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

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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>
This commit is contained in:
Tarik Moussa
2026-06-13 20:22:55 +02:00
parent aee00515f4
commit 4d361fd8dc
2 changed files with 264 additions and 4 deletions
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194
codex/cli.py
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@@ -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.")