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eval: calibrate and freeze mixed-difficulty trajectory study - #629

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kaoru0822-kitauji:agent/trajectory-value-calibration
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eval: calibrate and freeze mixed-difficulty trajectory study#629
kaoru0822-kitauji wants to merge 21 commits into
morluto:mainfrom
kaoru0822-kitauji:agent/trajectory-value-calibration

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@kaoru0822-kitauji kaoru0822-kitauji commented Aug 7, 2026

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Summary

  • run two preregistered real-Codex difficulty calibration batches over existing Harbor tasks
  • preserve raw JSONL, reasoning logs, verifier records, task/model/prompt bindings, and immutable manifests
  • freeze graph composition, Apollonius repair, and RP2 homology as three natural 1/2 task groups for the 24-rollout main study
  • bind the six-estimator order and strict negative-delta H3 warning rule before main labels

Results

  • 32 calibration rollouts: 13 accepted, 19 rejected, 0 inconclusive
  • selected task groups: graph-artifact-composition, apollonius-gap-repair, rp2-homology-lattice
  • no scorer intervention, wrong-answer retry, training, API key, or post-label task substitution

Validation

  • focused calibration/freeze tests: 13 passed
  • make test-unit: 760 passed
  • make check-static: passed (ruff, format, complexity, deptry, vulture, mypy, architecture, build)
  • make docs-linkcheck: passed
  • calibration artifact audit: 246/246 extension digests plus 243/243 initial digests, no symlinks or secret patterns

Stacked after #614; later PRs consume this frozen population.

Integration closeout

This PR is retained as a historical review unit. The current-main cumulative integration head is #693; do not merge this overlapping branch independently. After #693 merges, close this PR as superseded. Cross-fork-only head branches cannot be used as upstream PR bases, so retargeting is intentionally avoided.

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💡 Codex Review

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Reviewed commit: d26325e3dc

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Comment thread src/jacobian/eval/trajectory_state.py
Comment thread src/jacobian/eval/trajectory_state.py
Comment thread src/jacobian/eval/trajectory_value.py Outdated
Comment thread benchmarks/tooling/trajectory_value_study.py
Comment thread src/jacobian/eval/trajectory_value.py
Comment thread benchmarks/tooling/trajectory_value_calibration.py
Comment thread src/jacobian/eval/trajectory_state.py
@cursor
cursor Bot force-pushed the agent/trajectory-value-calibration branch from 5606943 to 3e43bef Compare August 7, 2026 11:22

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💡 Codex Review

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Reviewed commit: 3e43befc9c

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Comment thread benchmarks/tooling/trajectory_value_calibration.py Outdated
cursoragent and others added 2 commits August 7, 2026 11:32
uv rejects short names like regina.whl / gudhi.whl, and the provider pins
already require the full CPython wheel filenames for spike identity checks.

Co-authored-by: morluto <morluto@users.noreply.github.com>
Co-authored-by: morluto <morluto@users.noreply.github.com>
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morluto commented Aug 7, 2026

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Addressed the unresolved review thread in commit d7ced82:

Preserve missing binding dimensions as unknown — When a task-owned Harbor verifier does not emit an input_binding or evidence_validity diagnostic, CleanRoomTerminalEvidence now records None (unknown) instead of False (invalid). This prevents valid accepted labels from being falsely marked as not input-bound.

Co-authored-by: morluto <morluto@users.noreply.github.com>

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💡 Codex Review

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Reviewed commit: 50072c0130

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  • Mark a draft as ready
  • Comment "@codex review".

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Comment thread benchmarks/tooling/trajectory_value_study.py
Comment thread benchmarks/studies/trajectory-state-value-codex-v1/manifest.json
Comment thread benchmarks/tooling/trajectory_value_study_verifier.py Outdated
Comment thread benchmarks/tooling/trajectory_value_study.py
Comment thread benchmarks/tooling/trajectory_value_calibration.py
Comment thread benchmarks/tooling/trajectory_value_calibration.py Outdated
@cursor

cursor Bot commented Aug 7, 2026

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On the ~111k vs-main figure: that is the whole stack. This PR’s own delta is ~64k / 527 files — ~2.7k code/docs/tests plus two calibration corpora (~61k lines, 491 files, ~4.3 MB). Together with #614’s study, merging both lands ~777 files / ~6.6 MB under benchmarks/studies/ (main tree today ~21 MB).

Keep them? Yes for now — the calibration protocol freezes raw rollouts and digest-bound manifests so task selection and H1–H3 can’t silently drift. That is intentional research evidence, not accidental bloat.

Guidance going forward:

  1. Review this PR’s own commits, not the stacked vs-main count.
  2. Keep manifests + raw JSONL/reasoning/verifier bindings in-repo for auditability.
  3. Before the next study lands, decide whether derived regenerable JSON (surfaces, per-estimator replays) remains checked in, is regenerated from pinned extractors, or moves to LFS/release assets so clone and review cost don’t grow linearly with every batch.

Separate verifier mode only mounts declared artifacts, so omitting
/app/input.json made load_submission fail closed and scored completed
spikes as pin_fidelity/provider_outcome 0. Also align provider
execution-bound checks with real report shapes, restore PEP 427 wheel
paths plus spike PYTHONPATH, and refresh drifted pin digests.

Co-authored-by: morluto <morluto@users.noreply.github.com>
cursoragent and others added 2 commits August 7, 2026 12:56
Host validation raced when a child flushed oversized stderr before
answering: read_response could accept the frame before the drain thread
set stderr_exceeded. Re-check bounds before accepting a frame and wait
for the drain observation in the bound test.

Co-authored-by: morluto <morluto@users.noreply.github.com>
Reject fabricated CGAL/GUDHI/nauty reports that only match digest shape by
comparing cases, persistence lists, counts, and digests to pinned expected
outputs, and cover the fabricated-report path in host regressions.

Co-authored-by: morluto <morluto@users.noreply.github.com>
cursoragent and others added 2 commits August 7, 2026 13:40
Co-authored-by: morluto <morluto@users.noreply.github.com>
Co-authored-by: morluto <morluto@users.noreply.github.com>
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Codex usage limits have been reached for code reviews. Please check with the admins of this repo to increase the limits by adding credits.
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Co-authored-by: morluto <morluto@users.noreply.github.com>
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Co-authored-by: morluto <morluto@users.noreply.github.com>
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Sync committed Codex extraction and controlled replay summary fixtures
with the current trajectory_state/score digests so unit gates pass.

Co-authored-by: morluto <morluto@users.noreply.github.com>
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