feat: add pipeline.py — single command for full ingestion pipeline

Runs seed → converters → ingest → align → export in one shot.
Flags: --fresh (wipe DB), --skip-converters, --schemas (specific files),
--bump, --agent.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EXeTeJsXisxTRXay6EoBSQ

Author: claude

neuro_ghost/pipeline.py

@@ -0,0 +1,111 @@
+"""
+pipeline.py — Run the full NeuroGhost ingestion pipeline in one command.
+
+Steps
+-----
+1. (Optional) Delete the database file for a clean rebuild
+2. Seed schema.org as the base vocabulary
+3. (Optional) Fetch + convert external schemas via converters/run_all.py
+4. Ingest every .yml file found in the schemas directory
+5. Compute cross-schema alignments
+6. Export registry.json + version snapshot
+
+Usage
+-----
+    # Fresh rebuild — wipe DB, fetch external schemas, ingest everything
+    python neuro_ghost/pipeline.py --fresh
+
+    # Re-ingest local schemas only (skip external fetch)
+    python neuro_ghost/pipeline.py --fresh --skip-converters
+
+    # Incremental — add one schema to an existing DB
+    python neuro_ghost/pipeline.py --skip-converters --schemas schemas/bbqs.yml
+"""
+
+from __future__ import annotations
+import subprocess
+import sys
+from pathlib import Path
+
+import click
+
+HERE     = Path(__file__).parent
+ROOT     = HERE.parent
+SCHEMAS  = ROOT / "schemas"
+DB_PATH  = str(ROOT / "registry.lbug")
+
+
+def _run(cmd: list[str]) -> None:
+    print(f"\n$ {' '.join(cmd)}")
+    result = subprocess.run(cmd, check=False)
+    if result.returncode != 0:
+        print(f"\nERROR: command exited with code {result.returncode}")
+        sys.exit(result.returncode)
+
+
+@click.command()
+@click.option("--db",               default=DB_PATH, show_default=True,
+              help="Path to the LadybugDB file.")
+@click.option("--fresh",            is_flag=True,
+              help="Delete the DB before starting (clean rebuild).")
+@click.option("--skip-converters",  is_flag=True,
+              help="Skip fetching external schemas (BIDS, NWB, DANDI, …).")
+@click.option("--schemas",          default=None, multiple=True,
+              help="Specific .yml files to ingest. Defaults to all files in schemas/.")
+@click.option("--bump",             default="minor", show_default=True,
+              type=click.Choice(["major", "minor", "patch"]),
+              help="Version bump type for the registry export.")
+@click.option("--agent",            default="local", show_default=True,
+              help="Who is running this pipeline (recorded in provenance).")
+def cli(db: str, fresh: bool, skip_converters: bool,
+        schemas: tuple, bump: str, agent: str) -> None:
+    """Run the full NeuroGhost ingestion pipeline."""
+
+    py = sys.executable
+
+    # 1. Fresh wipe
+    if fresh:
+        db_path = Path(db)
+        if db_path.exists():
+            db_path.unlink()
+            print(f"Deleted {db_path}")
+
+    # 2. Seed schema.org
+    _run([py, str(HERE / "seed.py"), "--db", db])
+
+    # 3. External converters
+    if not skip_converters:
+        _run([py, str(HERE / "converters" / "run_all.py")])
+
+    # 4. Ingest schemas
+    targets: list[Path] = (
+        [Path(s) for s in schemas]
+        if schemas
+        else sorted(p for p in SCHEMAS.glob("*.yml")
+                    if p.name != "meta_model.yaml")
+    )
+
+    if not targets:
+        print("No schemas found to ingest.")
+        sys.exit(1)
+
+    for schema_file in targets:
+        _run([py, str(HERE / "ingest_linkml.py"),
+              "--file", str(schema_file),
+              "--db",   db,
+              "--agent", agent])
+
+    # 5. Align
+    _run([py, str(HERE / "align.py"), "--db", db])
+
+    # 6. Export
+    _run([py, str(HERE / "export_json.py"),
+          "--db",    db,
+          "--bump",  bump,
+          "--agent", agent])
+
+    print("\nPipeline complete.")
+
+
+if __name__ == "__main__":
+    cli()