newlife 0.1.0__tar.gz

newlife-0.1.0/.gitignore

@@ -0,0 +1,8 @@
+__pycache__/
+*.py[cod]
+.venv/
+*.egg-info/
+dist/
+build/
+.pytest_cache/
+.DS_Store

newlife-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
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newlife-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: newlife
+Version: 0.1.0
+Summary: Preregistration harness for simulation: freeze what would count as an answer in git, compute the verdict mechanically, and prove from commit ancestry that the outputs post-date the freeze.
+Project-URL: Homepage, https://github.com/hzshen88/newlife
+Project-URL: Repository, https://github.com/hzshen88/newlife
+Author: hzshen88
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: preregistration,provenance,reproducibility,scientific-workflow,simulation,systems-biology
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Requires-Dist: proofroot<0.2,>=0.1
+Provides-Extra: process-bigraph
+Requires-Dist: process-bigraph==1.8.3; extra == 'process-bigraph'
+Provides-Extra: spatio-flux
+Requires-Dist: spatio-flux==1.4.0; extra == 'spatio-flux'
+Description-Content-Type: text/markdown
+
+# 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`.
+
+```bash
+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:
+
+```bash
+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>

newlife-0.1.0/README.md

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+# 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`.
+
+```bash
+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:
+
+```bash
+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>

newlife-0.1.0/pyproject.toml

@@ -0,0 +1,48 @@
+[project]
+name = "newlife"
+version = "0.1.0"
+description = "Preregistration harness for simulation: freeze what would count as an answer in git, compute the verdict mechanically, and prove from commit ancestry that the outputs post-date the freeze."
+readme = "README.md"
+requires-python = ">=3.12"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+authors = [{ name = "hzshen88" }]
+keywords = ["preregistration", "reproducibility", "simulation", "provenance",
+            "systems-biology", "scientific-workflow"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = ["proofroot>=0.1,<0.2"]
+
+[project.optional-dependencies]
+process-bigraph = ["process-bigraph==1.8.3"]
+# 第十六个里程碑：一个真正独立的第三方包。走 optional extra，不进主依赖面
+spatio-flux = ["spatio-flux==1.4.0"]
+
+[project.scripts]
+newlife = "newlife.cli:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.uv.sources]
+proofroot = { workspace = true }
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/newlife"]
+# 模板与 vendored 的 prereg.sh 不是 .py，必须显式带进 wheel——
+# 「冻结工具不随库发布」是用户拿不到时间证明的直接原因。
+artifacts = ["src/newlife/scaffold/prereg.sh", "src/newlife/scaffold/templates/*",
+             "src/newlife/skills/*/SKILL.md"]
+
+[dependency-groups]
+dev = ["pytest>=8"]
+
+[project.urls]
+Homepage = "https://github.com/hzshen88/newlife"
+Repository = "https://github.com/hzshen88/newlife"

newlife-0.1.0/src/newlife/__init__.py

@@ -0,0 +1,11 @@
+"""newlife — a verifiable profile layer for composable biological simulation.
+
+Owns the scientific semantics the bare runtime does not provide (proposal
+v0.6, §3): StateClaim / MechanismSpec / Effect / Resolver contracts, path
+authority, read-only alias protection, single-path lowering (the only write
+path into any runtime), and canonical evidence traces.
+
+Vendor types (Process, Composite, ...) never leak past the adapter layer;
+`process-bigraph` is an optional extra and may only be imported inside
+`newlife.adapters.process_bigraph`.
+"""

newlife-0.1.0/src/newlife/adapters/__init__.py

@@ -0,0 +1 @@
+"""adapters subpackage (skeleton — filled per v0.1 schedule; no lowering code before preregistration freeze)."""

newlife-0.1.0/src/newlife/adapters/process_bigraph/__init__.py

@@ -0,0 +1 @@
+"""adapters/process_bigraph subpackage (skeleton — filled per v0.1 schedule; no lowering code before preregistration freeze)."""

newlife-0.1.0/src/newlife/adapters/process_bigraph/bare_control.py

@@ -0,0 +1,144 @@
+"""Bare process-bigraph controls that deliberately bypass newlife."""
+
+from __future__ import annotations
+
+from typing import Any
+
+from process_bigraph import Composite, allocate_core
+from process_bigraph.processes.growth_division import Grow
+
+
+def bare_trajectory(*, initial_mass: float, rate: float, steps: int) -> list[float]:
+    """Run ``Grow`` on bare process-bigraph and return the mass trajectory."""
+    core = _core()
+    state: dict[str, Any] = {
+        "mass": initial_mass,
+        "grow": {
+            "_type": "process",
+            "address": "local:Grow",
+            "config": {"rate": rate},
+            "inputs": {"mass": ["mass"]},
+            "outputs": {"mass": ["mass"]},
+            "interval": 1.0,
+        },
+    }
+    composite = Composite({"state": state}, core=core)
+    trajectory = [float(composite.state["mass"])]
+    for _ in range(steps):
+        composite.run(1.0)
+        trajectory.append(float(composite.state["mass"]))
+    return trajectory
+
+
+def _core():
+    core = allocate_core()
+    core.register_link("Grow", Grow)
+    return core
+
+
+# --- 第十六个里程碑：一个真正独立的第三方包（spatio-flux 1.4.0）---
+
+
+def monod_trajectory(
+    *, initial_mass: float, glucose: float, steps: int
+) -> list[tuple[float, dict[str, float]]]:
+    """Run ``MonodKinetics`` on bare process-bigraph and return its trajectory."""
+    try:
+        import spatio_flux
+        from spatio_flux.processes.monod_kinetics import MonodKinetics
+    except ImportError as exc:
+        raise SystemExit(
+            "spatio-flux is not installed; this is an environment error, not a verdict. "
+            "Install with: uv sync --package newlife --extra process-bigraph "
+            f"--extra spatio-flux. Original error: {exc}"
+        ) from exc
+
+    core = allocate_core()
+    spatio_flux.register_types(core)          # 第三方交付的类型词表
+    core.register_link("MonodKinetics", MonodKinetics)
+
+    state: dict[str, Any] = {
+        "mass": initial_mass,
+        "local": {"glucose": glucose},
+        "exchange": {"glucose": 0.0},
+        "kin": {
+            "_type": "process",
+            "address": "local:MonodKinetics",
+            "config": {},
+            "inputs": {"biomass": ["mass"], "substrates": ["local"]},
+            "outputs": {"biomass": ["mass"], "substrates": ["exchange"]},
+            "interval": 1.0,
+        },
+    }
+    composite = Composite({"state": state}, core=core)
+    out = [(float(composite.state["mass"]), dict(composite.state["exchange"]))]
+    for _ in range(steps):
+        composite.run(1.0)
+        out.append((float(composite.state["mass"]), dict(composite.state["exchange"])))
+    return out
+
+
+# --- 第十七个里程碑：一个求解器背后的第三方 process（spatio-flux 的 dFBA）---
+
+FIELDS = ("glucose", "acetate", "biomass")
+
+
+def dfba_trajectory(
+    *, glucose: float, acetate: float, biomass: float, steps: int
+) -> list[dict[str, float]]:
+    """Run ``DynamicFBA`` on bare process-bigraph with its bundled E. coli model."""
+    try:
+        import spatio_flux
+        from spatio_flux.processes.dfba import MODEL_REGISTRY_DFBA, DynamicFBA
+    except ImportError as exc:
+        raise SystemExit(
+            "spatio-flux or cobra is not installed; this is an environment error, "
+            "not a verdict. Install with: uv sync --package newlife "
+            f"--extra process-bigraph --extra spatio-flux. Original error: {exc}"
+        ) from exc
+
+    core = allocate_core()
+    spatio_flux.register_types(core)
+    core.register_link("DynamicFBA", DynamicFBA)
+
+    state: dict[str, Any] = {
+        "fields": {"glucose": glucose, "acetate": acetate, "biomass": biomass},
+        "fba": {
+            "_type": "process",
+            "address": "local:DynamicFBA",
+            "config": dict(MODEL_REGISTRY_DFBA["ecoli core"]),
+            "inputs": {
+                "substrates": {"glucose": ["fields", "glucose"],
+                               "acetate": ["fields", "acetate"]},
+                "biomass": ["fields", "biomass"],
+            },
+            "outputs": {
+                "substrates": {"glucose": ["fields", "glucose"],
+                               "acetate": ["fields", "acetate"]},
+                "biomass": ["fields", "biomass"],
+            },
+            "interval": 1.0,
+        },
+    }
+    composite = Composite({"state": state}, core=core)
+    out = [normalise_fields(composite.state["fields"])]
+    for _ in range(steps):
+        composite.run(1.0)
+        out.append(normalise_fields(composite.state["fields"]))
+    return out
+
+
+def normalise_fields(fields: Any) -> dict[str, float]:
+    """Normalize third-party numeric scalar values to Python ``float``."""
+    return {k: float(fields[k]) for k in FIELDS}
+
+
+def solver_identity() -> dict[str, str]:
+    """Return the optimization interface and solver version used by dFBA."""
+    from cobra.io import load_model
+    import swiglpk
+
+    return {
+        "optlang_interface": load_model("textbook").solver.interface.__name__,
+        "glpk_version": str(swiglpk.glp_version()),
+    }