feat(cli): wire all commands via Typer (ingest, search, discover, provenance, ask-stub)
- Implement all CLI commands as specified in F-07: ingest, search, and discover subcommands (leads, citing, cited-by, cocited), and provenance subcommands (scan, add-link, links, bib). - Add ask command stub that exits with code 1 (not yet implemented). - Implement comprehensive tests with mocked dependencies (no real DB/API calls). Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
This commit is contained in:
Tarik Moussa
155
codex/cli.py
155
codex/cli.py
@@ -1,8 +1,157 @@
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"""codex CLI — commands wired to domain modules."""
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from __future__ import annotations
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import json
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from typing import Optional
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import typer
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app = typer.Typer(help="codex — personal knowledge base for scientific papers.")
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discover_app = typer.Typer(help="Discovery queries over the citation graph.")
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prov_app = typer.Typer(help="Provenance: @cite scan, code_links, bib export.")
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app.add_typer(discover_app, name="discover")
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app.add_typer(prov_app, name="provenance")
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@app.callback()
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def _main() -> None:
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"""codex CLI — commands land here in F-07."""
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@app.command()
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def ingest(
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paper_id: str = typer.Argument(..., help="arXiv ID, DOI, or OpenAlex W-ID"),
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source: Optional[str] = typer.Option(None, "--source", "-s", help="Path to .tex or .pdf"), # noqa: UP045
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) -> None:
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"""Ingest a paper into the knowledge base."""
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from codex.ingest import ingest_paper
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result = ingest_paper(paper_id, source_path=source)
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typer.echo(
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f"Ingested {result.paper_id}: {result.chunks_upserted} chunks, "
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f"{result.citations_upserted} citations"
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)
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@app.command()
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def search(
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query: str = typer.Argument(..., help="Natural-language search query"),
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limit: int = typer.Option(10, "--limit", "-n", help="Number of results"),
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) -> None:
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"""Semantic similarity search over paper abstracts."""
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from codex.db import get_conn
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from codex.embed import get_embedder
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emb = get_embedder().encode_dense([query])[0].tolist()
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with get_conn() as conn:
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rows = conn.execute(
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"""
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SELECT id, title, year,
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abstract_emb <-> %(emb)s AS distance
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FROM papers
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WHERE abstract_emb IS NOT NULL
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ORDER BY abstract_emb <-> %(emb)s
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LIMIT %(limit)s
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""",
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{"emb": emb, "limit": limit},
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).fetchall()
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for row in rows:
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typer.echo(f"[{row['distance']:.3f}] {row['id']} ({row['year']}) — {row['title']}")
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@discover_app.command("leads")
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def discover_leads(
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limit: int = typer.Option(20, "--limit", "-n"),
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) -> None:
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"""Show discovery leads: cited papers not yet ingested, ranked by pull."""
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from codex.discover import discovery_leads
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for item in discovery_leads(limit=limit):
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typer.echo(f"{item['pull']:>4}× {item['cited_id']}")
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@discover_app.command("citing")
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def discover_citing(paper_id: str = typer.Argument(...)) -> None:
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"""List papers that cite PAPER_ID."""
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from codex.discover import citing_papers
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for pid in citing_papers(paper_id):
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typer.echo(pid)
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@discover_app.command("cited-by")
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def discover_cited_by(paper_id: str = typer.Argument(...)) -> None:
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"""List papers that PAPER_ID cites."""
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from codex.discover import cited_by
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for pid in cited_by(paper_id):
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typer.echo(pid)
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@discover_app.command("cocited")
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def discover_cocited(
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paper_id: str = typer.Argument(...),
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limit: int = typer.Option(10, "--limit", "-n"),
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) -> None:
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"""List papers frequently co-cited with PAPER_ID."""
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from codex.discover import cocited_papers
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for item in cocited_papers(paper_id, limit=limit):
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typer.echo(f"{item['co_citations']:>4}× {item['paper_id']}")
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@prov_app.command("scan")
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def prov_scan(root_dir: str = typer.Argument(..., help="Root directory to scan")) -> None:
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"""Scan C++ sources for @cite tags."""
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from codex.provenance import scan_cite_tags
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hits = scan_cite_tags(root_dir)
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typer.echo(json.dumps(hits, indent=2))
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@prov_app.command("add-link")
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def prov_add_link(
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symbol: str = typer.Argument(...),
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paper_id: Optional[str] = typer.Option(None, "--paper-id"), # noqa: UP045
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role: Optional[str] = typer.Option(None, "--role"), # noqa: UP045
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note: Optional[str] = typer.Option(None, "--note"), # noqa: UP045
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) -> None:
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"""Add a code → paper link."""
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from codex.provenance import add_code_link
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link = add_code_link(symbol, paper_id=paper_id, role=role, note=note)
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typer.echo(f"Created code_link id={link.id}: {symbol} → {paper_id}")
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@prov_app.command("links")
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def prov_links(
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paper_id: Optional[str] = typer.Option(None, "--paper-id"), # noqa: UP045
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) -> None:
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"""List code → paper links."""
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from codex.provenance import list_code_links
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for link in list_code_links(paper_id=paper_id):
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typer.echo(f"[{link.id}] {link.symbol} → {link.paper_id} ({link.role})")
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@prov_app.command("bib")
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def prov_bib(
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paper_ids: Optional[list[str]] = typer.Argument(None), # noqa: UP045, B008
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output: Optional[str] = typer.Option( # noqa: UP045
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None, "--output", "-o", help="Write to file instead of stdout"
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),
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) -> None:
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"""Export papers as BibTeX."""
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from codex.provenance import export_bib
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bib = export_bib(paper_ids if paper_ids else None)
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if output:
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from pathlib import Path
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Path(output).write_text(bib, encoding="utf-8")
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typer.echo(f"Wrote {output}")
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else:
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typer.echo(bib)
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@app.command()
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def ask(question: str = typer.Argument(..., help="Question to answer")) -> None:
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"""Ask a question (RAG — not yet implemented)."""
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typer.echo("ask: not yet implemented", err=True)
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raise typer.Exit(1)
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0
tests/cli/__init__.py
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0
tests/cli/__init__.py
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291
tests/cli/test_cli.py
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291
tests/cli/test_cli.py
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@@ -0,0 +1,291 @@
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"""Tests for codex.cli — Typer command-line interface.
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All external calls (ingest, DB, embed, discovery, provenance) are mocked
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so the suite runs offline without real API calls.
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"""
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from __future__ import annotations
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from typing import Any
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from unittest.mock import MagicMock, patch
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import numpy as np
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from typer.testing import CliRunner
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from codex.cli import app
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from codex.ingest import IngestResult
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from codex.models import CodeLink
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runner = CliRunner()
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class TestIngest:
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"""Tests for `codex ingest` command."""
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def test_ingest_command(self) -> None:
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"""Test basic ingest command with mocked ingest_paper."""
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with patch("codex.ingest.ingest_paper") as mock_ingest:
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mock_ingest.return_value = IngestResult(
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paper_id="2301.07041",
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chunks_upserted=5,
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citations_upserted=3,
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)
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result = runner.invoke(app, ["ingest", "2301.07041"])
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assert result.exit_code == 0
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assert "2301.07041" in result.stdout
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assert "5 chunks" in result.stdout
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assert "3 citations" in result.stdout
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class TestSearch:
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"""Tests for `codex search` command."""
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def test_search_command(self) -> None:
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"""Test search command with mocked embedder and DB."""
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with (
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patch("codex.embed.get_embedder") as mock_embedder,
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patch("codex.db.get_conn") as mock_get_conn,
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):
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# Mock embedder - return numpy array with one row
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mock_emb_instance = MagicMock()
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mock_emb_instance.encode_dense.return_value = np.array([[0.1, 0.2, 0.3]])
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mock_embedder.return_value = mock_emb_instance
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# Mock DB connection
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mock_conn = MagicMock()
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mock_conn.__enter__.return_value = mock_conn
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mock_conn.__exit__.return_value = None
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mock_conn.execute.return_value.fetchall.return_value = [
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{
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"id": "2301.07041",
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"title": "Test Paper",
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"year": 2023,
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"distance": 0.123,
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},
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{
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"id": "2301.07042",
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"title": "Another Paper",
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"year": 2023,
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"distance": 0.456,
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},
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]
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mock_get_conn.return_value = mock_conn
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result = runner.invoke(app, ["search", "machine learning", "--limit", "2"])
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assert result.exit_code == 0
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assert "2301.07041" in result.stdout
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assert "2301.07042" in result.stdout
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assert "Test Paper" in result.stdout
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assert "0.123" in result.stdout
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class TestDiscoverLeads:
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"""Tests for `codex discover leads` command."""
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def test_discover_leads_command(self) -> None:
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"""Test discover leads command with mocked discovery_leads."""
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with patch("codex.discover.discovery_leads") as mock_leads:
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mock_leads.return_value = [
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{"cited_id": "2301.07041", "pull": 5},
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{"cited_id": "2301.07042", "pull": 3},
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]
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result = runner.invoke(app, ["discover", "leads", "--limit", "2"])
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assert result.exit_code == 0
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assert "2301.07041" in result.stdout
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assert "2301.07042" in result.stdout
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assert "5×" in result.stdout
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assert "3×" in result.stdout
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class TestDiscoverCiting:
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"""Tests for `codex discover citing` command."""
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def test_discover_citing_command(self) -> None:
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"""Test discover citing command with mocked citing_papers."""
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with patch("codex.discover.citing_papers") as mock_citing:
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mock_citing.return_value = ["2301.07041", "2301.07042"]
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result = runner.invoke(app, ["discover", "citing", "2301.07043"])
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assert result.exit_code == 0
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assert "2301.07041" in result.stdout
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assert "2301.07042" in result.stdout
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class TestDiscoverCitedBy:
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"""Tests for `codex discover cited-by` command."""
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def test_discover_cited_by_command(self) -> None:
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"""Test discover cited-by command with mocked cited_by."""
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with patch("codex.discover.cited_by") as mock_cited:
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mock_cited.return_value = ["2301.07041", "2301.07042"]
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result = runner.invoke(app, ["discover", "cited-by", "2301.07043"])
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assert result.exit_code == 0
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assert "2301.07041" in result.stdout
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assert "2301.07042" in result.stdout
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class TestDiscoverCocited:
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"""Tests for `codex discover cocited` command."""
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def test_discover_cocited_command(self) -> None:
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"""Test discover cocited command with mocked cocited_papers."""
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with patch("codex.discover.cocited_papers") as mock_cocited:
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mock_cocited.return_value = [
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{"paper_id": "2301.07041", "co_citations": 5},
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{"paper_id": "2301.07042", "co_citations": 3},
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]
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result = runner.invoke(app, ["discover", "cocited", "2301.07043"])
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assert result.exit_code == 0
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assert "2301.07041" in result.stdout
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assert "2301.07042" in result.stdout
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assert "5×" in result.stdout
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assert "3×" in result.stdout
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class TestProvScan:
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"""Tests for `codex provenance scan` command."""
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def test_prov_scan_command(self) -> None:
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"""Test provenance scan command with mocked scan_cite_tags."""
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with patch("codex.provenance.scan_cite_tags") as mock_scan:
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mock_scan.return_value = [
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{
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"file": "src/main.cpp",
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"line": "42",
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"symbol": "compute_embedding",
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"bibkey": "2301.07041",
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},
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{
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"file": "src/utils.h",
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"line": "10",
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"symbol": "helper_func",
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"bibkey": "2301.07042",
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},
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]
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result = runner.invoke(app, ["provenance", "scan", "/path/to/src"])
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assert result.exit_code == 0
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assert "src/main.cpp" in result.stdout
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assert "2301.07041" in result.stdout
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assert "compute_embedding" in result.stdout
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class TestProvAddLink:
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"""Tests for `codex provenance add-link` command."""
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def test_prov_add_link_command(self) -> None:
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"""Test provenance add-link command with mocked add_code_link."""
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with patch("codex.provenance.add_code_link") as mock_add:
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mock_link = CodeLink(
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id=1,
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symbol="my_func",
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paper_id="2301.07041",
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role="core_algorithm",
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note="Primary reference",
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added_at="2023-01-01T00:00:00Z",
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)
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mock_add.return_value = mock_link
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result = runner.invoke(
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app,
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[
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"provenance",
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"add-link",
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"my_func",
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"--paper-id",
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"2301.07041",
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"--role",
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"core_algorithm",
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"--note",
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"Primary reference",
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],
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)
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assert result.exit_code == 0
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assert "Created code_link" in result.stdout
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assert "my_func" in result.stdout
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assert "2301.07041" in result.stdout
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class TestProvLinks:
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"""Tests for `codex provenance links` command."""
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def test_prov_links_command(self) -> None:
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"""Test provenance links command with mocked list_code_links."""
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with patch("codex.provenance.list_code_links") as mock_links:
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mock_links.return_value = [
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CodeLink(
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id=1,
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symbol="my_func",
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paper_id="2301.07041",
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role="core",
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note=None,
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added_at="2023-01-01T00:00:00Z",
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),
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CodeLink(
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id=2,
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symbol="another_func",
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paper_id="2301.07042",
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role="utility",
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note=None,
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added_at="2023-01-02T00:00:00Z",
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),
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]
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result = runner.invoke(app, ["provenance", "links"])
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assert result.exit_code == 0
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assert "[1]" in result.stdout
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assert "[2]" in result.stdout
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assert "my_func" in result.stdout
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assert "another_func" in result.stdout
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class TestProvBib:
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"""Tests for `codex provenance bib` command."""
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def test_prov_bib_command(self) -> None:
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"""Test provenance bib command with mocked export_bib."""
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with patch("codex.provenance.export_bib") as mock_export:
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mock_export.return_value = "@article{2301.07041,\n title = {Test},\n}"
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result = runner.invoke(app, ["provenance", "bib"])
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assert result.exit_code == 0
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assert "@article" in result.stdout
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assert "2301.07041" in result.stdout
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def test_prov_bib_with_output_file(self, tmp_path: Any) -> None:
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"""Test provenance bib command writing to file."""
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with patch("codex.provenance.export_bib") as mock_export:
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mock_export.return_value = "@article{2301.07041,\n title = {Test},\n}"
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output_file = tmp_path / "refs.bib"
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result = runner.invoke(app, ["provenance", "bib", "--output", str(output_file)])
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assert result.exit_code == 0
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assert "Wrote" in result.stdout
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assert output_file.exists()
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assert "@article" in output_file.read_text()
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class TestAsk:
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"""Tests for `codex ask` command."""
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def test_ask_command_exits_1(self) -> None:
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"""Test that ask command exits with code 1 (not yet implemented)."""
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result = runner.invoke(app, ["ask", "what is machine learning?"])
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assert result.exit_code == 1
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assert "not yet implemented" in result.stdout or "not yet implemented" in result.stderr
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