codes/3_coding_llm.py

import json
import os
from tqdm import tqdm
import sys
import copy
from utils import extract_planning, content_to_json, extract_code_from_content,extract_code_from_content2, print_response, print_log_cost, load_accumulated_cost, save_accumulated_cost
from transformers import AutoTokenizer
from vllm import LLM, SamplingParams

import argparse

parser = argparse.ArgumentParser()

parser.add_argument('--paper_name',type=str)

parser.add_argument('--model_name',type=str, default="deepseek-ai/DeepSeek-Coder-V2-Lite-Instruct") 
parser.add_argument('--tp_size',type=int, default=2)
parser.add_argument('--temperature',type=float, default=1.0)
parser.add_argument('--max_model_len',type=int, default=128000)

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()

paper_name = args.paper_name

model_name = args.model_name
tp_size = args.tp_size
max_model_len = args.max_model_len
temperature = args.temperature

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])

if 'Task list' in task_list:
    todo_file_lst = task_list['Task list']
elif 'task_list' in task_list:
    todo_file_lst = task_list['task_list']
elif 'task list' in task_list:
    todo_file_lst = task_list['task list']
else:
    print(f"[ERROR] 'Task list' does not exist. Please re-generate the planning.")
    sys.exit(0)

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

model_name = args.model_name
tokenizer = AutoTokenizer.from_pretrained(model_name)


if "Qwen" in model_name:
    llm = LLM(model=model_name, 
            tensor_parallel_size=tp_size, 
            max_model_len=max_model_len,
            gpu_memory_utilization=0.95,
            trust_remote_code=True, enforce_eager=True, 
            rope_scaling={"factor": 4.0, "original_max_position_embeddings": 32768, "type": "yarn"})
    sampling_params = SamplingParams(temperature=temperature, max_tokens=131072)

elif "deepseek" in model_name:
    llm = LLM(model=model_name, 
              tensor_parallel_size=tp_size, 
              max_model_len=max_model_len,
              gpu_memory_utilization=0.95,
              trust_remote_code=True, enforce_eager=True)
    sampling_params = SamplingParams(temperature=temperature, max_tokens=128000, stop_token_ids=[tokenizer.eos_token_id])


def run_llm(msg):
    # vllm
    prompt_token_ids = [tokenizer.apply_chat_template(messages, add_generation_prompt=True) for messages in [msg]]

    outputs = llm.generate(prompt_token_ids=prompt_token_ids, sampling_params=sampling_params)

    completion = [output.outputs[0].text for output in outputs]
    
    return completion[0] 
    

# 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_trajectories.json", encoding='utf8') as f:
        detailed_logic_analysis_trajectories = json.load(f)

    detailed_logic_analysis_dict[todo_file_name] = detailed_logic_analysis_trajectories[0]['content']

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

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 = run_llm(trajectories)
    
    # response
    completion_json = {
        'text': completion
    }
    responses.append(completion_json)

    # trajectories
    trajectories.append({'role': 'assistant', 'content': completion})

    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("/", "_")

    # print and logging
    print_response(completion_json, is_llm=True)

    # save artifacts
    with open(f'{artifact_output_dir}/{save_todo_file_name}_coding.txt', 'w', encoding='utf-8') as f:
        f.write(completion)

    # extract code save 
    try:
        code = extract_code_from_content(completion)
    except Exception as e:
        code = extract_code_from_content2(completion) 

    if len(code) == 0:
        code = completion

    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)

    with open(f"{output_repo_dir}/{todo_file_name}", 'w', encoding='utf-8') as f:
        f.write(code)