c4106b0f51
find_gaps defaulted its probe topics to paper titles, so a title — which retrieves mostly its own single bibkey — fell below synthesis_gap_min_coverage and flagged almost every paper as a 'gap'. Coverage-map gaps now run only for explicitly-requested topics; the CLI gains a repeatable --topic option. The code-vs-corpus gap path (precise) is unchanged and still default. Tests: the two cases that relied on default-title coverage gaps now pass explicit topics; added a regression that no coverage gaps appear without --topic. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
655 lines
22 KiB
Python
655 lines
22 KiB
Python
"""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 datetime import UTC, datetime
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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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wiki_app = typer.Typer(help="Wiki-compile: grounded concept pages over the RAG substrate.")
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synth_app = typer.Typer(help="Synthesis: grounded leads and quarantined conjectures (F-13).")
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quality_app = typer.Typer(help="Chunk quality gate and section classification (F-16).")
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graph_app = typer.Typer(help="Citation graph analytics: PageRank, coupling, dangling leads (F-15).")
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# F-09: search sub-app with paper (semantic) and formula (FTS) subcommands
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search_app = typer.Typer(
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help="Search: semantic paper search and formula full-text search.",
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invoke_without_command=True,
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)
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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.add_typer(wiki_app, name="wiki")
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app.add_typer(synth_app, name="synthesis")
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app.add_typer(quality_app, name="quality")
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app.add_typer(graph_app, name="graph")
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app.add_typer(search_app, name="search")
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@app.command()
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def migrate() -> None:
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"""Apply infra/schema.sql to bring the database schema up to date (idempotent).
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Must connect as a role that can run DDL (owns / can CREATE + ALTER the tables).
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The application's DATABASE_URL is usually a least-privilege DML role and will
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fail with InsufficientPrivilege; set MIGRATION_DATABASE_URL to a privileged
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(owner/superuser) connection (audit M-1).
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"""
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import psycopg
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import psycopg.rows
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from codex.config import get_settings
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from codex.db import apply_schema
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settings = get_settings()
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url = settings.migration_database_url or settings.database_url
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try:
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with psycopg.connect(url, row_factory=psycopg.rows.dict_row) as conn:
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apply_schema(conn)
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except psycopg.errors.InsufficientPrivilege as exc:
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typer.echo(
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"ERROR: schema migration needs a role that owns the tables "
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"(CREATE/ALTER). Set MIGRATION_DATABASE_URL to a privileged connection "
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f"and retry. ({exc})",
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err=True,
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)
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raise typer.Exit(1) from exc
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typer.echo("Schema applied — database is up to date.")
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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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rich: bool = typer.Option( # noqa: A002
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False,
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"--rich",
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help="Extract formulas and figures (requires PDF source, F-09).",
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),
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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, rich=rich)
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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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f"{result.formulas_upserted} formulas, "
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f"{result.figures_upserted} figures"
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)
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# ---------------------------------------------------------------------------
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# F-09: Search command group
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# ---------------------------------------------------------------------------
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@search_app.callback(invoke_without_command=True)
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def search_callback(ctx: typer.Context) -> None:
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"""Search subcommands: ``paper`` for semantic search, ``formula`` for LaTeX FTS."""
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if ctx.invoked_subcommand is None:
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typer.echo(ctx.get_help())
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raise typer.Exit(0)
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@search_app.command("paper")
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def search_paper(
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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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cite_boost: bool = typer.Option(
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False,
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"--cite-boost",
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help="Weight results by citation PageRank (F-15). Graceful when corpus < 5 papers.",
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),
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) -> None:
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"""Semantic similarity search over paper abstracts."""
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from codex.config import get_settings
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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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if cite_boost and rows:
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from codex.graph import build_citation_graph, citation_pagerank
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settings = get_settings()
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graph = build_citation_graph(conn)
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pr = citation_pagerank(graph)
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alpha = settings.graph_cite_boost_alpha
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results = []
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for row in rows:
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pr_score = pr.get(row["id"], 0.0)
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# distance is lower=better; divide to reduce distance for high-PR papers
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boosted = row["distance"] / (1.0 + alpha * pr_score)
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results.append((boosted, row))
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results.sort(key=lambda x: x[0])
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for boosted_dist, row in results:
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typer.echo(f"[{boosted_dist:.3f}] {row['id']} ({row['year']}) — {row['title']}")
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return
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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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@search_app.command("formula")
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def search_formula(
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query: str = typer.Argument(..., help="LaTeX snippet or keyword to search in formulas"),
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limit: int = typer.Option(10, "--limit", "-n", help="Number of results"),
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) -> None:
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"""Full-text search over extracted LaTeX formulas (F-09)."""
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from codex.db import get_conn
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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 paper_id, page, raw_latex, context,
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ts_rank(to_tsvector('english', raw_latex || ' ' || coalesce(context, '')),
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plainto_tsquery('english', %(query)s)) AS rank
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FROM formulas
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WHERE to_tsvector('english', raw_latex || ' ' || coalesce(context, ''))
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@@ plainto_tsquery('english', %(query)s)
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ORDER BY rank DESC
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LIMIT %(limit)s
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""",
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{"query": query, "limit": limit},
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).fetchall()
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if not rows:
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typer.echo("No matching formulas found.")
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return
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for row in rows:
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typer.echo(
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f"[{row['rank']:.3f}] {row['paper_id']} p.{row['page']} {row['raw_latex'][:80]}"
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)
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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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# ---------------------------------------------------------------------------
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# F-12: Wiki command group
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# ---------------------------------------------------------------------------
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@wiki_app.command("compile")
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def wiki_compile(
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concept: Optional[str] = typer.Option( # noqa: UP045
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None, "--concept", help="Compile only this concept slug."
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),
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all_concepts: bool = typer.Option(
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False, "--all", help="Force full recompile (ignore change detection)."
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),
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top_k: int = typer.Option(0, "--top-k", help="Override config.wiki_top_k (0 = use config)."),
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output_dir: Optional[str] = typer.Option( # noqa: UP045
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None, "--output-dir", help="Override config.wiki_dir."
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),
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) -> None:
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"""Compile concept pages from retrieved chunks via local LLM.
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By default only recompiles concepts whose source chunks have changed
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(hash-based incremental). Use --all to force full recompile.
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"""
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from codex.wiki import compile_all
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report = compile_all(
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changed_only=not all_concepts,
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top_k=top_k if top_k > 0 else None,
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concept_filter=concept,
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output_dir=output_dir,
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)
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if report.compiled:
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typer.echo(f"Compiled: {', '.join(report.compiled)}")
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if report.skipped:
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typer.echo(f"Skipped (unchanged): {', '.join(report.skipped)}")
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if report.ungrounded:
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typer.echo(f"⚠ Ungrounded claims: {len(report.ungrounded)}", err=True)
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for slug, text in report.ungrounded:
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typer.echo(f" [{slug}] {text[:100]}", err=True)
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@wiki_app.command("list")
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def wiki_list(
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output_dir: Optional[str] = typer.Option( # noqa: UP045
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None, "--output-dir", help="Override config.wiki_dir."
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),
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) -> None:
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"""List compiled concept pages with freshness information."""
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import json as _json
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from pathlib import Path
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from codex.config import get_settings
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settings = get_settings()
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wiki_dir = Path(output_dir or settings.wiki_dir)
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state_path = wiki_dir / ".compile-state.json"
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state: dict[str, str] = {}
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if state_path.exists():
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try:
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state = _json.loads(state_path.read_text(encoding="utf-8"))
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except (_json.JSONDecodeError, OSError):
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state = {}
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pages = sorted(wiki_dir.glob("*.md"))
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if not pages:
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typer.echo("No compiled pages found.")
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return
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for page in pages:
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if page.name in ("index.md", "log.md"):
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continue
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slug = page.stem
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hash_val = state.get(slug, "—")[:8]
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content = page.read_text(encoding="utf-8")
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n_claims = content.count("[")
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n_ungrounded = content.count("⚠")
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mtime = datetime.fromtimestamp(page.stat().st_mtime, tz=UTC).strftime("%Y-%m-%d %H:%M")
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typer.echo(
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f"{slug:40s} last={mtime} hash={hash_val} claims≈{n_claims} ⚠={n_ungrounded}"
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)
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@wiki_app.command("check")
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def wiki_check(
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output_dir: Optional[str] = typer.Option( # noqa: UP045
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None, "--output-dir", help="Override config.wiki_dir."
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),
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) -> None:
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"""Check all compiled pages for ungrounded claims.
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Exits with code 0 if all claims are grounded, 1 if any are ungrounded.
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Suitable for CI pipelines.
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"""
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from pathlib import Path
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from codex.config import get_settings
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settings = get_settings()
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wiki_dir = Path(output_dir or settings.wiki_dir)
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pages = sorted(wiki_dir.glob("*.md"))
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found_ungrounded = False
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for page in pages:
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if page.name in ("index.md", "log.md"):
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continue
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content = page.read_text(encoding="utf-8")
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if "⚠" in content:
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typer.echo(f"⚠ Ungrounded claim(s) in: {page.name}", err=True)
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found_ungrounded = True
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# Check for quarantined pages in wiki/draft/
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draft_dir = wiki_dir / "draft"
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draft_pages = sorted(draft_dir.glob("*.md")) if draft_dir.exists() else []
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if draft_pages:
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n = len(draft_pages)
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typer.echo(
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f"⚠ {n} page(s) quarantined in wiki/draft/ (grounding rate below threshold)",
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err=True,
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)
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for dp in draft_pages:
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typer.echo(f" - {dp.name}", err=True)
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raise typer.Exit(2)
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if found_ungrounded:
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raise typer.Exit(1)
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else:
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typer.echo("All claims grounded.")
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# ---------------------------------------------------------------------------
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# F-13: Synthesis command group
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# ---------------------------------------------------------------------------
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@synth_app.command("leads")
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def synthesis_leads(
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lib_path: Optional[str] = typer.Option( # noqa: UP045
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None,
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"--lib-path",
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help=(
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"Path to a C++ source tree. Enables improvement leads (@cite-aware) and "
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"code-vs-corpus gap detection."
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),
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),
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topic: list[str] | None = typer.Option( # noqa: B008
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None,
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"--topic",
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help=(
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"Topic to check for coverage gaps (repeatable). Opt-in: without --topic "
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"no coverage-map gaps run (avoids per-paper false positives, audit R-8)."
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),
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),
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output_dir: Optional[str] = typer.Option( # noqa: UP045
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None, "--output-dir", help="Override config.leads_dir."
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),
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) -> None:
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"""Generate grounded leads (stages 2-4) and write them to leads/grounded/."""
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from codex.config import get_settings
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from codex.synthesis import (
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default_llm_client,
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find_connections,
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find_gaps,
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find_improvements,
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write_leads,
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)
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settings = get_settings()
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leads_dir = output_dir or settings.leads_dir
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llm = default_llm_client()
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connections = find_connections(top_k=settings.synthesis_top_k, llm=llm)
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gaps = find_gaps(lib_path=lib_path, llm=llm, topics=topic or None)
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improvements = (
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find_improvements(lib_path, top_k=settings.synthesis_top_k, llm=llm) if lib_path else []
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)
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all_leads = connections + gaps + improvements
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write_leads(all_leads, leads_dir)
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typer.echo(
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f"Grounded leads written to {leads_dir}/grounded/: "
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f"{len(connections)} connection · {len(gaps)} gap · {len(improvements)} improvement"
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)
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@synth_app.command("conjectures")
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def synthesis_conjectures(
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output_dir: Optional[str] = typer.Option( # noqa: UP045
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||
None, "--output-dir", help="Override config.leads_dir."
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||
),
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||
) -> None:
|
||
"""Generate stage-5 conjecture leads — quarantined to leads/conjectures/.
|
||
|
||
INVARIANT (F-13 HARD): conjectures are NEVER written to wiki/. They
|
||
require a ``suggested_validation`` spike before they may be promoted.
|
||
"""
|
||
from codex.config import get_settings
|
||
from codex.synthesis import default_llm_client, propose_conjectures, write_leads
|
||
|
||
settings = get_settings()
|
||
leads_dir = output_dir or settings.leads_dir
|
||
llm = default_llm_client()
|
||
|
||
conjectures = propose_conjectures(top_k=settings.synthesis_top_k, llm=llm)
|
||
write_leads(conjectures, leads_dir)
|
||
|
||
typer.echo(f"Conjectures (UNVERIFIED) written to {leads_dir}/conjectures/: {len(conjectures)}")
|
||
|
||
|
||
@synth_app.command("report")
|
||
def synthesis_report(
|
||
output_dir: Optional[str] = typer.Option( # noqa: UP045
|
||
None, "--output-dir", help="Override config.leads_dir."
|
||
),
|
||
) -> None:
|
||
"""Show grounded leads and conjectures — visibly separated."""
|
||
from pathlib import Path
|
||
|
||
from codex.config import get_settings
|
||
|
||
settings = get_settings()
|
||
leads_dir = Path(output_dir or settings.leads_dir)
|
||
grounded_dir = leads_dir / "grounded"
|
||
conj_dir = leads_dir / "conjectures"
|
||
|
||
grounded_files = sorted(grounded_dir.glob("*.md")) if grounded_dir.exists() else []
|
||
conj_files = sorted(conj_dir.glob("*.md")) if conj_dir.exists() else []
|
||
|
||
typer.echo("=" * 72)
|
||
typer.echo(f"GROUNDED LEADS ({len(grounded_files)}) → {grounded_dir}")
|
||
typer.echo("=" * 72)
|
||
if not grounded_files:
|
||
typer.echo("(none)")
|
||
for f in grounded_files:
|
||
first = f.read_text(encoding="utf-8").splitlines()[0]
|
||
typer.echo(f" {first}")
|
||
|
||
typer.echo("")
|
||
typer.echo("=" * 72)
|
||
typer.echo(f"CONJECTURES ({len(conj_files)}) → {conj_dir} [UNVERIFIED — never in wiki/]")
|
||
typer.echo("=" * 72)
|
||
if not conj_files:
|
||
typer.echo("(none)")
|
||
for f in conj_files:
|
||
first = f.read_text(encoding="utf-8").splitlines()[0]
|
||
typer.echo(f" {first}")
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# F-16 — quality sub-commands
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
@quality_app.command("run")
|
||
def quality_run(
|
||
paper_id: Optional[str] = typer.Option( # noqa: UP045
|
||
None,
|
||
"--paper-id",
|
||
help="Restrict pass to one paper (omit to process all papers).",
|
||
),
|
||
) -> None:
|
||
"""Apply quality gate + section classification to existing chunks.
|
||
|
||
Iterates over chunks in the database, removes those that fail the
|
||
quality thresholds, and back-fills the ``section`` column for the rest.
|
||
"""
|
||
from codex.config import get_settings
|
||
from codex.db import get_conn
|
||
from codex.quality import run_quality_pass
|
||
|
||
settings = get_settings()
|
||
with get_conn() as conn:
|
||
stats = run_quality_pass(paper_id=paper_id, conn=conn, settings=settings)
|
||
|
||
scope = f"paper {paper_id}" if paper_id else "all papers"
|
||
typer.echo(
|
||
f"Quality pass ({scope}): "
|
||
f"{stats['kept']} kept, "
|
||
f"{stats['removed']} removed, "
|
||
f"{stats['tagged']} section-tagged"
|
||
)
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# F-15 — graph sub-commands
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
@graph_app.command("report")
|
||
def graph_report(
|
||
top_n: int = typer.Option(10, "--top-n", "-n", help="Number of hub papers to show."),
|
||
output_json: bool = typer.Option(False, "--json", help="Output as JSON."),
|
||
) -> None:
|
||
"""Show citation graph report: top hub papers, dangling citations, cluster summary."""
|
||
from codex.config import get_settings
|
||
from codex.db import get_conn
|
||
from codex.graph import build_citation_graph, citation_pagerank, dangling_citations
|
||
|
||
settings = get_settings()
|
||
with get_conn() as conn:
|
||
graph = build_citation_graph(conn)
|
||
known_ids = {row["id"] for row in conn.execute("SELECT id FROM papers").fetchall()}
|
||
|
||
if graph.number_of_nodes() == 0:
|
||
typer.echo("Citation graph is empty — ingest some papers first.")
|
||
return
|
||
|
||
n_papers = len(known_ids)
|
||
pr = citation_pagerank(graph)
|
||
hubs = sorted(pr.items(), key=lambda x: -x[1])[:top_n]
|
||
dangling = sorted(dangling_citations(graph, known_ids))
|
||
|
||
if output_json:
|
||
typer.echo(
|
||
json.dumps(
|
||
{
|
||
"nodes": graph.number_of_nodes(),
|
||
"edges": graph.number_of_edges(),
|
||
"hubs": [{"paper_id": pid, "pagerank": score} for pid, score in hubs],
|
||
"dangling_count": len(dangling),
|
||
"dangling": dangling,
|
||
},
|
||
indent=2,
|
||
)
|
||
)
|
||
return
|
||
|
||
if n_papers < settings.graph_min_corpus_size:
|
||
typer.echo(
|
||
f"Warning: only {n_papers} ingested papers "
|
||
f"(recommended ≥ {settings.graph_min_corpus_size} for meaningful ranking).",
|
||
err=True,
|
||
)
|
||
typer.echo(f"Graph: {graph.number_of_nodes()} nodes, {graph.number_of_edges()} edges")
|
||
typer.echo("")
|
||
typer.echo(f"TOP-{top_n} HUB PAPERS (PageRank)")
|
||
typer.echo("-" * 48)
|
||
for pid, score in hubs:
|
||
typer.echo(f" {score:.4f} {pid}")
|
||
typer.echo("")
|
||
typer.echo(f"DANGLING CITATIONS ({len(dangling)} cited but not ingested)")
|
||
typer.echo("-" * 48)
|
||
for pid in dangling[:top_n]:
|
||
typer.echo(f" {pid}")
|
||
if len(dangling) > top_n:
|
||
typer.echo(f" … and {len(dangling) - top_n} more")
|
||
|
||
|
||
@graph_app.command("related")
|
||
def graph_related(
|
||
paper_id: str = typer.Argument(..., help="Paper ID to find related papers for."),
|
||
min_shared: int = typer.Option(
|
||
2, "--min-shared", help="Minimum shared references for bibliographic coupling."
|
||
),
|
||
) -> None:
|
||
"""List bibliographically related papers (shared references ≥ min-shared)."""
|
||
from codex.db import get_conn
|
||
from codex.graph import build_citation_graph, find_related
|
||
|
||
with get_conn() as conn:
|
||
graph = build_citation_graph(conn)
|
||
|
||
related = find_related(paper_id, graph, min_shared=min_shared)
|
||
if not related:
|
||
typer.echo(f"No papers with ≥ {min_shared} shared references found for {paper_id}.")
|
||
return
|
||
typer.echo(
|
||
f"Papers related to {paper_id} (bibliographic coupling, ≥ {min_shared} shared refs):"
|
||
)
|
||
for pid in related:
|
||
typer.echo(f" {pid}")
|