codes/3_coding.py

import json
import os
from tqdm import tqdm
import re
import sys
import copy
from utils import extract_planning, content_to_json, extract_code_from_content, print_response, print_log_cost, load_accumulated_cost, save_accumulated_cost
from llm_provider import get_provider, get_default_model
import argparse

parser = argparse.ArgumentParser()

parser.add_argument('--paper_name', type=str)
parser.add_argument('--gpt_version', type=str, default="o3-mini", help='Model version (deprecated, use --model)')
parser.add_argument('--model', type=str, help='Model name')
parser.add_argument('--provider', type=str, default='gemini', choices=['openai', 'gemini', 'gemma'], help='LLM provider')
parser.add_argument('--paper_format', type=str, default="JSON", choices=["JSON", "LaTeX"])
parser.add_argument('--pdf_json_path', type=str) # json format
parser.add_argument('--pdf_latex_path', type=str) # latex format
parser.add_argument('--output_dir',type=str, default="")
parser.add_argument('--output_repo_dir',type=str, default="")

args = parser.parse_args()

# Initialize LLM provider
provider_name = args.provider
llm_provider = get_provider(provider_name)
model = args.model or args.gpt_version or get_default_model(provider_name)

print(f"🤖 Using {provider_name.upper()} with model: {model}")

paper_name = args.paper_name
gpt_version = args.gpt_version
paper_format = args.paper_format
pdf_json_path = args.pdf_json_path
pdf_latex_path = args.pdf_latex_path
output_dir = args.output_dir
output_repo_dir = args.output_repo_dir

if paper_format == "JSON":
    with open(f'{pdf_json_path}') as f:
        paper_content = json.load(f)
elif paper_format == "LaTeX":
    with open(f'{pdf_latex_path}') as f:
        paper_content = f.read()
else:
    print(f"[ERROR] Invalid paper format. Please select either 'JSON' or 'LaTeX.")
    sys.exit(0)

with open(f'{output_dir}/planning_config.yaml') as f: 
    config_yaml = f.read()

context_lst = extract_planning(f'{output_dir}/planning_trajectories.json')
# 0: overview, 1: detailed, 2: PRD
# file_list = content_to_json(context_lst[1])
task_list = content_to_json(context_lst[2])

todo_file_lst = task_list['Task list']
done_file_lst = ['config.yaml']
done_file_dict = {}

code_msg = [
    {"role": "system", "content": f"""You are an expert researcher and software engineer with a deep understanding of experimental design and reproducibility in scientific research.
You will receive a research paper in {paper_format} format, an overview of the plan, a Design in JSON format consisting of "Implementation approach", "File list", "Data structures and interfaces", and "Program call flow", followed by a Task in JSON format that includes "Required packages", "Required other language third-party packages", "Logic Analysis", and "Task list", along with a configuration file named "config.yaml". 
Your task is to write code to reproduce the experiments and methodologies described in the paper. 

The code you write must be elegant, modular, and maintainable, adhering to Google-style guidelines. 
The code must strictly align with the paper's methodology, experimental setup, and evaluation metrics. 
Write code with triple quoto."""}]

def get_write_msg(todo_file_name, detailed_logic_analysis, done_file_lst): 
    code_files = ""
    for done_file in done_file_lst:
        if done_file.endswith(".yaml"): continue
        code_files += f"""
```python
{done_file_dict[done_file]}
```

"""

    write_msg=[
{'role': 'user', "content": f"""# Context
## Paper
{paper_content}

-----

## Overview of the plan
{context_lst[0]}

-----

## Design
{context_lst[1]}

-----

## Task
{context_lst[2]}

-----

## Configuration file
```yaml
{config_yaml}
```
-----

## Code Files
{code_files}

-----

# Format example
## Code: {todo_file_name}
```python
## {todo_file_name}
...
```

-----

# Instruction
Based on the paper, plan, design, task and configuration file(config.yaml) specified previously, follow "Format example", write the code. 

We have {done_file_lst}.
Next, you must write only the "{todo_file_name}".
1. Only One file: do your best to implement THIS ONLY ONE FILE.
2. COMPLETE CODE: Your code will be part of the entire project, so please implement complete, reliable, reusable code snippets.
3. Set default value: If there is any setting, ALWAYS SET A DEFAULT VALUE, ALWAYS USE STRONG TYPE AND EXPLICIT VARIABLE. AVOID circular import.
4. Follow design: YOU MUST FOLLOW "Data structures and interfaces". DONT CHANGE ANY DESIGN. Do not use public member functions that do not exist in your design.
5. CAREFULLY CHECK THAT YOU DONT MISS ANY NECESSARY CLASS/FUNCTION IN THIS FILE.
6. Before using a external variable/module, make sure you import it first.
7. Write out EVERY CODE DETAIL, DON'T LEAVE TODO.
8. REFER TO CONFIGURATION: you must use configuration from "config.yaml". DO NOT FABRICATE any configuration values.

{detailed_logic_analysis}

## Code: {todo_file_name}"""}]
    return write_msg


def api_call(msg):
    """Make API call using the configured provider"""
    if "o3-mini" in model and provider_name == 'openai':
        completion = llm_provider.create_completion(
            messages=msg,
            model=model,
            reasoning_effort="high"
        )
    else:
        completion = llm_provider.create_completion(
            messages=msg,
            model=model
        )
    return completion
    

# testing for checking
detailed_logic_analysis_dict = {}
retrieved_section_dict = {}
for todo_file_name in todo_file_lst:
    # simple analysis
    save_todo_file_name = todo_file_name.replace("/", "_")

    if todo_file_name == "config.yaml":
        continue
    
    with open(f"{output_dir}/{save_todo_file_name}_simple_analysis_response.json") as f:
        detailed_logic_analysis_response = json.load(f)
    detailed_logic_analysis_dict[todo_file_name] = detailed_logic_analysis_response[0]['choices'][0]['message']['content']

artifact_output_dir=f'{output_dir}/coding_artifacts'
os.makedirs(artifact_output_dir, exist_ok=True)

total_accumulated_cost = load_accumulated_cost(f"{output_dir}/accumulated_cost.json")
for todo_idx, todo_file_name in enumerate(tqdm(todo_file_lst)):
    responses = []
    trajectories = copy.deepcopy(code_msg)

    current_stage = f"[CODING] {todo_file_name}"
    print(current_stage)

    if todo_file_name == "config.yaml":
        continue

    instruction_msg = get_write_msg(todo_file_name, detailed_logic_analysis_dict[todo_file_name], done_file_lst)
    trajectories.extend(instruction_msg)

    completion = api_call(trajectories)
    
    # Extract response using provider abstraction
    response_text = llm_provider.get_response_text(completion)
    usage_info = llm_provider.get_usage_info(completion)
    
    # Create completion JSON for logging
    completion_json = {
        'choices': [{'message': {'role': 'assistant', 'content': response_text}}],
        'usage': usage_info,
        'model': model
    }

    # print and logging
    print_response(completion_json)
    temp_total_accumulated_cost = print_log_cost(completion_json, model, current_stage, output_dir, total_accumulated_cost)
    total_accumulated_cost = temp_total_accumulated_cost

    responses.append(completion_json)

    # trajectories
    message = {'role': 'assistant', 'content': response_text}
    trajectories.append(message)

    done_file_lst.append(todo_file_name)

    # save
    # save_dir_name = f"{paper_name}_repo"
    os.makedirs(f'{output_repo_dir}', exist_ok=True)
    save_todo_file_name = todo_file_name.replace("/", "_")


    # save artifacts - create subdirectories if needed
    artifact_file_path = f'{artifact_output_dir}/{save_todo_file_name}_coding.txt'
    artifact_file_dir = os.path.dirname(artifact_file_path)
    os.makedirs(artifact_file_dir, exist_ok=True)
    
    with open(artifact_file_path, 'w') as f:
        f.write(completion_json['choices'][0]['message']['content'])

    # extract code save 
    code = extract_code_from_content(completion_json['choices'][0]['message']['content'])
    if len(code) == 0:
        code = completion_json['choices'][0]['message']['content']

    done_file_dict[todo_file_name] = code
    if save_todo_file_name != todo_file_name:
        todo_file_dir = '/'.join(todo_file_name.split("/")[:-1])
        os.makedirs(f"{output_repo_dir}/{todo_file_dir}", exist_ok=True)

    # save code file - create subdirectories if needed
    code_file_path = f"{output_repo_dir}/{todo_file_name}"
    code_file_dir = os.path.dirname(code_file_path)
    os.makedirs(code_file_dir, exist_ok=True)
    
    with open(code_file_path, 'w') as f:
        f.write(code)

save_accumulated_cost(f"{output_dir}/accumulated_cost.json", total_accumulated_cost)