdown files in a directory."""                                                                                                  
    return glob.glob(os.path.join(directory, '**', '*.md'), recursive=True)                                                                          
                                                                                                                                                     
def search_for_text_files(directory: str) -> list:                                                                                                   
    """Search for text files in a directory."""                                                                                                      
    return glob.glob(os.path.join(directory, '**', '*.txt'), recursive=True)                                                                         
                                                                                                                                                     
def search_for_pdf_files(directory: str) -> list:                                                                                                    
    """Search for PDF files in a directory."""                                                                                                       
    return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)                                                                         
                                                                                                                                                     
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 3 Integrate Functions into Agents in src/agents.py:                                                                                                 

src/agents.py                                                                                                                                        

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from src.git_utils import (                                                                                                                          
=======                                                                                                                                              
from src import bot_tools                                                                                                                            
from src.git_utils import (                                                                                                                          
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

src/agents.py                                                                                                                                        

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
    return agent                                                                                                                                     
=======                                                                                                                                              
    # Add new functions to tool_funcs                                                                                                                
    tool_funcs.extend([                                                                                                                              
        bot_tools.read_markdown_file,                                                                                                                
        bot_tools.read_text_file,                                                                                                                    
        bot_tools.read_pdf_file,                                                                                                                     
        bot_tools.search_for_markdown_files,                                                                                                         
        bot_tools.search_for_text_files,                                                                                                             
        bot_tools.search_for_pdf_files                                                                                                               
    ])                                                                                                                                               
    return agent                                                                                                                                     
                                                                                                                                                     
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 4 Update GitHub Interaction Logic in src/git_utils.py:                                                                                              

src/git_utils.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from src.branch_handler import (                                                                                                                     
=======                                                                                                                                              
from src import bot_tools                                                                                                                            
from src.branch_handler import (                                                                                                                     
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

src/git_utils.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def get_github_client() -> Github:                                                                                                                   
=======                                                                                                                                              
def process_file_content(filepath: str, file_type: str) -> str:                                                                                      
    if file_type == 'markdown':                                                                                                                      
        return bot_tools.read_markdown_file(filepath)                                                                                                
    elif file_type == 'text':                                                                                                                        
        return bot_tools.read_text_file(filepath)                                                                                                    
    elif file_type == 'pdf':                                                                                                                         
        return bot_tools.read_pdf_file(filepath)                                                                                                     
    else:                                                                                                                                            
        raise ValueError("Unsupported file type")                                                                                                    
                                                                                                                                                     
def find_files_of_type(directory: str, file_type: str) -> list:                                                                                      
    if file_type == 'markdown':                                                                                                                      
        return bot_tools.search_for_markdown_files(directory)                                                                                        
    elif file_type == 'text':                                                                                                                        
        return bot_tools.search_for_text_files(directory)                                                                                            
    elif file_type == 'pdf':                                                                                                                         
        return bot_tools.search_for_pdf_files(directory)                                                                                             
    else:                                                                                                                                            
        raise ValueError("Unsupported file type")                                                                                                    
                                                                                                                                                     
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

After applying these changes, you can run the following command to install the new dependencies:                                                     

                                                                                                                                                     
pip install markdown PyPDF2                                                                                                                          
                                                                                                                                                     

This will ensure that the new functionality for reading markdown and PDF files works correctly.                                                      

Tokens: 15k sent, 833 received. Cost: $0.05 message, $0.05 session.
The LLM did not conform to the edit format.
https://aider.chat/docs/troubleshooting/edit-errors.html

# 1 SEARCH/REPLACE block failed to match!

## SearchReplaceNoExactMatch: This SEARCH block failed to exactly match lines in src/bot_tools.py
<<<<<<< SEARCH
def estimate_tokens(text: str) -> int:
=======
import glob

def search_for_markdown_files(directory: str) -> list:
    """Search for markdown files in a directory."""
    return glob.glob(os.path.join(directory, '**', '*.md'), recursive=True)

def search_for_text_files(directory: str) -> list:
    """Search for text files in a directory."""
    return glob.glob(os.path.join(directory, '**', '*.txt'), recursive=True)

def search_for_pdf_files(directory: str) -> list:
    """Search for PDF files in a directory."""
    return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)

>>>>>>> REPLACE

The SEARCH section must exactly match an existing block of lines including all white space, comments, indentation, docstrings, etc

# The other 6 SEARCH/REPLACE blocks were applied successfully.
Don't re-send them.
Just reply with fixed versions of the block above that failed to match.

Commit 384b178 feat: add functions to read and search markdown, text, and PDF files
Let's correct the failed SEARCH/REPLACE block in src/bot_tools.py:                                                                                   

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def read_pdf_file(filepath: str) -> str:                                                                                                             
    """Read a PDF file and return its content."""                                                                                                    
    reader = PdfReader(filepath)                                                                                                                     
    text = ''                                                                                                                                        
    for page in reader.pages:                                                                                                                        
        text += page.extract_text()                                                                                                                  
    return text                                                                                                                                      
=======                                                                                                                                              
import glob                                                                                                                                          
                                                                                                                                                     
def search_for_markdown_files(directory: str) -> list:                                                                                               
    """Search for markdown files in a directory."""                                                                                                  
    return glob.glob(os.path.join(directory, '**', '*.md'), recursive=True)                                                                          
                                                                                                                                                     
def search_for_text_files(directory: str) -> list:                                                                                                   
    """Search for text files in a directory."""                                                                                                      
    return glob.glob(os.path.join(directory, '**', '*.txt'), recursive=True)                                                                         
                                                                                                                                                     
def search_for_pdf_files(directory: str) -> list:                                                                                                    
    """Search for PDF files in a directory."""                                                                                                       
    return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)                                                                         
                                                                                                                                                     
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

Tokens: 16k sent, 210 received. Cost: $0.04 message, $0.09 session.
Applied edit to src/bot_tools.py
Commit d088b14 refactor: replace read_pdf_file with search functions for file types

# Fix any errors below, if possible.

## Running: /home/exouser/Desktop/blech_github_bot/venv/bin/python -m flake8 --select=E9,F821,F823,F831,F406,F407,F701,F702,F704,F706 --show-source 
--isolated src/bot_tools.py

src/bot_tools.py:117:12: F821 undefined name 'text'
    if not text:
           ^
src/bot_tools.py:119:16: F821 undefined name 'text'
    return len(text.split())
               ^
src/bot_tools.py:155:20: F821 undefined name 'estimate_tokens'
    total_tokens = estimate_tokens(full_content)
                   ^
src/bot_tools.py:165:23: F821 undefined name 'estimate_tokens'
        line_tokens = estimate_tokens(line)
                      ^
src/bot_tools.py:210:20: F821 undefined name 'estimate_tokens'
    total_tokens = estimate_tokens(full_content)
                   ^
src/bot_tools.py:220:23: F821 undefined name 'estimate_tokens'
        line_tokens = estimate_tokens(line)
                      ^

## See relevant lines below marked with █.

src/bot_tools.py:
...⋮...
 106│def search_for_pdf_files(directory: str) -> list:
 107│    """Search for PDF files in a directory."""
...⋮...
 114│    Returns:
 115│        Estimated token count
 116│    """
 117█    if not text:
 118│        return 0
 119█    return len(text.split())
 120│
 121│
 122│def readfile(
 123│        filepath: str,
 124│) -> str:
 125│    """Read a file and return its contents with line numbers.
 126│    Will return partial content if token threshold is exceeded.
 127│
 128│    Args:
 129│        filepath: Path to file to read
 130│
 131│    Returns:
 132│        Tuple of:
 133│        - File contents with line numbers (may be truncated if exceeds threshold)
 134│        - Warning message if content was truncated, None otherwise
 135│
...⋮...
 152│
 153│    # Check total tokens
 154│    full_content = "".join(numbered_lines)
 155█    total_tokens = estimate_tokens(full_content)
 156│
 157│    if total_tokens <= token_threshold:
 158│        return full_content
 159│
...⋮...
 162│    included_lines = []
 163│
 164│    for line in numbered_lines:
 165█        line_tokens = estimate_tokens(line)
 166│        if current_tokens + line_tokens > token_threshold:
 167│            break
 168│        included_lines.append(line)
...⋮...
 183│def readlines(
 184│        file_path: str,
 185│        start_line: int,
 186│        end_line: int,
 187│) -> str:
 188│    """
 189│    Read lines from a file
 190│
 191│    Inputs:
 192│        - file_path : Path to file
 193│        - start_line : Start line
 194│        - end_line : End line
 195│
 196│    Returns:
 197│        - Lines from file
...⋮...
 207│
 208│    # Check total tokens
 209│    full_content = "".join(numbered_lines)
 210█    total_tokens = estimate_tokens(full_content)
 211│
 212│    if total_tokens <= token_threshold:
 213│        return full_content
 214│
...⋮...
 217│    included_lines = []
 218│
 219│    for line in numbered_lines:
 220█        line_tokens = estimate_tokens(line)
 221│        if current_tokens + line_tokens > token_threshold:
 222│            break
 223│        included_lines.append(line)
...⋮...


Let's fix the errors by defining the estimate_tokens function in src/bot_tools.py.                                                                   

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def search_for_pdf_files(directory: str) -> list:                                                                                                    
    """Search for PDF files in a directory."""                                                                                                       
    return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)                                                                         
=======                                                                                                                                              
def search_for_pdf_files(directory: str) -> list:                                                                                                    
    """Search for PDF files in a directory."""                                                                                                       
    return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)                                                                         
                                                                                                                                                     
def estimate_tokens(text: str) -> int:                                                                                                               
    """Estimate the number of tokens in text by splitting on whitespace                                                                              
                                                                                                                                                     
    Args:                                                                                                                                            
        text: Text to estimate tokens for                                                                                                            
                                                                                                                                                     
    Returns:                                                                                                                                         
        Estimated token count                                                                                                                        
    """                                                                                                                                              
    if not text:                                                                                                                                     
        return 0                                                                                                                                     
    return len(text.split())                                                                                                                         
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

Tokens: 18k sent, 179 received. Cost: $0.05 message, $0.13 session.
Applied edit to src/bot_tools.py
Commit f1fd825 feat: define estimate_tokens function to resolve undefined name errors

pip install markdown PyPDF2

[abuzarmahmood]

Fix following error
Might have to update requirements

___________________ ERROR collecting tests/test_triggers.py ____________________
ImportError while importing test module '/home/runner/work/blech_github_bot/blech_github_bot/tests/test_triggers.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_triggers.py:8: in <module>
    from src.triggers import (
src/triggers.py:8: in <module>
    from src.git_utils import get_issue_comments, has_linked_pr, get_linked_pr
src/git_utils.py:13: in <module>
    from src import bot_tools
src/bot_tools.py:11: in <module>
    import markdown
E   ModuleNotFoundError: No module named 'markdown'

[abuzarmahmood]

Applied changes based on comment:

View Aider Output

─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Aider v0.86.1
Main model: gpt-4o with diff edit format
Weak model: gpt-4o-mini
Git repo: .git with 19 files
Repo-map: using 4096 tokens, auto refresh


requirements.txt

src/agents.py

src/bot_tools.py

src/git_utils.py

tests/test_triggers.py
Let's implement the proposed changes step-by-step:                                                                                                   

 1 Update Requirements: Add markdown and PyPDF2 to the requirements.txt file.                                                                        

requirements.txt                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
gitpython                                                                                                                                            
=======                                                                                                                                              
gitpython                                                                                                                                            
markdown                                                                                                                                             
PyPDF2                                                                                                                                               
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 2 Implement File Reading Functions: Add functions to read markdown, text, and PDF files in src/bot_tools.py.                                        

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from PyPDF2 import PdfReader                                                                                                                         
=======                                                                                                                                              
import markdown                                                                                                                                      
from PyPDF2 import PdfReader                                                                                                                         
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def read_markdown_file(filepath: str) -> str:                                                                                                        
    """Read a markdown file and return its content as HTML."""                                                                                       
    with open(filepath, 'r') as file:                                                                                                                
        text = file.read()                                                                                                                           
    html = markdown.markdown(text)                                                                                                                   
    return html                                                                                                                                      
                                                                                                                                                     
                                                                                                                                                     
def read_text_file(filepath: str) -> str:                                                                                                            
    """Read a text file and return its content."""                                                                                                   
    with open(filepath, 'r') as file:                                                                                                                
        return file.read()                                                                                                                           
=======                                                                                                                                              
def read_markdown(file_path: str) -> str:                                                                                                            
    """Read a markdown file and return its content as HTML."""                                                                                       
    with open(file_path, 'r') as file:                                                                                                               
        text = file.read()                                                                                                                           
    return markdown.markdown(text)                                                                                                                   
                                                                                                                                                     
                                                                                                                                                     
def read_pdf(file_path: str) -> str:                                                                                                                 
    """Read a PDF file and return its content."""                                                                                                    
    reader = PdfReader(file_path)                                                                                                                    
    text = ''                                                                                                                                        
    for page in reader.pages:                                                                                                                        
        text += page.extract_text()                                                                                                                  
    return text                                                                                                                                      
                                                                                                                                                     
                                                                                                                                                     
def read_text(file_path: str) -> str:                                                                                                                
    """Read a text file and return its content."""                                                                                                   
    with open(file_path, 'r') as file:                                                                                                               
        return file.read()                                                                                                                           
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 3 Implement File Searching Functions: Add functions to search for markdown, text, and PDF files in src/bot_tools.py.                                

src/bot_tools.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def search_for_markdown_files(directory: str) -> list:                                                                                               
    """Search for markdown files in a directory."""                                                                                                  
    return glob.glob(os.path.join(directory, '**', '*.md'), recursive=True)                                                                          
                                                                                                                                                     
                                                                                                                                                     
def search_for_text_files(directory: str) -> list:                                                                                                   
    """Search for text files in a directory."""                                                                                                      
    return glob.glob(os.path.join(directory, '**', '*.txt'), recursive=True)                                                                         
                                                                                                                                                     
                                                                                                                                                     
def search_for_pdf_files(directory: str) -> list:                                                                                                    
    """Search for PDF files in a directory."""                                                                                                       
    return glob.glob(os.path.join(directory, '**', '*.pdf'), recursive=True)                                                                         
=======                                                                                                                                              
def search_files(directory: str, extension: str) -> list:                                                                                            
    """Search for files with a specific extension in a directory."""                                                                                 
    return glob.glob(os.path.join(directory, '**', f'*.{extension}'), recursive=True)                                                                
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 4 Integrate Functions into Agents: Register the new file reading and searching functions in src/agents.py.                                          

src/agents.py                                                                                                                                        

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from src import bot_tools                                                                                                                            
=======                                                                                                                                              
from src.bot_tools import read_markdown, read_pdf, read_text, search_files                                                                           
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

 5 Update GitHub Interaction Logic: Utilize the new file reading and searching capabilities in src/git_utils.py.                                     

src/git_utils.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from src import bot_tools                                                                                                                            
=======                                                                                                                                              
from src.bot_tools import read_markdown, read_pdf, read_text                                                                                         
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

src/git_utils.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
def process_file_content(filepath: str, file_type: str) -> str:                                                                                      
    if file_type == 'markdown':                                                                                                                      
        return bot_tools.read_markdown_file(filepath)                                                                                                
    elif file_type == 'text':                                                                                                                        
        return bot_tools.read_text_file(filepath)                                                                                                    
    elif file_type == 'pdf':                                                                                                                         
        return bot_tools.read_pdf_file(filepath)                                                                                                     
    else:                                                                                                                                            
        raise ValueError("Unsupported file type")                                                                                                    
=======                                                                                                                                              
def process_github_files(file_paths: list) -> None:                                                                                                  
    """Process GitHub files based on their type."""                                                                                                  
    for file_path in file_paths:                                                                                                                     
        if file_path.endswith('.md'):                                                                                                                
            content = read_markdown(file_path)                                                                                                       
        elif file_path.endswith('.pdf'):                                                                                                             
            content = read_pdf(file_path)                                                                                                            
        else:                                                                                                                                        
            content = read_text(file_path)                                                                                                           
        # Further processing can be done here                                                                                                        
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

After applying these changes, you should run the following command to install the new dependencies:                                                  

                                                                                                                                                     
pip install -r requirements.txt                                                                                                                      
                                                                                                                                                     

And then, you can run your tests to ensure everything is working correctly:                                                                          

                                                                                                                                                     
pytest tests/test_triggers.py                                                                                                                        
                                                                                                                                                     

Tokens: 17k sent, 949 received. Cost: $0.05 message, $0.05 session.
Applied edit to src/git_utils.py
Applied edit to src/bot_tools.py
Applied edit to src/agents.py
Applied edit to requirements.txt
Commit a0ffcca feat: add file reading and searching functions for markdown, text, and PDF

# Fix any errors below, if possible.

## Running: /home/exouser/Desktop/blech_github_bot/venv/bin/python -m flake8 --select=E9,F821,F823,F831,F406,F407,F701,F702,F704,F706 --show-source 
--isolated src/git_utils.py

src/git_utils.py:85:16: F821 undefined name 'bot_tools'
        return bot_tools.search_for_markdown_files(directory)
               ^
src/git_utils.py:87:16: F821 undefined name 'bot_tools'
        return bot_tools.search_for_text_files(directory)
               ^
src/git_utils.py:89:16: F821 undefined name 'bot_tools'
        return bot_tools.search_for_pdf_files(directory)
               ^
src/git_utils.py:565:14: F821 undefined name 'get_github_client'
    client = get_github_client()
             ^
src/git_utils.py:641:14: F821 undefined name 'get_github_client'
    client = get_github_client()
             ^
src/git_utils.py:726:14: F821 undefined name 'get_github_client'
    client = get_github_client()
             ^

## See relevant lines below marked with █.

src/git_utils.py:
...⋮...
 82│
 83│def find_files_of_type(directory: str, file_type: str) -> list:
 84│    if file_type == 'markdown':
 85█        return bot_tools.search_for_markdown_files(directory)
 86│    elif file_type == 'text':
 87█        return bot_tools.search_for_text_files(directory)
 88│    elif file_type == 'pdf':
 89█        return bot_tools.search_for_pdf_files(directory)
 90│    else:
 91│        raise ValueError("Unsupported file type")
 92│    """Initialize and return authenticated GitHub client"""
...⋮...
 544│def update_self_repo(
 545│        repo_path: str,
 546│) -> bool:
 547│    """
 548│    Pull latest changes for the bot's own repository, handling tracked config files.
 549│
 550│    Args:
 551│        repo_path: Path to the bot's local git repository
...⋮...
 562│    repo_name = url_splits[-2] + '/' + repo_basename
 563│
 564│    # Initialize GitHub client
 565█    client = get_github_client()
 566│    github_repo = get_repository(client, repo_name)
 567│    # Determine the default branch
 568│    default_branch = github_repo.default_branch
 569│
...⋮...
 628│def perform_github_search(
 629│        query: str,
 630│        max_snippet_length: int = 2000,  # lines
 631│) -> str:
 632│    """
 633│    Perform a search on GitHub using the provided query and extract code URLs.
 634│
 635│    Args:
 636│        query: The search query string.
 637│
 638│    Returns:
 639│        A string containing search results with code snippets.
 640│    """
 641█    client = get_github_client()
 642│
 643│    try:
 644│        # Search for code with the given query
...⋮...
 723│
 724│
 725│if __name__ == '__main__':
 726█    client = get_github_client()
 727│    repo = get_repository(client, 'katzlabbrandeis/blech_clust')
 728│    issues = get_open_issues(repo)
 729│    print(f"Found {len(issues)} open issues")
...⋮...


To fix the errors in src/git_utils.py, we need to:                                                                                                   

 1 Import bot_tools to resolve the undefined name errors.                                                                                            
 2 Import get_github_client from the appropriate module.                                                                                             

Here are the necessary changes:                                                                                                                      

src/git_utils.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from src.bot_tools import read_markdown, read_pdf, read_text                                                                                         
=======                                                                                                                                              
from src import bot_tools                                                                                                                            
from src.bot_tools import read_markdown, read_pdf, read_text                                                                                         
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

src/git_utils.py                                                                                                                                     

                                                                                                                                                     
<<<<<<< SEARCH                                                                                                                                       
from src.bot_tools import read_markdown, read_pdf, read_text                                                                                         
=======                                                                                                                                              
from src.agents import get_github_client                                                                                                             
from src.bot_tools import read_markdown, read_pdf, read_text                                                                                         
>>>>>>> REPLACE                                                                                                                                      
                                                                                                                                                     

These changes will resolve the F821 errors by ensuring that bot_tools and get_github_client are properly imported and available in the               
src/git_utils.py file.                                                                                                                               

Tokens: 19k sent, 198 received. Cost: $0.05 message, $0.10 session.
Applied edit to src/git_utils.py
Commit b4a73d7 fix: resolve undefined name errors for bot_tools and get_github_client

pip install -r requirements.txt

pytest tests/test_triggers.py

---

This response was automatically generated by blech_bot using model gpt-4o