codex-py/codex/cli.py

"""codex CLI — commands wired to domain modules."""

from __future__ import annotations

import json
from typing import Optional

import typer

app = typer.Typer(help="codex — personal knowledge base for scientific papers.")
discover_app = typer.Typer(help="Discovery queries over the citation graph.")
prov_app = typer.Typer(help="Provenance: @cite scan, code_links, bib export.")
app.add_typer(discover_app, name="discover")
app.add_typer(prov_app, name="provenance")


@app.command()
def ingest(
    paper_id: str = typer.Argument(..., help="arXiv ID, DOI, or OpenAlex W-ID"),
    source: Optional[str] = typer.Option(None, "--source", "-s", help="Path to .tex or .pdf"),  # noqa: UP045
) -> None:
    """Ingest a paper into the knowledge base."""
    from codex.ingest import ingest_paper

    result = ingest_paper(paper_id, source_path=source)
    typer.echo(
        f"Ingested {result.paper_id}: {result.chunks_upserted} chunks, "
        f"{result.citations_upserted} citations"
    )


@app.command()
def search(
    query: str = typer.Argument(..., help="Natural-language search query"),
    limit: int = typer.Option(10, "--limit", "-n", help="Number of results"),
) -> None:
    """Semantic similarity search over paper abstracts."""
    from codex.db import get_conn
    from codex.embed import get_embedder

    emb = get_embedder().encode_dense([query])[0].tolist()
    with get_conn() as conn:
        rows = conn.execute(
            """
            SELECT id, title, year,
                   abstract_emb <-> %(emb)s AS distance
            FROM   papers
            WHERE  abstract_emb IS NOT NULL
            ORDER  BY abstract_emb <-> %(emb)s
            LIMIT  %(limit)s
            """,
            {"emb": emb, "limit": limit},
        ).fetchall()
    for row in rows:
        typer.echo(f"[{row['distance']:.3f}] {row['id']} ({row['year']}) — {row['title']}")


@discover_app.command("leads")
def discover_leads(
    limit: int = typer.Option(20, "--limit", "-n"),
) -> None:
    """Show discovery leads: cited papers not yet ingested, ranked by pull."""
    from codex.discover import discovery_leads

    for item in discovery_leads(limit=limit):
        typer.echo(f"{item['pull']:>4}×  {item['cited_id']}")


@discover_app.command("citing")
def discover_citing(paper_id: str = typer.Argument(...)) -> None:
    """List papers that cite PAPER_ID."""
    from codex.discover import citing_papers

    for pid in citing_papers(paper_id):
        typer.echo(pid)


@discover_app.command("cited-by")
def discover_cited_by(paper_id: str = typer.Argument(...)) -> None:
    """List papers that PAPER_ID cites."""
    from codex.discover import cited_by

    for pid in cited_by(paper_id):
        typer.echo(pid)


@discover_app.command("cocited")
def discover_cocited(
    paper_id: str = typer.Argument(...),
    limit: int = typer.Option(10, "--limit", "-n"),
) -> None:
    """List papers frequently co-cited with PAPER_ID."""
    from codex.discover import cocited_papers

    for item in cocited_papers(paper_id, limit=limit):
        typer.echo(f"{item['co_citations']:>4}×  {item['paper_id']}")


@prov_app.command("scan")
def prov_scan(root_dir: str = typer.Argument(..., help="Root directory to scan")) -> None:
    """Scan C++ sources for @cite tags."""
    from codex.provenance import scan_cite_tags

    hits = scan_cite_tags(root_dir)
    typer.echo(json.dumps(hits, indent=2))


@prov_app.command("add-link")
def prov_add_link(
    symbol: str = typer.Argument(...),
    paper_id: Optional[str] = typer.Option(None, "--paper-id"),  # noqa: UP045
    role: Optional[str] = typer.Option(None, "--role"),  # noqa: UP045
    note: Optional[str] = typer.Option(None, "--note"),  # noqa: UP045
) -> None:
    """Add a code → paper link."""
    from codex.provenance import add_code_link

    link = add_code_link(symbol, paper_id=paper_id, role=role, note=note)
    typer.echo(f"Created code_link id={link.id}: {symbol} → {paper_id}")


@prov_app.command("links")
def prov_links(
    paper_id: Optional[str] = typer.Option(None, "--paper-id"),  # noqa: UP045
) -> None:
    """List code → paper links."""
    from codex.provenance import list_code_links

    for link in list_code_links(paper_id=paper_id):
        typer.echo(f"[{link.id}] {link.symbol} → {link.paper_id}  ({link.role})")


@prov_app.command("bib")
def prov_bib(
    paper_ids: Optional[list[str]] = typer.Argument(None),  # noqa: UP045, B008
    output: Optional[str] = typer.Option(  # noqa: UP045
        None, "--output", "-o", help="Write to file instead of stdout"
    ),
) -> None:
    """Export papers as BibTeX."""
    from codex.provenance import export_bib

    bib = export_bib(paper_ids if paper_ids else None)
    if output:
        from pathlib import Path

        Path(output).write_text(bib, encoding="utf-8")
        typer.echo(f"Wrote {output}")
    else:
        typer.echo(bib)


@app.command()
def ask(question: str = typer.Argument(..., help="Question to answer")) -> None:
    """Ask a question (RAG — not yet implemented)."""
    typer.echo("ask: not yet implemented", err=True)
    raise typer.Exit(1)