Chemotaxis III in Lean Partial Lean 4 formalization · release v0.1.1
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Reproducing the formal checks

Git downloads the source. Elan installs the Lean version named by lean-toolchain. Lake is Lean’s package/build tool; Mathlib is the pinned mathematical library. Its cache avoids recompiling dependencies, but the scientific project still builds from source.

One command

From a clean checkout run ./verify.sh. Git, elan, a C toolchain, Python 3 and network access are required. Start with three Lean threads (LEAN_NUM_THREADS=3) and allow several minutes or more depending on hardware and cache downloads.

Transparent route

lake exe cache get
lake build
./scripts/check_umbrella.sh
./scripts/check_no_proof_escapes.sh
./scripts/test_proof_escape_gate.sh
./scripts/audit_axioms.sh

The audit writes .verification/positive.raw.json and a separate negative-control transcript. It audits the complete owned environment, including generated helpers. Success includes PASS: complete live axiom inventory and compiled negative control. The negative scratch theorem is expected to fail the audit; it never enters the positive library.

For receipt and comparator verification, install lean-pkg and follow its receipt-check commands against the committed .lean-receipts files. A local source-only gate additionally runs scripts/verify-local.sh from a committed fresh source clone and prints every indexed type/axiom query. Comparator Challenge/Solution modules are separate targets; their intentional Challenge admissions are not library proofs.

Troubleshooting

If lake is missing, add elan’s bin directory to PATH and restart the shell. Network/cache failure is not a mathematical failure: retain the error and rerun the cache fetch. Lower LEAN_NUM_THREADS if resources are tight. Never change the pinned toolchain or dependencies to make a check appear green. A complete build proves the Lean statements elaborate; it does not prove their transcription from the manuscript is faithful, construct their hypothesis objects, or certify the entire PDE paper.