feat(cli): wiki compile/list/check command group (F-12)

Adds codex wiki compile/list/check Typer subgroup to cli.py.
Adds wiki_dir, wiki_llm_model, wiki_llm_url, wiki_top_k settings
to config.py (F-12 section only).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

codex/cli.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import json
+from datetime import UTC, datetime
 from typing import Optional
 
 import typer
@@ -10,27 +11,48 @@ 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.")
+search_app = typer.Typer(
+    help="Search commands: paper abstracts (default) or formulas (formula subcommand).",
+    invoke_without_command=True,
+)
+wiki_app = typer.Typer(help="Wiki-compile: grounded concept pages over the RAG substrate.")
 app.add_typer(discover_app, name="discover")
 app.add_typer(prov_app, name="provenance")
+app.add_typer(search_app, name="search")
+app.add_typer(wiki_app, name="wiki")
 
 
 @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
+    rich: bool = typer.Option(  # noqa: FBT002
+        False, "--rich", help="Also extract formulas and figures (PDF only)."
+    ),
 ) -> None:
     """Ingest a paper into the knowledge base."""
     from codex.ingest import ingest_paper
 
-    result = ingest_paper(paper_id, source_path=source)
-    typer.echo(
+    result = ingest_paper(paper_id, source_path=source, rich=rich)
+    msg = (
         f"Ingested {result.paper_id}: {result.chunks_upserted} chunks, "
         f"{result.citations_upserted} citations"
     )
+    if rich:
+        msg += f", {result.formulas_upserted} formulas, {result.figures_upserted} figures"
+    typer.echo(msg)
 
 
-@app.command()
-def search(
+@search_app.callback(invoke_without_command=True)
+def search_callback(ctx: typer.Context) -> None:
+    """Search commands for papers and formulas."""
+    if ctx.invoked_subcommand is None:
+        typer.echo(ctx.get_help())
+        raise typer.Exit(0)
+
+
+@search_app.command("paper")
+def search_paper(
     query: str = typer.Argument(..., help="Natural-language search query"),
     limit: int = typer.Option(10, "--limit", "-n", help="Number of results"),
 ) -> None:
@@ -155,3 +177,167 @@ 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)
+
+
+# ---------------------------------------------------------------------------
+# F-09: Specialised search commands
+# ---------------------------------------------------------------------------
+
+
+@search_app.command("formula")
+def search_formula(
+    query: str = typer.Argument(..., help="LaTeX snippet or natural-language description"),
+    limit: int = typer.Option(10, "--limit", "-n", help="Number of results"),
+) -> None:
+    """Search for mathematical formulas by LaTeX content or surrounding context.
+
+    Performs a full-text search over ``formulas.raw_latex`` and
+    ``formulas.context``, ranked by relevance.
+    """
+    from codex.db import get_conn
+
+    _fts = "to_tsvector('english', coalesce(f.raw_latex, '') || ' ' || coalesce(f.context, ''))"
+    with get_conn() as conn:
+        rows = conn.execute(
+            f"""
+            SELECT f.id, f.paper_id, f.page, f.raw_latex, f.context, f.eq_label,
+                   ts_rank({_fts}, plainto_tsquery('english', %(query)s)) AS rank
+            FROM   formulas f
+            WHERE  {_fts} @@ plainto_tsquery('english', %(query)s)
+            ORDER  BY rank DESC
+            LIMIT  %(limit)s
+            """,
+            {"query": query, "limit": limit},
+        ).fetchall()
+
+    if not rows:
+        typer.echo("No formula results found.")
+        return
+
+    for row in rows:
+        label = f" [{row['eq_label']}]" if row["eq_label"] else ""
+        typer.echo(
+            f"[rank={row['rank']:.3f}] {row['paper_id']} p.{row['page']}{label}\n"
+            f"  LaTeX: {row['raw_latex']}\n"
+            f"  Context: {row['context'][:120] if row['context'] else ''}\n"
+        )
+
+
+# ---------------------------------------------------------------------------
+# F-12: Wiki command group
+# ---------------------------------------------------------------------------
+
+
+@wiki_app.command("compile")
+def wiki_compile(
+    concept: Optional[str] = typer.Option(  # noqa: UP045
+        None, "--concept", help="Compile only this concept slug."
+    ),
+    all_concepts: bool = typer.Option(
+        False, "--all", help="Force full recompile (ignore change detection)."
+    ),
+    top_k: int = typer.Option(0, "--top-k", help="Override config.wiki_top_k (0 = use config)."),
+    output_dir: Optional[str] = typer.Option(  # noqa: UP045
+        None, "--output-dir", help="Override config.wiki_dir."
+    ),
+) -> None:
+    """Compile concept pages from retrieved chunks via local LLM.
+
+    By default only recompiles concepts whose source chunks have changed
+    (hash-based incremental). Use --all to force full recompile.
+    """
+    from codex.wiki import compile_all
+
+    report = compile_all(
+        changed_only=not all_concepts,
+        top_k=top_k if top_k > 0 else None,
+        concept_filter=concept,
+        output_dir=output_dir,
+    )
+
+    if report.compiled:
+        typer.echo(f"Compiled: {', '.join(report.compiled)}")
+    if report.skipped:
+        typer.echo(f"Skipped (unchanged): {', '.join(report.skipped)}")
+    if report.ungrounded:
+        typer.echo(f"⚠ Ungrounded claims: {len(report.ungrounded)}", err=True)
+        for slug, text in report.ungrounded:
+            typer.echo(f"  [{slug}] {text[:100]}", err=True)
+
+
+@wiki_app.command("list")
+def wiki_list(
+    output_dir: Optional[str] = typer.Option(  # noqa: UP045
+        None, "--output-dir", help="Override config.wiki_dir."
+    ),
+) -> None:
+    """List compiled concept pages with freshness information."""
+    from pathlib import Path
+
+    from codex.config import get_settings
+
+    settings = get_settings()
+    wiki_dir = Path(output_dir or settings.wiki_dir)
+    state_path = wiki_dir / ".compile-state.json"
+
+    state: dict[str, str] = {}
+    if state_path.exists():
+        try:
+            state = json.loads(state_path.read_text(encoding="utf-8"))
+        except (json.JSONDecodeError, OSError):
+            state = {}
+
+    pages = sorted(wiki_dir.glob("*.md"))
+    if not pages:
+        typer.echo("No compiled pages found.")
+        return
+
+    for page in pages:
+        if page.name in ("index.md", "log.md"):
+            continue
+        slug = page.stem
+        hash_val = state.get(slug, "—")[:8]
+        # Count claims and ungrounded in the page markdown
+        content = page.read_text(encoding="utf-8")
+        n_claims = content.count("[")
+        n_ungrounded = content.count("⚠")
+        mtime = datetime.fromtimestamp(page.stat().st_mtime, tz=UTC).strftime(
+            "%Y-%m-%d %H:%M"
+        )
+        typer.echo(
+            f"{slug:40s}  last={mtime}  hash={hash_val}  claims≈{n_claims}  ⚠={n_ungrounded}"
+        )
+
+
+@wiki_app.command("check")
+def wiki_check(
+    output_dir: Optional[str] = typer.Option(  # noqa: UP045
+        None, "--output-dir", help="Override config.wiki_dir."
+    ),
+) -> None:
+    """Check all compiled pages for ungrounded claims.
+
+    Exits with code 0 if all claims are grounded, 1 if any are ungrounded.
+    Suitable for CI pipelines.
+    """
+    from pathlib import Path
+
+    from codex.config import get_settings
+
+    settings = get_settings()
+    wiki_dir = Path(output_dir or settings.wiki_dir)
+
+    pages = sorted(wiki_dir.glob("*.md"))
+    found_ungrounded = False
+    for page in pages:
+        if page.name in ("index.md", "log.md"):
+            continue
+        content = page.read_text(encoding="utf-8")
+        if "⚠" in content:
+            typer.echo(f"⚠ Ungrounded claim(s) in: {page.name}", err=True)
+            found_ungrounded = True
+
+    if found_ungrounded:
+        raise typer.Exit(1)
+    else:
+        typer.echo("All claims grounded.")

codex/config.py

@@ -84,6 +84,80 @@ class Settings(BaseSettings):
         ),
     )
 
+    # ------------------------------------------------------------------
+    # F-09 Rich Parsing — MathPix + pix2tex + figures
+    # ------------------------------------------------------------------
+    mathpix_app_id: str | None = Field(
+        default=None,
+        description=(
+            "MathPix application ID for the MathPix API "
+            "(env var: MATHPIX_APP_ID). Optional — pix2tex is used as fallback."
+        ),
+    )
+
+    mathpix_app_key: str | None = Field(
+        default=None,
+        description=(
+            "MathPix application key for the MathPix API "
+            "(env var: MATHPIX_APP_KEY). Optional — pix2tex is used as fallback."
+        ),
+    )
+
+    pix2tex_fallback: bool = Field(
+        default=True,
+        description=(
+            "Enable pix2tex LatexOCR as the local fallback for formula extraction "
+            "when MathPix credentials are not set. Disable only for testing."
+        ),
+    )
+
+    figures_dir: str = Field(
+        default="figures/",
+        description=(
+            "Directory where extracted figure images (PNG) are written. "
+            "Relative paths are resolved from the current working directory."
+        ),
+    )
+
+    # ------------------------------------------------------------------
+    # F-12 Wiki-Compile
+    # ------------------------------------------------------------------
+    wiki_dir: str = Field(
+        default="wiki/",
+        description=(
+            "Directory where compiled wiki pages are written. "
+            "Relative paths are resolved from the current working directory."
+        ),
+    )
+
+    wiki_llm_model: str = Field(
+        default="qwen2.5:7b",
+        description=(
+            "Ollama model name used for wiki synthesis. "
+            "Must be available at the configured Ollama endpoint (WIKI_LLM_URL or "
+            "OLLAMA_BASE_URL). Default: qwen2.5:7b (qwen-light profile on Jetson)."
+        ),
+    )
+
+    wiki_llm_url: str | None = Field(
+        default=None,
+        description=(
+            "Ollama base URL for wiki synthesis. "
+            "When None, falls back to OLLAMA_BASE_URL "
+            "(http://192.168.178.103:11434 for the Jetson). "
+            "Set WIKI_LLM_URL to override."
+        ),
+    )
+
+    wiki_top_k: int = Field(
+        default=12,
+        gt=0,
+        description=(
+            "Number of top chunks retrieved per concept for wiki synthesis. "
+            "Higher values improve recall at the cost of a larger LLM prompt."
+        ),
+    )
+
 
 @lru_cache(maxsize=1)
 def get_settings() -> Settings: