auto-sync 2026-07-04T05:22:54Z workspace (part 3)

workspace/scripts/audit_action_bounds.py

@@ -35,6 +35,11 @@ def main(argv: list[str] | None = None) -> int:
     parser.add_argument("--low", type=float, default=-1.0)
     parser.add_argument("--high", type=float, default=1.0)
     parser.add_argument("--tolerance", type=float, default=1.0e-6)
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     if args.low >= args.high:
@@ -85,7 +90,7 @@ def main(argv: list[str] | None = None) -> int:
     }
     (out_dir / "metrics.json").write_text(json.dumps(payload, indent=2, sort_keys=True) + "\n")
     (out_dir / "table.tex").write_text(_latex_table(rows) + "\n")
-    (out_dir / "report.md").write_text(_report(payload) + "\n")
+    _write_markdown_report(out_dir, payload, no_markdown_report=args.no_markdown_report)
     (out_dir / "eval.log").write_text(
         "\n".join(f"{row['split']}: {row['num_rows']} rows" for row in rows) + "\n"
     )
@@ -430,6 +435,19 @@ def _report(payload: dict[str, Any]) -> str:
     return "\n".join(lines)
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    payload: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(payload) + "\n")
+
+
 def _write_provenance(out_dir: Path, args: argparse.Namespace) -> None:
     config = {key: str(value) for key, value in sorted(vars(args).items())}
     (out_dir / "config.yaml").write_text(

workspace/scripts/audit_chart_feature_sources.py

@@ -34,6 +34,11 @@ def main(argv: list[str] | None = None) -> int:
         ],
     )
     parser.add_argument("--out-dir", type=Path, default=Path("runs/chart_feature_audit"))
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     out_dir = args.out_dir
@@ -137,7 +142,7 @@ def main(argv: list[str] | None = None) -> int:
     (out_dir / "metrics_by_task.json").write_text(_metrics_by_task(split_rows) + "\n")
     (out_dir / "metrics_by_seed.json").write_text("{}\n")
     (out_dir / "table.tex").write_text(_table(split_rows) + "\n")
-    (out_dir / "report.md").write_text(_report(metrics) + "\n")
+    _write_markdown_report(out_dir, metrics, no_markdown_report=args.no_markdown_report)
     (out_dir / "train.log").write_text("not a training run; audited chart feature sources\n")
     (out_dir / "eval.log").write_text("audited chart feature sources in exported chart indexes\n")
     print(json.dumps({"out_dir": str(out_dir), "splits": len(split_rows)}, indent=2))
@@ -244,6 +249,19 @@ def _report(metrics: dict[str, Any]) -> str:
     return "\n".join(lines)
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    metrics: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(metrics) + "\n")
+
+
 def _write_provenance(out_dir: Path, args: argparse.Namespace) -> None:
     (out_dir / "config.yaml").write_text(
         "\n".join(f"{key}: {value}" for key, value in sorted(vars(args).items())) + "\n"

workspace/scripts/audit_cil_charts.py

@@ -16,6 +16,11 @@ def main(argv: list[str] | None = None) -> int:
     parser.add_argument("--chart-root", type=Path, default=Path("data/cil_charts"))
     parser.add_argument("--run-root", type=Path, default=Path("runs"))
     parser.add_argument("--out-dir", type=Path, default=Path("runs/leakage_audit"))
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     indexes = _load_indexes(args.chart_root)
@@ -52,11 +57,24 @@ def main(argv: list[str] | None = None) -> int:
     out_dir = args.out_dir
     out_dir.mkdir(parents=True, exist_ok=True)
     (out_dir / "report.json").write_text(json.dumps(report, indent=2, sort_keys=True) + "\n")
-    (out_dir / "report.md").write_text(_markdown(report) + "\n")
+    _write_markdown_report(out_dir, report, no_markdown_report=args.no_markdown_report)
     print(json.dumps({"status": report["status"], "violations": len(violations)}, indent=2))
     return 1 if violations else 0
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    report: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_markdown(report) + "\n")
+
+
 def _load_indexes(chart_root: Path) -> dict[str, tuple[Path, dict[str, Any]]]:
     output: dict[str, tuple[Path, dict[str, Any]]] = {}
     for split in REQUIRED_SPLITS:

workspace/scripts/build_action_scale_vector.py

@@ -54,6 +54,11 @@ def main(argv: list[str] | None = None) -> int:
         default=1.0,
         help="Maximum allowed scale value.",
     )
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     if args.floor <= 0.0:
@@ -133,7 +138,7 @@ def main(argv: list[str] | None = None) -> int:
     )
     (out_dir / "eval.log").write_text("no eval; action convention artifact only\n")
     (out_dir / "table.tex").write_text(_table(payload) + "\n")
-    (out_dir / "report.md").write_text(_report(payload) + "\n")
+    _write_markdown_report(out_dir, payload, no_markdown_report=args.no_markdown_report)
     print(json.dumps({"out_dir": str(out_dir), "scale_env": payload["scale_env"]}, indent=2))
     return 0
 
@@ -178,6 +183,19 @@ def _report(payload: dict[str, Any]) -> str:
     )
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    payload: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(payload) + "\n")
+
+
 def _latex_escape(value: str) -> str:
     return value.replace("_", "\\_").replace("%", "\\%").replace("&", "\\&")
 

workspace/scripts/build_data_accounting.py

@@ -35,6 +35,11 @@ def main(argv: list[str] | None = None) -> int:
         "--base-candidate-types",
         default=",".join(DEFAULT_BASE_CANDIDATE_TYPES),
     )
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     fractions = _parse_split_fractions(args.split_fractions)
@@ -103,11 +108,24 @@ def main(argv: list[str] | None = None) -> int:
     out_dir.mkdir(parents=True, exist_ok=True)
     (out_dir / "table.json").write_text(json.dumps(payload, indent=2, sort_keys=True) + "\n")
     (out_dir / "table.tex").write_text(_latex_table(materialized) + "\n")
-    (out_dir / "report.md").write_text(_markdown_report(payload) + "\n")
+    _write_markdown_report(out_dir, payload, no_markdown_report=args.no_markdown_report)
     print(json.dumps({"out_dir": str(out_dir), "split_hash": payload["split_hash"]}, indent=2))
     return 0
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    payload: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_markdown_report(payload) + "\n")
+
+
 def _empty_row(split: str) -> dict[str, Any]:
     return {
         "split": split,

workspace/scripts/calibrate_dominance.py

@@ -21,6 +21,11 @@ def main(argv: list[str] | None = None) -> int:
     parser.add_argument("--input", type=Path, required=True, help="Measured calibration JSON rows.")
     parser.add_argument("--out-dir", type=Path, default=Path("runs/dominance_calibration"))
     parser.add_argument("--alpha", type=float, default=0.1)
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
     if not 0.0 < args.alpha < 1.0:
         parser.error("--alpha must be in (0, 1)")
@@ -66,7 +71,7 @@ def main(argv: list[str] | None = None) -> int:
     (out_dir / "train.log").write_text("fit conformal residual quantile from measured calibration rows\n")
     (out_dir / "eval.log").write_text("no held-out dominance eval in calibration script\n")
     (out_dir / "table.tex").write_text(_table(payload) + "\n")
-    (out_dir / "report.md").write_text(_report(payload) + "\n")
+    _write_markdown_report(out_dir, payload, no_markdown_report=args.no_markdown_report)
     print(json.dumps({"out_dir": str(out_dir), "residual_quantile": quantile}, indent=2))
     return 0
 
@@ -125,6 +130,19 @@ def _report(payload: dict[str, Any]) -> str:
     )
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    payload: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(payload) + "\n")
+
+
 def _run(command: list[str]) -> str:
     try:
         return subprocess.check_output(command, cwd=PROJECT_ROOT, text=True).strip()

workspace/scripts/check_tangent_reconstruction.py

@@ -31,6 +31,11 @@ def main(argv: list[str] | None = None) -> int:
     )
     parser.add_argument("--chart-root", type=Path, default=Path("data/cil_charts"))
     parser.add_argument("--out-dir", type=Path, default=Path("runs/tangent_reconstruction"))
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     indexes = args.chart_index or sorted(args.chart_root.glob("*/index.json"))
@@ -61,7 +66,7 @@ def main(argv: list[str] | None = None) -> int:
     (out_dir / "train.log").write_text("no training; checked exported tangent summaries\n")
     (out_dir / "eval.log").write_text(f"checked {len(rows)} rows across {len(indexes)} indexes\n")
     (out_dir / "table.tex").write_text(_table(summary) + "\n")
-    (out_dir / "report.md").write_text(_report(summary) + "\n")
+    _write_markdown_report(out_dir, summary, no_markdown_report=args.no_markdown_report)
     print(json.dumps({"out_dir": str(out_dir), **summary}, indent=2))
     return 0
 
@@ -167,6 +172,19 @@ def _report(summary: dict[str, Any]) -> str:
     )
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    summary: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(summary) + "\n")
+
+
 def _run(command: list[str]) -> str:
     try:
         return subprocess.check_output(command, cwd=PROJECT_ROOT, text=True).strip()

workspace/scripts/eval_chart_positive_memory_proxy.py

@@ -47,6 +47,11 @@ def main(argv: list[str] | None = None) -> int:
     parser.add_argument("--neighbors", type=int, default=8)
     parser.add_argument("--max-target-charts", type=int, default=100000)
     parser.add_argument("--thresholds", default="0.20,0.40")
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     thresholds = [float(item) for item in args.thresholds.split(",") if item.strip()]
@@ -129,7 +134,13 @@ def main(argv: list[str] | None = None) -> int:
         + "\n"
     )
     (out_dir / "table.tex").write_text(_table(summary) + "\n")
-    (out_dir / "report.md").write_text(_report(args.mode, args.k, summary) + "\n")
+    _write_markdown_report(
+        out_dir,
+        args.mode,
+        args.k,
+        summary,
+        no_markdown_report=args.no_markdown_report,
+    )
     print(json.dumps({"out_dir": str(out_dir), "num_rows": len(rows)}, indent=2))
     return 0
 
@@ -304,6 +315,21 @@ def _report(method: str, k: int, summary: dict[str, Any]) -> str:
     return "\n".join(lines)
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    method: str,
+    k: int,
+    summary: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(method, k, summary) + "\n")
+
+
 def _latex_escape(value: str) -> str:
     return value.replace("_", "\\_").replace("%", "\\%").replace("&", "\\&")
 

workspace/scripts/export_chart_object_embeddings.py

@@ -46,6 +46,11 @@ def main(argv: list[str] | None = None) -> int:
         default=Path("runs/chart_object_embeddings_rgb_refs"),
     )
     parser.add_argument("--overwrite", action="store_true")
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     out_dir = args.out_dir
@@ -75,7 +80,7 @@ def main(argv: list[str] | None = None) -> int:
     (out_dir / "metrics_by_task.json").write_text(_metrics_by_task(split_rows) + "\n")
     (out_dir / "metrics_by_seed.json").write_text("{}\n")
     (out_dir / "table.tex").write_text(_table(split_rows) + "\n")
-    (out_dir / "report.md").write_text(_report(metrics) + "\n")
+    _write_markdown_report(out_dir, metrics, no_markdown_report=args.no_markdown_report)
     (out_dir / "train.log").write_text("not a training run; exported object-layout embeddings\n")
     (out_dir / "eval.log").write_text(
         "decoded observation_ref JPEGs only; no outcomes, labels, or hidden branches read\n"
@@ -348,6 +353,19 @@ def _report(metrics: dict[str, Any]) -> str:
     return "\n".join(lines)
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    metrics: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(metrics) + "\n")
+
+
 def _write_provenance(out_dir: Path, args: argparse.Namespace) -> None:
     (out_dir / "config.yaml").write_text(
         "\n".join(f"{key}: {value}" for key, value in sorted(vars(args).items())) + "\n"

workspace/scripts/export_chart_observation_embeddings.py

@@ -43,6 +43,11 @@ def main(argv: list[str] | None = None) -> int:
         default=Path("runs/chart_observation_embeddings_rgb_refs"),
     )
     parser.add_argument("--overwrite", action="store_true")
+    parser.add_argument(
+        "--no-markdown-report",
+        action="store_true",
+        help="Do not write report.md; persistent prose is consolidated in README.md.",
+    )
     args = parser.parse_args(argv)
 
     out_dir = args.out_dir
@@ -76,7 +81,7 @@ def main(argv: list[str] | None = None) -> int:
     (out_dir / "metrics_by_task.json").write_text(_metrics_by_task(split_rows) + "\n")
     (out_dir / "metrics_by_seed.json").write_text("{}\n")
     (out_dir / "table.tex").write_text(_table(split_rows) + "\n")
-    (out_dir / "report.md").write_text(_report(metrics) + "\n")
+    _write_markdown_report(out_dir, metrics, no_markdown_report=args.no_markdown_report)
     (out_dir / "train.log").write_text("not a training run; exported observation embeddings\n")
     (out_dir / "eval.log").write_text("decoded observation_ref JPEGs only; no outcomes read\n")
     print(json.dumps({"out_dir": str(out_dir), "splits": len(split_rows)}, indent=2))
@@ -284,6 +289,19 @@ def _report(metrics: dict[str, Any]) -> str:
     return "\n".join(lines)
 
 
+def _write_markdown_report(
+    out_dir: Path,
+    metrics: dict[str, Any],
+    *,
+    no_markdown_report: bool,
+) -> None:
+    report_path = out_dir / "report.md"
+    if no_markdown_report:
+        report_path.unlink(missing_ok=True)
+        return
+    report_path.write_text(_report(metrics) + "\n")
+
+
 def _write_provenance(out_dir: Path, args: argparse.Namespace) -> None:
     (out_dir / "config.yaml").write_text(
         "\n".join(f"{key}: {value}" for key, value in sorted(vars(args).items())) + "\n"

workspace/scripts/slurm/reexport_rgb_ref_cil_charts.sbatch

@@ -51,8 +51,10 @@ common_args=(
 
 "$PYTHON" scripts/audit_cil_charts.py \
   --chart-root "$OUT_ROOT" \
-  --out-dir runs/leakage_audit_rgb_refs
+  --out-dir runs/leakage_audit_rgb_refs \
+  --no-markdown-report
 
 "$PYTHON" scripts/audit_chart_feature_sources.py \
   --indexes "$OUT_ROOT/train/index.json" "$OUT_ROOT/val/index.json" "$OUT_ROOT/test/index.json" \
-  --out-dir runs/chart_feature_audit_rgb_refs
+  --out-dir runs/chart_feature_audit_rgb_refs \
+  --no-markdown-report