Fix CLI/tooling robustness gaps and dedupe the Conditioning enum

- run_create_manifest gains --force; it previously overwrote an
  existing manifest (including holdout.manifest, which
  check_holdout_overlap exists specifically to protect) with no
  warning or backup on a second run.
- _git_user_name only caught OSError, not subprocess.TimeoutExpired (a
  SubprocessError, not an OSError) — a slow/loaded shared portal
  machine could crash `dwarf bump-gen`/`bump-schema` instead of
  degrading to by=None as intended.
- `dwarf convert --jobs`/`make-root --jobs` now warn (never block) when
  the requested count exceeds ~1/4 of the machine's CPUs, matching the
  same shared-machine etiquette check added to giant train in the
  previous commit.
- The Conditioning enum was independently redefined in both
  giant/cli.py and scripts/dwarf.py; moved to a single
  giant.config.Conditioning both now import, removing the drift risk
  of a third conditioning mode being added to one but not the other.

Each fix has a regression test.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

giant/cli.py

@@ -211,9 +211,10 @@ class Mode(str, Enum):
     wgan = "wgan"
 
 
-class Conditioning(str, Enum):
-    physical = "physical"
-    embedding = "embedding"
+# Conditioning itself lives in giant.config (imported below as gconfig) —
+# shared with scripts/dwarf.py's Typer commands so the two CLIs can't
+# silently drift apart on the option's valid values.
+Conditioning = gconfig.Conditioning
 
 
 class Coord(str, Enum):

giant/config.py

@@ -4,11 +4,23 @@ import subprocess
 import sys
 import tomllib
 from datetime import datetime, timezone
+from enum import Enum
 from pathlib import Path
 
 import numpy as np
 import torch
 
+
+class Conditioning(str, Enum):
+    """`model.conditioning` choices — shared by `giant.cli` and `scripts.dwarf`'s
+    Typer commands so the two CLIs can't silently drift apart on the option's
+    valid values (see DEFAULT_CONFIG["model"]["conditioning"] for what each
+    value means)."""
+
+    physical = "physical"
+    embedding = "embedding"
+
+
 DEFAULT_CONFIG: dict = {
     "train": {
         "mode": "flow",

scripts/bump_dataset_version.py

@@ -85,7 +85,12 @@ def _git_user_name() -> str | None:
         out = subprocess.run(
             ["git", "config", "user.name"], capture_output=True, text=True, timeout=2
         )
-    except OSError:
+    except (OSError, subprocess.SubprocessError):
+        # OSError (e.g. git not on PATH) and subprocess.SubprocessError
+        # (e.g. TimeoutExpired) are unrelated hierarchies — TimeoutExpired
+        # is not an OSError, so catching only OSError (as before) let a
+        # slow/loaded NFS-backed portal machine crash this instead of
+        # degrading to by=None as intended.
         return None
     name = out.stdout.strip()
     return name or None
@@ -730,6 +735,7 @@ def run_create_manifest(
     pool: str | None = None,
     type_: str | None = None,
     root: str = "/ceph/lbogner/geant_steps",
+    force: bool = False,
 ) -> None:
     if (output is None) == (pool is None):
         raise SystemExit("error: exactly one of --output or --pool is required")
@@ -745,6 +751,12 @@ def run_create_manifest(
     parquet_files = [Path(f) for f in files]
     lines, missing, resolved = plan_create_manifest(output_path, parquet_files)
     overlaps = check_holdout_overlap(output_path, resolved)
+    # Unlike missing/overlaps this is a hard stop even without --execute
+    # reaching the write, since create_manifest has no in-place "update" mode
+    # (unlike update_manifest) — a second run against the same output_path
+    # (e.g. holdout.manifest, the file check_holdout_overlap exists to
+    # protect) would otherwise silently clobber it with no diff/backup.
+    already_exists = output_path.exists() and not force
 
     print(f"=== {'EXECUTING' if execute else 'DRY RUN'} ===")
     print(f"manifest: {output_path.resolve()}")
@@ -761,7 +773,10 @@ def run_create_manifest(
         for name, f in overlaps:
             print(f"  {f}  (also in {name})")
 
-    if (missing or overlaps) and execute:
+    if already_exists:
+        print(f"\n{output_path} already exists — pass --force to overwrite it.")
+
+    if (missing or overlaps or already_exists) and execute:
         raise SystemExit("error: refusing to write manifest (see above)")
 
     if not execute:

scripts/dwarf.py

@@ -5,6 +5,7 @@ simulation-fanout tools into one Typer app so there's a single command name
 (and `--help`) to remember instead of five differently-hyphenated ones.
 """
 
+import os
 from enum import Enum
 from pathlib import Path
 from typing import Optional
@@ -12,6 +13,7 @@ from typing import Optional
 import typer
 from typing_extensions import Annotated
 
+from giant.config import Conditioning
 from scripts.bump_dataset_version import (
     run_bump_gen,
     run_bump_schema,
@@ -37,6 +39,25 @@ def _main() -> None:
     """dwarf — dataset/tooling CLI (ROOT<->parquet conversion, dataset versioning, sim fanout)."""
 
 
+def _warn_if_exceeds_shared_quota(n: int, flag: str) -> None:
+    """Soft warning (never blocks) when a worker/job count looks likely to
+    grab more than this repo's documented shared-portal-machine etiquette
+    (CLAUDE.md's Compute environment: stay within ~1/4 of CPU/RAM and a
+    single GPU, since portal1/deepthought{,2}/bms{1..3} are shared with
+    other users). Not a hard cap — a legitimate big machine or a
+    deliberately aggressive run is still the caller's call.
+    """
+    cpu_count = os.cpu_count() or 1
+    quota = max(1, cpu_count // 4)
+    if n > quota:
+        typer.echo(
+            f"warning: {flag}={n} exceeds ~1/4 of this machine's "
+            f"{cpu_count} CPU(s) ({quota}) — portal machines are shared "
+            "with other users (see CLAUDE.md's Compute environment section)",
+            err=True,
+        )
+
+
 class Compression(str, Enum):
     snappy = "snappy"
     lz4 = "lz4"
@@ -106,6 +127,7 @@ def convert(
     if jobs < 1:
         typer.echo("error: --jobs must be >= 1", err=True)
         raise typer.Exit(1)
+    _warn_if_exceeds_shared_quota(jobs, "--jobs")
 
     compression_value = (
         "uncompressed" if compression is Compression.none else compression.value
@@ -327,6 +349,10 @@ def create_manifest(
     execute: Annotated[
         bool, typer.Option("--execute", help="Write the manifest (default: dry run)")
     ] = False,
+    force: Annotated[
+        bool,
+        typer.Option("--force", help="Overwrite the manifest if it already exists"),
+    ] = False,
 ) -> None:
     """Create a new manifest from a list of parquet files."""
     run_create_manifest(
@@ -336,6 +362,7 @@ def create_manifest(
         pool=pool,
         type_=type_.value if type_ is not None else None,
         root=str(root),
+        force=force,
     )
 
 
@@ -391,6 +418,7 @@ def make_root(
     ] = False,
 ) -> None:
     """Generate new ROOT shards via a minicalosim executable."""
+    _warn_if_exceeds_shared_quota(jobs, "--jobs")
     run_make_root(
         executable=executable,
         detector=detector,
@@ -472,11 +500,6 @@ def build_geometry_oracle(
     )
 
 
-class Conditioning(str, Enum):
-    physical = "physical"
-    embedding = "embedding"
-
-
 @app.command("warm-cache")
 def warm_cache(
     data: Annotated[

tests/test_bump_dataset_version.py

@@ -1,4 +1,6 @@
 import os
+import subprocess
+
 from scripts import bump_dataset_version
 
 plan_bump_gen = bump_dataset_version.plan_bump_gen
@@ -11,6 +13,14 @@ apply_create_manifest = bump_dataset_version.apply_create_manifest
 check_holdout_overlap = bump_dataset_version.check_holdout_overlap
 
 
+def test_git_user_name_returns_none_on_timeout(monkeypatch):
+    def _raise_timeout(*args, **kwargs):
+        raise subprocess.TimeoutExpired(cmd=["git"], timeout=2)
+
+    monkeypatch.setattr(subprocess, "run", _raise_timeout)
+    assert bump_dataset_version._git_user_name() is None
+
+
 def test_bump_gen_starts_at_gen1_when_none_exist(tmp_path):
     dirs, log_line = plan_bump_gen(
         tmp_path, "steps", "first generation", None, "2026-01-01"
@@ -401,6 +411,36 @@ def test_create_manifest_creates_parent_dirs(tmp_path):
     assert output.exists()
 
 
+def test_run_create_manifest_refuses_to_overwrite_existing_output(tmp_path):
+    pq = tmp_path / "a.parquet"
+    pq.touch()
+    output = tmp_path / "pools" / "pbwo4" / "holdout.manifest"
+    output.parent.mkdir(parents=True)
+    output.write_text("original contents\n")
+
+    try:
+        bump_dataset_version.run_create_manifest(
+            [str(pq)], execute=True, output=str(output)
+        )
+        assert False, "expected SystemExit"
+    except SystemExit:
+        pass
+    assert output.read_text() == "original contents\n"
+
+
+def test_run_create_manifest_force_overwrites_existing_output(tmp_path):
+    pq = tmp_path / "a.parquet"
+    pq.touch()
+    output = tmp_path / "pools" / "pbwo4" / "holdout.manifest"
+    output.parent.mkdir(parents=True)
+    output.write_text("original contents\n")
+
+    bump_dataset_version.run_create_manifest(
+        [str(pq)], execute=True, output=str(output), force=True
+    )
+    assert output.read_text() != "original contents\n"
+
+
 # ---------------------------------------------------------------------------
 # check_holdout_overlap
 # ---------------------------------------------------------------------------

tests/test_dwarf.py

@@ -1,12 +1,35 @@
 from typer.testing import CliRunner
 
+from giant import cli as giant_cli
+from giant.config import Conditioning
 from giant.data import setup_cache
+from scripts import dwarf
 from scripts.dwarf import app
 from test_pipeline import _make_synthetic_steps
 
 runner = CliRunner()
 
 
+def test_conditioning_enum_shared_across_both_clis():
+    """giant.cli and scripts.dwarf must use the one giant.config.Conditioning
+    enum, not independently redefined copies that could silently drift apart
+    on valid --conditioning values."""
+    assert dwarf.Conditioning is Conditioning
+    assert giant_cli.Conditioning is Conditioning
+
+
+def test_warn_if_exceeds_shared_quota_warns_over_quarter_cpu(monkeypatch, capsys):
+    monkeypatch.setattr(dwarf.os, "cpu_count", lambda: 8)  # quota = 2
+    dwarf._warn_if_exceeds_shared_quota(3, "--jobs")
+    assert "warning: --jobs=3 exceeds" in capsys.readouterr().err
+
+
+def test_warn_if_exceeds_shared_quota_silent_within_quota(monkeypatch, capsys):
+    monkeypatch.setattr(dwarf.os, "cpu_count", lambda: 8)  # quota = 2
+    dwarf._warn_if_exceeds_shared_quota(2, "--jobs")
+    assert capsys.readouterr().err == ""
+
+
 def test_convert_rejects_jobs_below_one(tmp_path):
     root_file = tmp_path / "shard.root"
     root_file.touch()