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Reproduce and verify

Verify the frozen evidence contract

From the repository root, run the dependency-free validator and the bundle checksum audit:

python scripts/validate_paper3_manifest.py
(cd docs/results/paper-iii/stationary-continuation/v1 && \
  sha256sum --check SHA256SUMS)

The validator checks:

  • the exact simulator, manuscript-science, figure-source, and immutable-data revisions;
  • the seven files named by the v1 SHA256SUMS manifest;
  • acceptance.passed=true, 96 states, and 780 of 780 passing gates;
  • all four stationary case IDs, analytical slopes, fitted mesh slopes, and observed orders;
  • the stationary and time-figure PNG/PDF hashes;
  • the two validated time-integration archives, constants, and featured runs;
  • absence of legacy run previews and provenance-only raw paths from the curated Results page; and
  • the exact four-family provenance-only boundary.

Expected output:

Paper III manifest valid: 4 stationary cases (96 states, 780/780 gates), 2 time-integration figures, 4 provenance-only archives.

Reproduce stationary continuation

Use the exact public simulator revision frozen by release 1.0.0:

git clone https://github.com/ianruau/Chemotaxis_simulation.git
cd Chemotaxis_simulation
git checkout 7c2a09b24fdebb9000b9b996eb34150d6de5ed17
python -m venv .venv
.venv/bin/pip install --editable .
.venv/bin/python stationary_branch_validation.py \
  --output-dir /tmp/paper3-stationary-validation \
  --check

The generator prescribes the signed first-cosine amplitude, eliminates the elliptic variable with the production solver, and solves the remaining stationary equations. For each of four cases it uses

  • meshes N=40,80,160;
  • amplitudes A=+/-{0.0025,0.005,0.01,0.02}; and
  • the constrained fit chi-chi_star_disc=c2*A^2+c4*A^4.

For minimal cases, one dependent flux equation is replaced in the Newton system by the fixed-mass constraint; the omitted endpoint equation is restored and checked in the published full residual.

The command writes:

branch-points.csv
fit-summary.json
states-index.json
stationary-continuation.pdf
stationary-continuation.png
stationary-profiles.csv
stationary-states.npz
SHA256SUMS

The published bundle was produced in two empty output directories. diff -qr reported no difference, including the deterministic NPZ archive and PDF.

Inspect the immutable data

The bundle is frozen at stationary-continuation/v1 in public data commit e62ffa1e99122f8fbbeb3df7586f4050c4ff5c58.

  • branch-points.csv is the compact 96-row scalar table.
  • stationary-profiles.csv is the long-form profile table.
  • stationary-states.npz stores every x, u, and v array.
  • states-index.json maps stable state IDs to NPZ array names and reflection partners.
  • fit-summary.json records coefficients, gates, methods, runtime versions, and full source revisions.

Version v1 is immutable. A changed method or regenerated artifact requires a new version directory.

Reproduce time-dependent diagnostics

The same simulator revision can reproduce or extend the two archived time-integration families. Use each family's config.yaml, constants.json, run_plan.json, and per-run run_meta.json together. Do not infer a current coefficient or classification from a historical folder name or old preview annotation.

The two current reader-facing composites are separately hashed in the release manifest. Historical per-run summary images are not part of the paper contract.

Build the companion site

python -m venv .venv-docs
.venv-docs/bin/pip install --requirement requirements-docs.txt
.venv-docs/bin/mkdocs build --strict

The Pages build omits raw arrays, CSV files, result PDFs, checksums, legacy galleries, and duplicate media. Git remains the complete archive; the site is the restrained reading layer.

Frozen provenance

Component Revision
Paper III numerical science fde25e17187bc3f247b36ce411f6f14eb93d52cf
Simulator and generator 7c2a09b24fdebb9000b9b996eb34150d6de5ed17
Immutable stationary data e62ffa1e99122f8fbbeb3df7586f4050c4ff5c58
Font-embedded time figures c0bfc431a19b81b1c45363dea472c29a745ad055