codex/cli.py

@@ -11,14 +11,9 @@ 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")
 
 
@@ -26,33 +21,19 @@ app.add_typer(wiki_app, name="wiki")
 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, rich=rich)
+    result = ingest_paper(paper_id, source_path=source)
-    msg = (
+    typer.echo(
         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)
 
 
-@search_app.callback(invoke_without_command=True)
+@app.command()
-def search_callback(ctx: typer.Context) -> None:
+def search(
-    """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:
@@ -179,50 +160,6 @@ def ask(question: str = typer.Argument(..., help="Question to answer")) -> None:
     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
 # ---------------------------------------------------------------------------
@@ -272,6 +209,7 @@ def wiki_list(
     ),
 ) -> None:
     """List compiled concept pages with freshness information."""
+    import json as _json
     from pathlib import Path
 
     from codex.config import get_settings
@@ -283,8 +221,8 @@ def wiki_list(
     state: dict[str, str] = {}
     if state_path.exists():
         try:
-            state = json.loads(state_path.read_text(encoding="utf-8"))
+            state = _json.loads(state_path.read_text(encoding="utf-8"))
-        except (json.JSONDecodeError, OSError):
+        except (_json.JSONDecodeError, OSError):
             state = {}
 
     pages = sorted(wiki_dir.glob("*.md"))
@@ -297,13 +235,10 @@ def wiki_list(
             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(
+        mtime = datetime.fromtimestamp(page.stat().st_mtime, tz=UTC).strftime("%Y-%m-%d %H:%M")
-            "%Y-%m-%d %H:%M"
-        )
         typer.echo(
             f"{slug:40s}  last={mtime}  hash={hash_val}  claims≈{n_claims}  ⚠={n_ungrounded}"
         )

codex/config.py

@@ -84,41 +84,6 @@ 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
     # ------------------------------------------------------------------