From 5109c8c9d69c8751ffd5744675db2a7b5173a407 Mon Sep 17 00:00:00 2001 From: Preston Williams Date: Sun, 1 Nov 2026 16:46:51 -0500 Subject: [PATCH 1/2] Add the repo crawler and an end-to-end ingest pipeline crawler.py keeps shallow clones of the org's public, active repos under a root folder with a manifest of commits and statuses; pipeline.py crawls and then chunks every synced repo into one chunks.jsonl. Co-Authored-By: Claude Opus 5.5 --- .gitignore | 3 + ingest/README.md | 16 ++++ ingest/crawler.py | 131 ++++++++++++++++++++++++++ ingest/pipeline.py | 73 +++++++++++++++ ingest/repos.toml | 4 + pyproject.toml | 1 + tests/test_crawler.py | 143 ++++++++++++++++++++++++++++ uv.lock | 211 ++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 582 insertions(+) create mode 100644 ingest/crawler.py create mode 100644 ingest/pipeline.py create mode 100644 ingest/repos.toml create mode 100644 tests/test_crawler.py diff --git a/.gitignore b/.gitignore index 5112c5f..9cb4fe5 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,6 @@ __pycache__/ dist/ build/ .DS_Store + +# local crawler output +data/ diff --git a/ingest/README.md b/ingest/README.md index 1f90e3a..0bd1c0c 100644 --- a/ingest/README.md +++ b/ingest/README.md @@ -2,6 +2,22 @@ Clone CDS repos, filter, secret-scan, and chunk them into chunks.jsonl (steps 3-4). +```bash +uv run python -m ingest.pipeline --root data/repos --out data/chunks.jsonl +``` + +`pipeline.py` runs the crawler, then chunks every synced repo into one file. Add +`--only FTM-Snake slurm-aware` or `--limit 5` to crawl a few repos; partial runs never delete +clones. Set `GITHUB_TOKEN` for higher API rate limits. + +`crawler.py` lists the org's public, non-fork, non-archived, non-empty repos (minus `exclude` +in `repos.toml`), keeps a shallow clone of each default branch under `--root`, and records +every repo's commit and status (`ok`, `stale`, `skipped`, `failed`, `removed`) in +`/manifest.json`. A clone with local changes is left alone, a failed update keeps the +last good copy, and a full run deletes clones of repos that are no longer listed. + +To chunk one checkout by hand: + ```bash uv run python -m ingest.chunker path/to/repo --repo CornellDataScience/name --out chunks.jsonl ``` diff --git a/ingest/crawler.py b/ingest/crawler.py new file mode 100644 index 0000000..af9cbd8 --- /dev/null +++ b/ingest/crawler.py @@ -0,0 +1,131 @@ +"""Keep shallow clones of the org's repos under a root folder, recorded in root/manifest.json.""" + +import json +import os +import shutil +import subprocess +import tomllib +from concurrent.futures import ThreadPoolExecutor +from dataclasses import asdict, dataclass +from datetime import datetime, timezone +from pathlib import Path + +CONFIG_PATH = Path(__file__).with_name("repos.toml") +GIT_TIMEOUT_SECONDS = 600 + + +@dataclass +class RepoInfo: + full_name: str # owner/name + clone_url: str + default_branch: str + fork: bool = False + archived: bool = False + empty: bool = False + + +@dataclass +class ManifestEntry: + full_name: str + path: str # relative to the root + default_branch: str + commit_sha: str | None + status: str # ok | stale | skipped | failed | removed + synced_at: str + error: str | None = None + + +def load_config(path: Path = CONFIG_PATH) -> dict: + with path.open("rb") as f: + return tomllib.load(f) + + +def list_org_repos(org: str, token: str | None = None) -> list[RepoInfo]: + from github import Auth, Github + + gh = Github(auth=Auth.Token(token)) if token else Github() + return [ + RepoInfo(r.full_name, r.clone_url, r.default_branch, r.fork, r.archived, r.size == 0) + for r in gh.get_organization(org).get_repos(type="public") + ] + + +def select_repos(repos: list[RepoInfo], exclude=(), only=(), limit: int | None = None) -> list[RepoInfo]: + names = lambda r: {r.full_name, r.full_name.split("/")[-1]} # noqa: E731 + selected = [ + r for r in sorted(repos, key=lambda r: r.full_name.lower()) + if not (r.fork or r.archived or r.empty) and not names(r) & set(exclude) and (not only or names(r) & set(only)) + ] + return selected[:limit] if limit else selected + + +def crawl(root: Path, repos: list[RepoInfo], jobs: int = 8, prune: bool = True) -> dict[str, ManifestEntry]: + """Clone or update each repo; with prune, delete clones of repos no longer listed.""" + root.mkdir(parents=True, exist_ok=True) + previous = read_manifest(root) + with ThreadPoolExecutor(max_workers=jobs) as pool: + entries = {e.full_name: e for e in pool.map(lambda r: sync_repo(root, r), repos)} + for name, old in previous.items(): + if name in entries: + continue + if prune and old.status != "removed": + shutil.rmtree(root / old.path, ignore_errors=True) + entries[name] = ManifestEntry(name, old.path, old.default_branch, None, "removed", _now()) + elif not prune: + entries[name] = old + write_manifest(root, entries) + return entries + + +def sync_repo(root: Path, repo: RepoInfo) -> ManifestEntry: + rel = repo.full_name + dest = root / rel + entry = lambda status, sha=None, error=None: ManifestEntry( # noqa: E731 + repo.full_name, rel, repo.default_branch, sha, status, _now(), error + ) + if not (dest / ".git").is_dir(): + shutil.rmtree(dest, ignore_errors=True) # leftovers of an interrupted clone + try: + _git(None, "clone", "--quiet", "--depth", "1", "--single-branch", "--branch", repo.default_branch, repo.clone_url, str(dest)) + except RuntimeError as e: + shutil.rmtree(dest, ignore_errors=True) + return entry("failed", error=str(e)) + return entry("ok", _git(dest, "rev-parse", "HEAD")) + + if _git(dest, "status", "--porcelain"): + return entry("skipped", _git(dest, "rev-parse", "HEAD"), "local changes in the clone") + try: + _git(dest, "fetch", "--quiet", "--depth", "1", "origin", repo.default_branch) + _git(dest, "reset", "--quiet", "--hard", "FETCH_HEAD") + except RuntimeError as e: + return entry("stale", _git(dest, "rev-parse", "HEAD"), str(e)) # keep indexing the last good copy + return entry("ok", _git(dest, "rev-parse", "HEAD")) + + +def read_manifest(root: Path) -> dict[str, ManifestEntry]: + path = root / "manifest.json" + if not path.is_file(): + return {} + return {name: ManifestEntry(**e) for name, e in json.loads(path.read_text())["repos"].items()} + + +def write_manifest(root: Path, entries: dict[str, ManifestEntry]): + data = {"synced_at": _now(), "repos": {name: asdict(entries[name]) for name in sorted(entries)}} + tmp = root / "manifest.json.tmp" + tmp.write_text(json.dumps(data, indent=2) + "\n") + tmp.replace(root / "manifest.json") + + +def _git(cwd: Path | None, *args: str) -> str: + env = {**os.environ, "GIT_TERMINAL_PROMPT": "0"} # fail instead of prompting for credentials + try: + result = subprocess.run(["git", *args], cwd=cwd, env=env, capture_output=True, text=True, timeout=GIT_TIMEOUT_SECONDS) + except subprocess.TimeoutExpired: + raise RuntimeError(f"git {args[0]} timed out") from None + if result.returncode != 0: + raise RuntimeError(f"git {args[0]} failed: {result.stderr.strip().splitlines()[-1] if result.stderr.strip() else result.returncode}") + return result.stdout.strip() + + +def _now() -> str: + return datetime.now(timezone.utc).isoformat(timespec="seconds") diff --git a/ingest/pipeline.py b/ingest/pipeline.py new file mode 100644 index 0000000..fdca604 --- /dev/null +++ b/ingest/pipeline.py @@ -0,0 +1,73 @@ +"""Crawl the org, then chunk every synced repo into one chunks.jsonl. + + uv run python -m ingest.pipeline --root data/repos --out data/chunks.jsonl --only FTM-Snake slurm-aware +""" + +import argparse +import json +import os +from collections import Counter +from pathlib import Path + +from ingest import crawler +from ingest.chunker import chunk_repo, llama_token_counter + +CHUNKABLE = {"ok", "stale"} + + +def run(root: Path, out: Path, repos: list[crawler.RepoInfo], count_tokens, jobs=8, prune=True, scan_secrets=True) -> dict: + entries = crawler.crawl(root, repos, jobs=jobs, prune=prune) + listed = {r.full_name for r in repos} + skipped, redacted, chunks = Counter(), [], Counter() + out.parent.mkdir(parents=True, exist_ok=True) + tmp = out.with_name(out.name + ".tmp") + with tmp.open("w") as f: + for name in sorted(listed): + entry = entries[name] + if entry.status not in CHUNKABLE: + continue + for record in chunk_repo(root / entry.path, name, count_tokens, skipped, redacted, scan_secrets): + f.write(json.dumps(record) + "\n") + chunks[name] += 1 + tmp.replace(out) # a failed run never leaves a half-written file + return {"entries": entries, "chunks": chunks, "skipped": skipped, "redacted": redacted} + + +def main(): + parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("--root", type=Path, default=Path("data/repos"), help="Where clones and manifest.json live") + parser.add_argument("--out", type=Path, default=Path("data/chunks.jsonl")) + parser.add_argument("--config", type=Path, default=crawler.CONFIG_PATH) + parser.add_argument("--only", nargs="+", default=(), help="Crawl just these repos (no pruning)") + parser.add_argument("--limit", type=int, help="Crawl the first N repos (no pruning)") + parser.add_argument("--jobs", type=int, default=8, help="Parallel clones") + parser.add_argument("--no-secret-scan", action="store_true", help="Skip gitleaks (never for real ingestion)") + args = parser.parse_args() + + config = crawler.load_config(args.config) + listing = crawler.list_org_repos(config["org"], os.environ.get("GITHUB_TOKEN")) + repos = crawler.select_repos(listing, config.get("exclude", []), args.only, args.limit) + if args.only and len(repos) < len(set(args.only)): + found = {r.full_name.split("/")[-1] for r in repos} + print(f"Not found or not indexable: {sorted(set(args.only) - found)}") + partial = bool(args.only or args.limit) + + result = run(args.root, args.out, repos, llama_token_counter(), args.jobs, prune=not partial, scan_secrets=not args.no_secret_scan) + + statuses = Counter(e.status for e in result["entries"].values()) + print(f"Repos: {dict(statuses)}") + for e in sorted(result["entries"].values(), key=lambda e: e.full_name): + if e.status in {"failed", "stale", "skipped"}: + print(f" {e.status}: {e.full_name}: {e.error}") + elif e.status == "removed": + print(f" removed: {e.full_name}") + print(f"Wrote {sum(result['chunks'].values())} chunks from {len(result['chunks'])} repos to {args.out}") + print(f"Skipped files: {dict(result['skipped']) or 'none'}") + if args.no_secret_scan: + print("WARNING: secret scan disabled") + for finding in result["redacted"]: + print(f"Redacted {finding.rule} at {finding.path}:{finding.line}") + + +if __name__ == "__main__": + main() diff --git a/ingest/repos.toml b/ingest/repos.toml new file mode 100644 index 0000000..e83fa3b --- /dev/null +++ b/ingest/repos.toml @@ -0,0 +1,4 @@ +# Which GitHub repos the crawler indexes: every public, non-fork, non-archived, +# non-empty repo in `org`, minus `exclude` (names without the org). +org = "CornellDataScience" +exclude = [] diff --git a/pyproject.toml b/pyproject.toml index 053b46c..3b557ac 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,6 +9,7 @@ dependencies = [ "huggingface-hub>=0.30", "nbformat>=5.11.1", "pathspec>=1.1.1", + "pygithub>=2.10.0", "torch==2.14.1", "transformers>=4.50", "tree-sitter>=0.26.0", diff --git a/tests/test_crawler.py b/tests/test_crawler.py new file mode 100644 index 0000000..f3b6878 --- /dev/null +++ b/tests/test_crawler.py @@ -0,0 +1,143 @@ +import json +import subprocess + +import pytest + +from ingest import crawler, pipeline +from ingest.crawler import RepoInfo, crawl, read_manifest, select_repos + + +def git(path, *args): + return subprocess.run( + ["git", "-C", str(path), "-c", "user.name=t", "-c", "user.email=t@t", *args], + check=True, capture_output=True, text=True, + ).stdout.strip() + + +def make_remote(tmp_path, name, files, branch="main"): + path = tmp_path / "remotes" / name + path.mkdir(parents=True) + git(path, "init", "-q", "-b", branch) + commit(path, files) + return RepoInfo(f"org/{name}", path.as_uri(), branch) + + +def commit(path, files): + for rel, text in files.items(): + (path / rel).parent.mkdir(parents=True, exist_ok=True) + (path / rel).write_text(text) + git(path, "add", ".") + git(path, "commit", "-qm", "change") + return git(path, "rev-parse", "HEAD") + + +def head(remote: RepoInfo): + return git(remote.clone_url.removeprefix("file://"), "rev-parse", "HEAD") + + +@pytest.fixture +def root(tmp_path): + return tmp_path / "root" + + +def test_select_repos(): + repos = [ + RepoInfo("org/b", "", "main"), + RepoInfo("org/a", "", "main"), + RepoInfo("org/fork", "", "main", fork=True), + RepoInfo("org/old", "", "main", archived=True), + RepoInfo("org/empty", "", "main", empty=True), + RepoInfo("org/skip", "", "main"), + ] + assert [r.full_name for r in select_repos(repos, exclude=["skip"])] == ["org/a", "org/b"] + assert [r.full_name for r in select_repos(repos, only=["b"])] == ["org/b"] + assert [r.full_name for r in select_repos(repos, only=["fork"])] == [] + assert [r.full_name for r in select_repos(repos, limit=1)] == ["org/a"] + + +def test_clone_then_update(tmp_path, root): + remote = make_remote(tmp_path, "app", {"main.py": "x = 1\n"}) + entries = crawl(root, [remote]) + assert entries["org/app"].status == "ok" + assert entries["org/app"].commit_sha == head(remote) + assert git(root / "org/app", "rev-parse", "--is-shallow-repository") == "true" + + new_sha = commit(tmp_path / "remotes/app", {"main.py": "x = 2\n"}) + entries = crawl(root, [remote]) + assert entries["org/app"].commit_sha == new_sha + assert (root / "org/app/main.py").read_text() == "x = 2\n" + assert read_manifest(root)["org/app"].commit_sha == new_sha + + +def test_non_main_default_branch(tmp_path, root): + remote = make_remote(tmp_path, "legacy", {"a.py": "x = 1\n"}, branch="master") + assert crawl(root, [remote])["org/legacy"].status == "ok" + + +def test_local_changes_are_left_alone(tmp_path, root): + remote = make_remote(tmp_path, "app", {"main.py": "x = 1\n"}) + old_sha = crawl(root, [remote])["org/app"].commit_sha + (root / "org/app/main.py").write_text("edited locally\n") + commit(tmp_path / "remotes/app", {"main.py": "x = 2\n"}) + entry = crawl(root, [remote])["org/app"] + assert entry.status == "skipped" and entry.commit_sha == old_sha + assert (root / "org/app/main.py").read_text() == "edited locally\n" + + +def test_failures_are_isolated(tmp_path, root): + good = make_remote(tmp_path, "good", {"a.py": "x = 1\n"}) + bad = RepoInfo("org/missing", (tmp_path / "nope").as_uri(), "main") + entries = crawl(root, [good, bad]) + assert entries["org/good"].status == "ok" + assert entries["org/missing"].status == "failed" and entries["org/missing"].error + assert not (root / "org/missing").exists() + + +def test_fetch_failure_keeps_last_good_copy(tmp_path, root): + remote = make_remote(tmp_path, "app", {"main.py": "x = 1\n"}) + sha = crawl(root, [remote])["org/app"].commit_sha + moved = RepoInfo("org/app", (tmp_path / "gone").as_uri(), "main") + git(root / "org/app", "remote", "set-url", "origin", moved.clone_url) + entry = crawl(root, [moved])["org/app"] + assert entry.status == "stale" and entry.commit_sha == sha + + +def test_prune_removes_only_repos_the_crawler_cloned(tmp_path, root): + a = make_remote(tmp_path, "a", {"a.py": "x = 1\n"}) + b = make_remote(tmp_path, "b", {"b.py": "x = 1\n"}) + crawl(root, [a, b]) + (root / "someone-elses-dir").mkdir() + + entries = crawl(root, [a], prune=False) # partial runs (--only/--limit) never delete + assert (root / "org/b").exists() and entries["org/b"].status == "ok" + + entries = crawl(root, [a]) + assert entries["org/b"].status == "removed" + assert not (root / "org/b").exists() + assert (root / "someone-elses-dir").exists() + assert "org/b" not in crawl(root, [a]) # reported once, then dropped + + +def test_pipeline_writes_combined_chunks(tmp_path, root): + a = make_remote(tmp_path, "a", {"src/app.py": "def main():\n return 1\n", "data/x.csv": "a,b\n"}) + b = make_remote(tmp_path, "b", {"README.md": "# B\n\nHello.\n"}) + out = tmp_path / "chunks.jsonl" + result = pipeline.run(root, out, [a, b], lambda t: len(t.split()), jobs=2, scan_secrets=False) + records = [json.loads(line) for line in out.read_text().splitlines()] + assert {(r["repo"], r["path"]) for r in records} == {("org/a", "src/app.py"), ("org/b", "README.md")} + assert {r["commit_sha"] for r in records if r["repo"] == "org/a"} == {head(a)} + assert result["chunks"] == {"org/a": 1, "org/b": 1} + assert not out.with_name(out.name + ".tmp").exists() + + +def test_pipeline_skips_repos_it_could_not_sync(tmp_path, root): + good = make_remote(tmp_path, "good", {"a.py": "x = 1\n"}) + bad = RepoInfo("org/missing", (tmp_path / "nope").as_uri(), "main") + result = pipeline.run(root, tmp_path / "out.jsonl", [good, bad], lambda t: len(t.split()), scan_secrets=False) + assert result["chunks"] == {"org/good": 1} + + +def test_default_config_is_valid(): + config = crawler.load_config() + assert config["org"] == "CornellDataScience" + assert isinstance(config["exclude"], list) diff --git a/uv.lock b/uv.lock index 1f35d31..bbaf1e7 100644 --- a/uv.lock +++ b/uv.lock @@ -22,6 +22,7 @@ dependencies = [ { name = "huggingface-hub" }, { name = "nbformat" }, { name = "pathspec" }, + { name = "pygithub" }, { name = "torch", version = "2.14.1", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux'" }, { name = "torch", version = "2.14.1+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux'" }, { name = "transformers" }, @@ -47,6 +48,7 @@ requires-dist = [ { name = "mamba-ssm", marker = "sys_platform == 'linux' and extra == 'cuda'", git = "https://github.com/state-spaces/mamba?rev=e9594ce1c732d97440f0332fdc43170a2294dbfa" }, { name = "nbformat", specifier = ">=5.11.1" }, { name = "pathspec", specifier = 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insertions(+), 3 deletions(-) diff --git a/ingest/crawler.py b/ingest/crawler.py index af9cbd8..8a75f0c 100644 --- a/ingest/crawler.py +++ b/ingest/crawler.py @@ -16,7 +16,7 @@ @dataclass class RepoInfo: - full_name: str # owner/name + full_name: str clone_url: str default_branch: str fork: bool = False diff --git a/ingest/repos.toml b/ingest/repos.toml index e83fa3b..d1dc167 100644 --- a/ingest/repos.toml +++ b/ingest/repos.toml @@ -1,4 +1,3 @@ -# Which GitHub repos the crawler indexes: every public, non-fork, non-archived, -# non-empty repo in `org`, minus `exclude` (names without the org). +# Indexed: public, non-fork, non-archived, non-empty repos in `org`, minus `exclude` (names only). org = "CornellDataScience" exclude = []