newlife

A preregistration harness for simulation. Freeze what would count as an answer before you run anything; let the machine — not your judgement after the fact — decide whether the criteria were met.

Install

Requires Python 3.12 or newer and git.

python -m pip install newlife
# Optional simulation backends:
python -m pip install "newlife[process-bigraph]"
python -m pip install "newlife[spatio-flux]"

Start in your own repository:

mkdir my-research && cd my-research
git init
git config user.name "Your Name"
git config user.email "you@example.com"
newlife init 2026-09-05-my-question   # scaffold a question folder; commits it,
                                      # deliberately leaving prereg.md uncommitted
$EDITOR questions/2026-09-05-my-question/prereg.md
newlife freeze questions/2026-09-05-my-question
$EDITOR questions/2026-09-05-my-question/verdict.py
newlife run questions/2026-09-05-my-question
newlife check questions/2026-09-05-my-question
git add questions/2026-09-05-my-question/results
git commit -m "record verdict"
newlife audit questions/2026-09-05-my-question

audit proves, from commit ancestry rather than forgeable dates: the registration has a freeze commit, the stamped hash matches it, the content was never edited afterwards, and every committed output post-dates the freeze. Questions are siblings, not a chain: a question's verdict never runs another question's runner.

What the contract layer does

BiologicalProfile enforces four contracts — StateClaim, MechanismSpec, Effect, Resolver. A mechanism declares which paths it owns and which effects it may emit; writing anywhere else raises newlife.core.errors.CommitAuthorityError from the contract layer, not from your solver. That distinction is load-bearing: "an exception was raised" is not the same as "the contract stopped it", and a negative control that conflates them proves nothing.

Third-party simulation processes are admitted unmodified. Verified against process-bigraph's own processes, spatio-flux (Monod kinetics, dynamic FBA behind a GLPK solver), and a hand-wrapped tellurium ODE model — trajectories byte-identical to running the same code without newlife.

Gates that ship with it

newlife check runs three checks against your files: criteria that are true by construction (a comprehension iterating a named constant while discarding the loop variable is a repetition, not a sweep); parse failures that silently fall back to a convenient default; and whether the units your registration declares are exactly the units your runner computes. Each of the three was written after that exact defect shipped undetected — the third one caught a real misalignment the first time it ran.

Also included: newlife skills install puts two AI skills (shaping a question into a decidable one; writing a registration that will not veto itself) where your assistant reads them.

proofroot is installed transitively and supplies RNG stream derivation, canonical serialization, and the evidence-tier vocabulary.

Source, design rationale, and the record of every milestone judged so far: https://github.com/hzshen88/newlife