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import os
os.chdir(os.path.dirname(os.path.abspath(__file__)))
from typing import List, Dict, Any, Optional
from pydantic import BaseModel
import pandas as pd
import shutil
import subprocess
import requests
import argparse
import asyncio
from pathlib import Path
from dotenv import load_dotenv
from datetime import datetime, timedelta
from util import init_logger, logger, call_llm, CODE_EXTENSIONS
from langchain_core.output_parsers import JsonOutputParser
# Pydantic models for structured output
class RelevanceResult(BaseModel):
relevant: str # YES or NO
reason: str
class ExpandedKeywords(BaseModel):
keywords: List[str]
def search_github_repos(keywords: List[str], token: str, output_csv: Path):
"""Search GitHub repos with incremental write per keyword using pending logic"""
headers = {"Authorization": f"Bearer {token}", "Accept": "application/vnd.github.v3+json"}
# Calculate pending keywords using set difference
all_keywords = set(k.lower() for k in keywords)
searched_keywords = set()
if output_csv.exists():
df_existing = pd.read_csv(output_csv)
searched_keywords = set(df_existing["keyword"].str.lower().unique())
logger.info(f"Resume: Already searched {len(searched_keywords)} keywords")
# Pending keywords = all - searched
pending_keywords = all_keywords - searched_keywords
pending = [k for k in keywords if k.lower() in pending_keywords]
logger.info(f"Pending: {len(pending)} keywords to search")
# Load existing URLs for global deduplication
global_seen = set()
if output_csv.exists():
global_seen = set(df_existing["url"].tolist())
def get_count(query: str) -> int:
"""Get total count without fetching data"""
try:
resp = requests.get(
"https://api.github.com/search/repositories",
headers=headers,
params={"q": query, "per_page": 1},
)
if resp.status_code == 200:
return resp.json().get("total_count", 0)
except:
pass
return 0
def fetch_repos(query: str, keyword: str, local_repos: List[Dict]):
"""Fetch all results for a single query"""
page = 1
while page <= 10:
try:
resp = requests.get(
"https://api.github.com/search/repositories",
headers=headers,
params={"q": query, "per_page": 100, "page": page},
)
if resp.status_code != 200:
break
items = resp.json().get("items", [])
if not items:
break
for r in items:
url = r.get("html_url", "")
if url and url not in global_seen:
global_seen.add(url)
repo_data = {
"keyword": keyword,
"name": r.get("name", ""),
"full_name": r.get("full_name", ""),
"owner": r.get("owner", {}).get("login", ""),
"url": url,
"description": r.get("description") or "",
"language": r.get("language") or "",
"topics": ",".join(r.get("topics", [])),
"stars": r.get("stargazers_count", 0),
"forks": r.get("forks_count", 0),
"created_at": r.get("created_at", ""),
"updated_at": r.get("updated_at", ""),
"pushed_at": r.get("pushed_at", ""),
"license": r.get("license", {}).get("spdx_id", "") if r.get("license") else "",
"default_branch": r.get("default_branch", ""),
"open_issues": r.get("open_issues_count", 0),
"size": r.get("size", 0),
"has_wiki": r.get("has_wiki", False),
"archived": r.get("archived", False),
}
local_repos.append(repo_data)
if len(items) < 100:
break
page += 1
except Exception as e:
logger.error(f"Fetch error: {e}")
break
def split_by_date(kw: str, keyword: str, start_date: datetime, end_date: datetime, local_repos: List[Dict]):
"""Recursive date splitting with stars>10 and in:readme filters"""
start_str = start_date.strftime("%Y-%m-%d")
end_str = end_date.strftime("%Y-%m-%d")
query = f"{kw} in:readme stars:>10 created:{start_str}..{end_str}"
count = get_count(query)
logger.info(f" {start_str} to {end_str}: {count} repos")
if count == 0:
return
elif count <= 1000:
fetch_repos(query, keyword, local_repos)
else:
days = (end_date - start_date).days
if days == 0:
logger.warning(f"Single day has {count} repos, getting first 1000: {start_str}")
fetch_repos(query, keyword, local_repos)
else:
mid_days = days // 2
mid_date = start_date + timedelta(days=mid_days)
split_by_date(kw, keyword, start_date, mid_date, local_repos)
split_by_date(kw, keyword, mid_date + timedelta(days=1), end_date, local_repos)
# Search each pending keyword and write immediately
for kw in pending:
logger.info(f"Searching keyword: {kw}")
keyword_repos = []
start = datetime(2008, 1, 1)
end = datetime.now()
split_by_date(kw, kw, start, end, keyword_repos)
# Write immediately after each keyword
if keyword_repos:
df_new = pd.DataFrame(keyword_repos)
df_new.to_csv(output_csv, mode="a", header=not output_csv.exists(), index=False, encoding="utf-8")
logger.info(f"✓ Saved {len(keyword_repos)} repos for keyword: {kw}")
else:
logger.info(f"✓ No new repos for keyword: {kw}")
logger.info(f"Total repos in CSV: {len(global_seen)}")
def get_readme(owner: str, repo: str, token: str) -> str:
"""Fetch README content from repo"""
try:
resp = requests.get(
f"https://api.github.com/repos/{owner}/{repo}/readme",
headers={"Authorization": f"Bearer {token}", "Accept": "application/vnd.github.v3.raw"},
)
return resp.text if resp.status_code == 200 else ""
except:
return ""
async def check_relevance(
repo: Dict, keywords: List[str], model: str, base_url: str, api_key: str, token: str, log_file: str
) -> bool:
"""Use LLM to check if repo is relevant to keywords"""
readme = get_readme(repo["owner"], repo["name"], token)[:8000]
prompt = f"""Determine if this GitHub repository is relevant to the keywords: {', '.join(keywords)}
Repository: {repo['name']}
Description: {repo['description']}
Language: {repo['language']}
README (truncated):
{readme}
Answer 'YES' if the repository is related to any of the keywords, 'NO' otherwise.
Provide your reasoning in the reason field."""
try:
result = await call_llm(
[{"role": "user", "content": prompt}],
model,
base_url,
api_key,
pydantic_object=RelevanceResult,
log_file=log_file,
temperature=0.1,
)
return result.get("relevant", "").upper() == "YES"
except Exception as e:
logger.error(f"LLM error for {repo['name']}: {e}")
return False
def save_csv(repos: List[Dict], path: str):
"""Save repos to CSV using pandas"""
df = pd.DataFrame(repos)
df.to_csv(path, index=False, encoding="utf-8")
logger.info(f"Saved {len(repos)} repos to {path}")
def clone_repos(csv_path: str, dest_dir: Path):
"""Clone repos with resume support using full_name"""
dest_dir.mkdir(parents=True, exist_ok=True)
df = pd.read_csv(csv_path)
to_clone = df.to_dict("records")
total_repos = len(to_clone)
existing_dirs = set(d.name for d in dest_dir.iterdir() if d.is_dir() and not d.name.startswith("."))
# Check if repo exists under any naming pattern
def is_cloned(full_name: str) -> bool:
owner, repo = full_name.split("/")
patterns = [f"{owner}___{repo}"]
return any(p in existing_dirs for p in patterns)
# Pending = repos not cloned under any pattern
pending = [r for r in to_clone if not is_cloned(r["full_name"])]
already_count = total_repos - len(pending)
logger.info(f"Resume: Already cloned {already_count}/{total_repos} repos")
logger.info(f"Pending: {len(pending)} repos to clone")
for i, row in enumerate(pending):
full_name = row["full_name"]
repo_path = dest_dir / full_name.replace("/", "___") # three underscores
try:
subprocess.run(
["git", "clone", "--depth", "1", row["url"], str(repo_path)], check=True, capture_output=True
)
logger.info(f"[{already_count + i + 1}/{total_repos}] Cloned: {full_name}")
except Exception as e:
logger.error(f"[{already_count + i + 1}/{total_repos}] Clone failed {full_name}: {e}")
async def main():
load_dotenv()
parser = argparse.ArgumentParser(description="GitHub Repo Crawler")
parser.add_argument(
"--keywords",
type=str,
default="Chemistry, Biology, Biochemistry, Omics, Medicine, Pharmacology, Toxicology, Bioinformatics, Bioengineering, Biophysics, Viral, Microbial, Prediction, Discovery, Protein, Gene, DNA, RNA, Vaccine, Computational Biology, Computational Biochemistry, Computational Chemistry, Computational Materials, Quantum Chemistry, Disease, Biomedical, Material, Pharmacogenetics, Pharmacogenomics, Modeling, Networks, In Silico, Pathology, Physiology, Genomics, Proteomics, Transcriptomics, Metabolomics, Glycomics, Lipidomics, Immunology, Microbiology, Molecular biology, Pharmaceutics, Network pharmacology, Epigenetics, Sequencing, Design, Multi-omics, Biomarker, System biology, Synthetic biology, Cell biology, Cancer biology, Ensemble, Personalized, Lipid, Metabolic, Genesis, Ion, Heterogeneity, Generative, Generate, Human, Receptor, Ligand, Organoid, Evolution, Pathogens, Homeostasis, Allele, Genotype, Phenotype, Antibody, Antigen, Nucleic acids, Carbohydrate, Substrate, Inhibition, Activation, Allosteric, Cofactor, Coenzyme, Enzyme, Redox, Hydrophilic, Hydrophobic, Codon, Transcription, Translation, Pathway, Cycle, Signaling, Dynamics, Kinetics, Docking, Spectrometry, Profiling, Diagnostics, CRISPR, Bio, Marker, Pharmacokinetics, Pharmacodynamics, Absorption, Mechanism of action, Agonist, Antagonist, Bioavailability, Half-life, Reaction, Drug, Biologics, Pharmacometrics, Beta-blocker, Regulatory networks, Multi-scale modeling, Single-cell, Spatial biology, Integration, Monte Carlo, System immunology, Metagenomics, QSAR, QAPR, Chemical space, AlphaFold, Folding, Mechanism, Digital twin, Virtual human, Gene editing, Bio foundation model, Biotechnology, Assay, Lead discovery, High-throughput, Screening, Hit-to-lead, Lead optimization, De novo, ADMET, Translational medicine, Drug repurpose, Conjugate, Agent-based model, Compartmental model, Reproduction number, Nowcasting, Phylodynamic model, Physiologically based pharmacokinetics model, PBPK model, Organ-on-a-chip, Anomaly detection, Stochastic modeling, Genomic surveillance, Antimicrobial resistance modeling, AMR, Pandemic, Digital PCR, Next-generation sequencing, Biosensors, Imaging, Sensors, Quantum mechanics, DFT, Ab initio, Hartree-Fock, Coupled cluster, Electronic structure, Homo-Lumo, Conformation, Cheminformatics, QM/MM, First-principles based DFT, Diffusion, Finite element method, Phase-field technique, Potential, Metamaterial, 2D, 3D, Porous, Crystal, Rosettafold, Gene regulatory networks, Cell atlas, Human atlas, Spatial transcriptomics, Pseudotime analysis, Quantum biology, Metabolic flux analysis, Free energy perturbation, Protein-protein, Explainable AI, Neurology, Reinforcement learning, Generative AI, Flow matching, Generative adversarial networks, GAN, Variational autoencoders, VAE, Autoregressive, Transformer, Recurrent neural networks, RNN, Score",
help="Comma-separated keywords",
)
parser.add_argument("--workdir", type=str, default="./workdir", help="Working directory")
parser.add_argument("--model", type=str, default=os.getenv("OPENAI_MODEL", "gpt-4o"))
parser.add_argument("--base_url", type=str, default=os.getenv("OPENAI_BASE_URL", "https://api.openai.com/v1"))
parser.add_argument("--api_key", type=str, default=os.getenv("OPENAI_API_KEY"))
args = parser.parse_args()
# Unified config
workdir = Path(args.workdir)
config = {
"workdir": workdir,
"keywords_expanded": workdir / "keywords_expanded.json",
"repos_searched": workdir / "repos_searched.csv",
"repos_checked": workdir / "repos_checked.csv",
"repos_raw": workdir / "repos_raw",
"repos_filtered": workdir / "repos_filtered",
"log_file": str(workdir / "calls_llm.jsonl"),
"model": args.model,
"base_url": args.base_url,
"api_key": args.api_key,
"github_token": os.environ.get("GITHUB_TOKEN"),
"keywords": [k.strip() for k in args.keywords.split(",") if k.strip()],
}
# Setup
os.makedirs(config["workdir"], exist_ok=True)
init_logger(str(config["workdir"] / "run.log"))
logger.info(f"Base keywords: {config['keywords']}")
logger.info(f"Model: {config['model']}")
# Step 0: Expand keywords with LLM (skip if keywords_expanded.json exists)
if config["keywords_expanded"].exists():
logger.info(f"[Skip] Step 0: {config['keywords_expanded']} exists")
import json
with open(config["keywords_expanded"], "r") as f:
expanded = json.load(f)["keywords"]
else:
logger.info("=" * 60 + "\nStep 0: Expand Keywords with LLM\n" + "=" * 60)
parser = JsonOutputParser(pydantic_object=ExpandedKeywords)
messages = [
{
"role": "system",
"content": f"You are an assistant that generates diverse and related keywords for scientific disciplines.\n{parser.get_format_instructions()}",
},
{
"role": "user",
"content": f"""Generate a list of exactly 5 diverse keywords related to these scientific fields: {', '.join(config['keywords'])}.
Make sure that the generated keywords do not stray away from these scientific disciplines and do not contain broad terms that will confuse the search (e.g. machine learning, algorithms, etc).
I would like to use these keywords to retrieve code repositories related to these specific scientific disciplines from GitHub and Papers with Code.""",
},
]
try:
result = await call_llm(
messages,
config["model"],
config["base_url"],
config["api_key"],
pydantic_object=ExpandedKeywords,
log_file=config["log_file"],
temperature=0.5,
)
# Merge with base keywords and dedupe
expanded = list(set(config["keywords"] + result.get("keywords", [])))
except Exception as e:
logger.error(f"Keyword expansion failed: {e}, using base keywords")
expanded = config["keywords"]
# Save expanded keywords
import json
with open(config["keywords_expanded"], "w") as f:
json.dump({"keywords": expanded}, f, indent=2)
logger.info(f"[Done] Step 0: {len(expanded)} keywords: {expanded}")
# Step 1: Search GitHub repos with pending logic
logger.info("=" * 60 + "\nStep 1: Search GitHub Repos\n" + "=" * 60)
search_github_repos(expanded, config["github_token"], config["repos_searched"])
# Check final results
if config["repos_searched"].exists():
df_final = pd.read_csv(config["repos_searched"])
logger.info(f"[Done] Step 1: {len(df_final)} total repos in CSV")
else:
logger.warning("No repos found")
pd.DataFrame(
columns=[
"keyword",
"name",
"full_name",
"owner",
"url",
"description",
"language",
"topics",
"stars",
"forks",
"created_at",
"updated_at",
"pushed_at",
"license",
"default_branch",
"open_issues",
"size",
"has_wiki",
"archived",
]
).to_csv(config["repos_searched"], index=False)
logger.info("[Done] Step 1: 0 repos saved")
# # Step 2: Concurrent relevance check with resume support (batch processing)
# repos_check_history = config["workdir"] / "repos_check_history.csv"
# if config["repos_checked"].exists():
# logger.info(f"[Skip] Step 2: {config['repos_checked']} exists")
# else:
# logger.info("=" * 60 + "\nStep 2: Check Relevance with LLM (Batch Concurrent)\n" + "=" * 60)
# # read to check list
# df_to_check = pd.read_csv(config["repos_searched"])
# total_repos = len(df_to_check)
# to_check_urls = set(df_to_check["url"].tolist())
# # read already checked list
# already_checked_urls = set()
# if repos_check_history.exists():
# df_checked = pd.read_csv(repos_check_history)
# already_checked_urls = set(df_checked["url"].tolist())
# logger.info(f"Resume: Already checked {len(already_checked_urls)}/{total_repos} repos")
# # pending repos to check
# pending_urls = to_check_urls - already_checked_urls
# unchecked = df_to_check[df_to_check["url"].isin(pending_urls)].to_dict("records")
# logger.info(f"Pending: {len(unchecked)} repos to check")
# if unchecked:
# # create parser
# parser = JsonOutputParser(pydantic_object=RelevanceResult)
# format_instructions = parser.get_format_instructions()
# keywords_str = ", ".join(expanded)
# system_content = f"""You are an expert at reading GitHub README.md files thoroughly and determining whether the repository hosts scientific code that is relevant to the scientific disciplines of {keywords_str}.
# Your task is to decide if the repository's scientific code is related to these disciplines.
# Only answer based on the information available in the README, repository description, and topics.
# {format_instructions}"""
# # concurrent check function
# async def check_one(repo):
# readme = get_readme(repo["owner"], repo["name"], config["github_token"])[:8000]
# messages = [
# {"role": "system", "content": system_content},
# {
# "role": "user",
# "content": f"""Think before you respond. Your answer should be based on your thorough understanding of the content of the README.md file.
# Does the README.md file indicate that the repository hosts code related to the scientific disciplines of {keywords_str}?
# Repository: {repo['full_name']}
# Description: {repo['description']}
# Topics: {repo['topics']}
# README: {readme}
# Answer by 'YES' or 'NO' in the relevant field. And provide your reasoning in the reason field.""",
# },
# ]
# try:
# result = await call_llm(
# messages,
# config["model"],
# config["base_url"],
# config["api_key"],
# pydantic_object=RelevanceResult,
# log_file=config["log_file"],
# temperature=0.1,
# )
# is_relevant = result.get("relevant", "").upper() == "YES"
# reason = result.get("reason", "")
# # return result for batch write
# return {
# "keyword": repo["keyword"],
# "full_name": repo["full_name"],
# "url": repo["url"],
# "description": repo["description"],
# "topics": repo["topics"],
# "is_relevant": "YES" if is_relevant else "NO",
# "reason": reason,
# "relevant": is_relevant,
# }
# except Exception as e:
# logger.error(f"Error checking {repo['full_name']}: {e}")
# return None
# # batch processing
# BATCH_SIZE = 10
# total_batches = (len(unchecked) + BATCH_SIZE - 1) // BATCH_SIZE
# for batch_idx in range(total_batches):
# start_idx = batch_idx * BATCH_SIZE
# end_idx = min(start_idx + BATCH_SIZE, len(unchecked))
# batch = unchecked[start_idx:end_idx]
# logger.info(f"Batch {batch_idx + 1}/{total_batches}: Processing {len(batch)} repos")
# # concurrent execute current batch
# batch_results = await asyncio.gather(*[check_one(r) for r in batch])
# # batch write result to history file
# valid_results = [r for r in batch_results if r is not None]
# if valid_results:
# df_batch = pd.DataFrame(valid_results)
# # only keep columns to write to CSV
# df_batch = df_batch[
# ["keyword", "full_name", "url", "description", "topics", "is_relevant", "reason"]
# ]
# df_batch.to_csv(
# repos_check_history,
# mode="a",
# header=not repos_check_history.exists(),
# index=False,
# encoding="utf-8",
# )
# for result in valid_results:
# status = "✓ Relevant" if result["relevant"] else "✗ Not relevant"
# logger.info(f" {status}: {result['full_name']}")
# logger.info(f"✓ Batch {batch_idx + 1}/{total_batches}: {len(valid_results)} repos saved")
# # collect all relevant repos from history file
# all_repos = df_to_check.to_dict("records")
# relevant_repos = []
# if repos_check_history.exists():
# df_history = pd.read_csv(repos_check_history)
# if not df_history.empty:
# relevant_urls = set(df_history[df_history["is_relevant"] == "YES"]["url"].tolist())
# relevant_repos = [r for r in all_repos if r["url"] in relevant_urls]
# # deduplicate by url and save
# if relevant_repos:
# df_relevant = pd.DataFrame(relevant_repos)
# df_relevant = df_relevant.drop_duplicates(subset=["url"])
# df_relevant.to_csv(config["repos_checked"], index=False, encoding="utf-8")
# logger.info(f"[Done] Step 2: {len(df_relevant)} relevant repos (deduplicated)")
# else:
# pd.DataFrame(columns=df_to_check.columns).to_csv(config["repos_checked"], index=False)
# logger.info("[Done] Step 2: 0 relevant repos")
# # Step 3: Clone repos with resume support
# if config["repos_checked"].exists():
# logger.info("=" * 60 + "\nStep 3: Clone Repos\n" + "=" * 60)
# # read and deduplicate repos
# df_checked = pd.read_csv(config["repos_checked"])
# if df_checked.empty:
# logger.info("[Skip] Step 3: No repos to clone")
# else:
# original_count = len(df_checked)
# df_checked = df_checked.drop_duplicates(subset=["url"])
# if len(df_checked) < original_count:
# logger.info(f"Deduplicated: {original_count} -> {len(df_checked)} repos")
# df_checked.to_csv(config["repos_checked"], index=False, encoding="utf-8")
# clone_repos(str(config["repos_checked"]), config["repos_raw"])
# logger.info("[Done] Step 3")
# else:
# logger.info(f"[Skip] Step 3: {config['repos_checked']} not found")
# # Step 4: Filter code files with resume support
# if config["repos_raw"].exists() and config["repos_raw"].is_dir():
# # Read repos to filter
# raw_repos = [d for d in config["repos_raw"].iterdir() if d.is_dir() and not d.name.startswith(".")]
# # Build full_name set from directory names
# raw_fullnames = set(d.name.replace("___", "/", 1) for d in raw_repos) # three underscores
# # Already filtered repos
# already_filtered_fullnames = set()
# if config["repos_filtered"].exists():
# already_filtered_fullnames = set(
# d.name.replace("___", "/", 1) # three underscores
# for d in config["repos_filtered"].iterdir()
# if d.is_dir() and not d.name.startswith(".")
# )
# # Pending repos to filter
# pending_fullnames = raw_fullnames - already_filtered_fullnames
# pending = [r for r in raw_repos if r.name.replace("___", "/", 1) in pending_fullnames]
# if not pending:
# logger.info(f"[Skip] Step 4: All {len(raw_repos)} repos already filtered")
# else:
# logger.info("=" * 60 + "\nStep 4: Filter Code Files\n" + "=" * 60)
# logger.info(f"Resume: Already filtered {len(already_filtered_fullnames)}/{len(raw_repos)} repos")
# logger.info(f"Pending: {len(pending)} repos to filter")
# config["repos_filtered"].mkdir(parents=True, exist_ok=True)
# for idx, repo in enumerate(pending):
# dest_repo = config["repos_filtered"] / repo.name # Keep same name format
# file_count = 0
# for root, dirs, files in os.walk(repo):
# dirs[:] = [
# d
# for d in dirs
# if not d.startswith(".")
# and d not in {"node_modules", "__pycache__", "venv", ".git", "build", "dist", "target"}
# ]
# for f in files:
# src = Path(root) / f
# if src.suffix.lower() in CODE_EXTENSIONS and src.exists():
# rel = src.relative_to(repo)
# dst = dest_repo / rel
# dst.parent.mkdir(parents=True, exist_ok=True)
# shutil.copy2(src, dst)
# file_count += 1
# if file_count > 0:
# full_name = repo.name.replace("___", "/", 1)
# logger.info(
# f"[{len(already_filtered_fullnames) + idx + 1}/{len(raw_repos)}] "
# f"{full_name}: {file_count} code files"
# )
# else:
# if dest_repo.exists():
# shutil.rmtree(dest_repo)
# logger.info("[Done] Step 4")
# else:
# logger.info(f"[Skip] Step 4: {config['repos_raw']} not found or empty")
if __name__ == "__main__":
asyncio.run(main())
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