analyze: default run directory to <repo>/analysis_runs, gitignored

giant analyze prep/submit previously defaulted the run directory to
next to the rollout parquet on /ceph. Default it instead to
<cwd>/analysis_runs/analysis_<id> so it lands inside the portal repo
checkout (/work) — gitignored, --run-dir still overrides it.
derive_run_dir/prep gained a default_base param; library callers that
don't pass one keep the old parquet-relative fallback.

.gitignore

@@ -17,3 +17,6 @@ checkpoints/
 
 # Scratch working directory
 /scratchpad/
+
+# giant analyze run directories (shared.json, reduced/, plots/, condor logs)
+/analysis_runs/

giant/analysis/condor.py

@@ -93,13 +93,26 @@ def load_rollout_yaml(path: str | Path) -> dict:
     return d
 
 
-def derive_run_dir(rollout_yaml: dict, run_dir: str | Path | None = None) -> Path:
+def derive_run_dir(
-    """Analysis output directory, next to the rollout parquet unless overridden."""
+    rollout_yaml: dict,
+    run_dir: str | Path | None = None,
+    default_base: str | Path | None = None,
+) -> Path:
+    """Analysis output directory.
+
+    Precedence: an explicit ``run_dir`` always wins. Otherwise
+    ``default_base / analysis_<tag>`` if ``default_base`` is given (the CLI
+    passes the repo's gitignored ``analysis_runs/``, so run directories don't
+    pile up on ``/ceph`` next to the rollout parquet). Falls back to next to
+    the rollout parquet — the original convention — for callers that don't
+    care where the run directory lives.
+    """
     if run_dir is not None:
         return Path(run_dir)
     rollout = Path(rollout_yaml["output"])
     tag = str(rollout_yaml.get("prediction_id") or rollout.stem)[:8]
-    return rollout.parent / f"analysis_{tag}"
+    base = Path(default_base) if default_base is not None else rollout.parent
+    return base / f"analysis_{tag}"
 
 
 def _plot_meta(rollout_yaml: dict) -> dict:
@@ -160,6 +173,7 @@ def prep(
     rollout_yaml: str | Path,
     run_dir: str | Path | None = None,
     n_chunks: int = 1,
+    default_base: str | Path | None = None,
     **ctx_kwargs,
 ) -> Path:
     """Read the rollout YAML, build the shared context, and lay out the run dir.
@@ -168,10 +182,11 @@ def prep(
     ``n_chunks`` is the run-level chunk count every ``compute-one``/``merge-one``
     job reads back out of ``run_meta.json`` (via ``RunMeta.n_chunks``), so it is
     resolved once here rather than re-passed (and risking disagreement) at every
-    later step.
+    later step. See ``derive_run_dir`` for how ``run_dir``/``default_base``
+    resolve the actual directory.
     """
     y = load_rollout_yaml(rollout_yaml)
-    run_path = derive_run_dir(y, run_dir)
+    run_path = derive_run_dir(y, run_dir, default_base=default_base)
     run_path.mkdir(parents=True, exist_ok=True)
 
     rollout, reference = y["output"], y["dataset"]

giant/cli.py

@@ -1144,7 +1144,7 @@ def analyze_prep(
         typer.Option(
             "--run-dir",
             "-o",
-            help="Override the run directory (default: next to the rollout parquet)",
+            help="Override the run directory (default: <cwd>/analysis_runs/analysis_<id>)",
         ),
     ] = None,
     n_energy_bins: Annotated[int, typer.Option("--energy-bins")] = 4,
@@ -1164,6 +1164,7 @@ def analyze_prep(
         rollout_yaml,
         run_dir,
         n_chunks=chunks,
+        default_base=Path.cwd() / "analysis_runs",
         n_energy_bins=n_energy_bins,
         n_marginal_bins=n_marginal_bins,
         top_k_pdg=top_k_pdg,
@@ -1244,7 +1245,11 @@ def analyze_submit(
     accounting_group: Annotated[str, typer.Option("--accounting-group")],
     run_dir: Annotated[
         Optional[Path],
-        typer.Option("--run-dir", "-o", help="Override the run directory"),
+        typer.Option(
+            "--run-dir",
+            "-o",
+            help="Override the run directory (default: <cwd>/analysis_runs/analysis_<id>)",
+        ),
     ] = None,
     docker_image: Annotated[
         str, typer.Option("--docker-image")
@@ -1277,6 +1282,7 @@ def analyze_submit(
         rollout_yaml,
         run_dir,
         n_chunks=chunks,
+        default_base=Path.cwd() / "analysis_runs",
         n_energy_bins=n_energy_bins,
         n_marginal_bins=n_marginal_bins,
         top_k_pdg=top_k_pdg,

tests/test_condor.py

@@ -89,6 +89,15 @@ def test_derive_run_dir_next_to_rollout():
     assert derive_run_dir(y, "/somewhere") == Path("/somewhere")
 
 
+def test_derive_run_dir_default_base():
+    y = {"output": "/data/roll.parquet", "prediction_id": "abcd1234ef", "dataset": "d"}
+    assert derive_run_dir(y, default_base="/work/lbogner/giant2/analysis_runs") == Path(
+        "/work/lbogner/giant2/analysis_runs/analysis_abcd1234"
+    )
+    # an explicit run_dir still wins over default_base
+    assert derive_run_dir(y, "/somewhere", default_base="/other") == Path("/somewhere")
+
+
 def test_prep_lays_out_run_dir(tmp_path: Path):
     yaml_path = _write_inputs(tmp_path)
     run_dir = _prep(yaml_path)