proofroot 0.1.0__tar.gz

proofroot-0.1.0/.gitignore

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

proofroot-0.1.0/LICENSE

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

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+Metadata-Version: 2.5
+Name: proofroot
+Version: 0.1.0
+Summary: Language-neutral trust core for reproducible simulation: named RNG stream derivation, run phases, evidence tiers, canonical serialization.
+Project-URL: Homepage, https://github.com/hzshen88/newlife
+Project-URL: Repository, https://github.com/hzshen88/newlife
+Project-URL: Documentation, https://github.com/hzshen88/newlife/tree/main/packages/proofroot
+Author: hzshen88
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: canonical-serialization,provenance,reproducibility,rng-streams,trust-core
+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
+Description-Content-Type: text/markdown
+
+# proofroot
+
+Language-neutral trust core for reproducible simulation. Zero dependencies,
+zero domain semantics.
+
+## Install and use
+
+Requires Python 3.12 or newer.
+
+```bash
+python -m pip install proofroot
+```
+
+```python
+import random
+
+from proofroot import EVIDENCECORE_RNG_V1, RngBank, canonical_bytes
+
+bank = RngBank(
+    root_seed=42,
+    names=["mutation", "selection"],
+    rng_strategy=EVIDENCECORE_RNG_V1,
+    stream_factory=random.Random,
+)
+mutation_rng = bank.rng_stream("mutation")
+print(bank.stream_seeds())
+print(mutation_rng.random())
+print(canonical_bytes({"answer": 42}))
+```
+
+Everything every simulation community needs and none of what any single one
+wants to own: named RNG stream seed derivation (`evidencecore-rng-v1`), bank
+semantics invariants (declared streams, lowercase normalization, forward-only),
+run phases, evidence tier vocabulary (exploration / confirmatory / unknown —
+missing fields default to unknown, never to confirmatory), and a canonical
+serialization spec (RFC 8785 structural rules; IEEE754 bit-pattern float
+comparison) with cross-language test vectors.
+
+**Charter boundary (frozen):** the cross-language contract ends at the derived
+seed. Seed derivation is byte-defined over SHA-256 and portable; random
+*sequences* depend on the host generator (Julia's Xoshiro, Python's choice)
+and are recorded in the run manifest, not standardized.
+
+**Oracle:** `EvidenceCore.jl` in the [ParaLife](https://github.com/hzshen88/paralife)
+monorepo is the frozen oracle generating this package's cross-language test
+vectors. ParaLife's legacy compatibility layers (legacy encodings, UPPER-CASE
+phase spellings) are deliberately **not** ported here.
+
+Design rationale: [proposal §5.10](https://github.com/hzshen88/newlife/blob/main/docs/design/proposal.md).

proofroot-0.1.0/README.md

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+# proofroot
+
+Language-neutral trust core for reproducible simulation. Zero dependencies,
+zero domain semantics.
+
+## Install and use
+
+Requires Python 3.12 or newer.
+
+```bash
+python -m pip install proofroot
+```
+
+```python
+import random
+
+from proofroot import EVIDENCECORE_RNG_V1, RngBank, canonical_bytes
+
+bank = RngBank(
+    root_seed=42,
+    names=["mutation", "selection"],
+    rng_strategy=EVIDENCECORE_RNG_V1,
+    stream_factory=random.Random,
+)
+mutation_rng = bank.rng_stream("mutation")
+print(bank.stream_seeds())
+print(mutation_rng.random())
+print(canonical_bytes({"answer": 42}))
+```
+
+Everything every simulation community needs and none of what any single one
+wants to own: named RNG stream seed derivation (`evidencecore-rng-v1`), bank
+semantics invariants (declared streams, lowercase normalization, forward-only),
+run phases, evidence tier vocabulary (exploration / confirmatory / unknown —
+missing fields default to unknown, never to confirmatory), and a canonical
+serialization spec (RFC 8785 structural rules; IEEE754 bit-pattern float
+comparison) with cross-language test vectors.
+
+**Charter boundary (frozen):** the cross-language contract ends at the derived
+seed. Seed derivation is byte-defined over SHA-256 and portable; random
+*sequences* depend on the host generator (Julia's Xoshiro, Python's choice)
+and are recorded in the run manifest, not standardized.
+
+**Oracle:** `EvidenceCore.jl` in the [ParaLife](https://github.com/hzshen88/paralife)
+monorepo is the frozen oracle generating this package's cross-language test
+vectors. ParaLife's legacy compatibility layers (legacy encodings, UPPER-CASE
+phase spellings) are deliberately **not** ported here.
+
+Design rationale: [proposal §5.10](https://github.com/hzshen88/newlife/blob/main/docs/design/proposal.md).

proofroot-0.1.0/pyproject.toml

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+[project]
+name = "proofroot"
+version = "0.1.0"
+description = "Language-neutral trust core for reproducible simulation: named RNG stream derivation, run phases, evidence tiers, canonical serialization."
+readme = "README.md"
+requires-python = ">=3.12"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+authors = [{ name = "hzshen88" }]
+keywords = ["reproducibility", "provenance", "rng-streams",
+            "canonical-serialization", "trust-core"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = []
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/proofroot"]
+
+[tool.hatch.build.targets.wheel.force-include]
+"vectors/canonical_vectors.json" = "proofroot/vectors/canonical_vectors.json"
+"vectors/evidencecore_rng_v1.json" = "proofroot/vectors/evidencecore_rng_v1.json"
+
+[dependency-groups]
+dev = ["pytest>=8"]
+
+[project.urls]
+Homepage = "https://github.com/hzshen88/newlife"
+Repository = "https://github.com/hzshen88/newlife"
+Documentation = "https://github.com/hzshen88/newlife/tree/main/packages/proofroot"

proofroot-0.1.0/src/proofroot/__init__.py

@@ -0,0 +1,54 @@
+"""proofroot — language-neutral trust core for reproducible simulation.
+
+Scope (frozen charter, see docs/design/proposal.md §5.10):
+- D1 current encoding (`evidencecore-rng-v1`) named RNG stream seed derivation
+- D4 bank semantics invariants (declared streams, lowercase normalization,
+  name regex, forward-only, seed snapshots as provenance)
+- D2 RunPhase + terminal-state decision; D5 evidence tier vocabulary
+  (exploration/confirmatory/unknown; missing fields default to unknown,
+  never to confirmatory)
+- Canonical serialization spec (RFC 8785 structural rules, IEEE754 bit-pattern
+  float comparison) + cross-language test vectors
+
+Excluded on purpose: Effect-typed trace schemas, attribution/compare logic,
+manifest assembly, and all domain semantics. Legacy ParaLife compatibility
+layers (parcells-rng-v1, parreact-rng-v1, parworlds-rng-v1 string encodings,
+legacy UPPER-CASE phase spellings) stay in ParaLife's EvidenceCore.jl and are
+deliberately NOT ported here.
+"""
+
+from .canonical import bits_to_float, canonical_bytes, float_to_bits
+from .phase import (
+    EVIDENCE_TIER_CONFIRMATORY,
+    EVIDENCE_TIER_EXPLORATION,
+    EVIDENCE_TIER_UNKNOWN,
+    EVIDENCE_TIERS,
+    RunPhase,
+    is_terminal,
+    parse_phase,
+    resolve_evidence_tier,
+)
+from .rng import (
+    EVIDENCECORE_RNG_V1,
+    RngBank,
+    RngDerivationError,
+    derive_stream_seed,
+)
+
+__all__ = [
+    "EVIDENCECORE_RNG_V1",
+    "bits_to_float",
+    "canonical_bytes",
+    "float_to_bits",
+    "EVIDENCE_TIER_CONFIRMATORY",
+    "EVIDENCE_TIER_EXPLORATION",
+    "EVIDENCE_TIER_UNKNOWN",
+    "EVIDENCE_TIERS",
+    "RunPhase",
+    "RngBank",
+    "RngDerivationError",
+    "derive_stream_seed",
+    "is_terminal",
+    "parse_phase",
+    "resolve_evidence_tier",
+]

proofroot-0.1.0/src/proofroot/canonical.py

@@ -0,0 +1,91 @@
+"""Canonical serialization spec + canonicalization function (§5.9).
+
+The 0th asset of any cross-language byte-level trace comparison is a
+canonical form that does not depend on the host language's float
+formatting. Rules (docs/design/proposal.md §5.9):
+
+- **Structural layer** — the ready-made parts of RFC 8785 (JCS): object keys
+  sorted, UTF-8 output, no insignificant whitespace. Key order is Unicode
+  *code point* order (the proposal pins this; note RFC 8785 itself sorts by
+  UTF-16 code units — the two differ only for keys mixing astral planes with
+  U+E000..U+FFFF, and proofroot's spec chooses code point order).
+- **Floats bypass text representation instead of praying to shortest
+  round-trip**: numeric comparison fields in a trace carry the IEEE754 binary
+ 64 bit pattern (16-digit lowercase hex via `float_to_bits`); human-readable
+  decimal may accompany as a comment field, but byte comparison only sees the
+  hex. Bit patterns are identical by definition across languages.
+- Consequently `canonical_bytes` **rejects raw floats** — a float that reached
+  the canonicalizer would be about to be formatted by host rules, which is
+  exactly the failure the spec exists to prevent. Callers pre-encode floats.
+
+The companion vectors (`vectors/canonical_vectors.json`, regenerated by
+`vectors/generate_canonical_vectors.py`) pin: key ordering incl. non-ASCII
+keys, string escaping, and the classic float traps (-0.0, subnormals, NaN
+payloads, infinities, 0.1).
+"""
+
+from __future__ import annotations
+
+import json
+import struct
+
+__all__ = ["canonical_bytes", "float_to_bits", "bits_to_float"]
+
+
+def float_to_bits(value: float) -> str:
+    """IEEE754 binary64 bit pattern of ``value`` as '0x' + 16 lowercase hex.
+
+    This is the *only* sanctioned float representation in comparison
+    fields: -0.0, subnormals and NaN payloads round-trip exactly.
+    """
+    return "0x" + struct.pack(">d", value).hex()
+
+
+def bits_to_float(bits: str) -> float:
+    """Inverse of `float_to_bits` (accepts with or without the '0x' prefix)."""
+    return struct.unpack(">d", bytes.fromhex(bits.removeprefix("0x")))[0]
+
+
+def _encode(value, level_key: str | None):
+    # bool before int: bool is an int subclass in Python.
+    if value is None or value is True or value is False:
+        return value
+    if isinstance(value, int):
+        return value
+    if isinstance(value, float):
+        raise TypeError(
+            "raw float in canonical input; pre-encode comparison fields with "
+            f"float_to_bits (got {value!r}"
+            + (f" at key {level_key!r}" if level_key is not None else "")
+            + ")"
+        )
+    if isinstance(value, str):
+        return value
+    if isinstance(value, list):
+        return [_encode(item, level_key) for item in value]
+    if isinstance(value, dict):
+        out = {}
+        for key in sorted(value):
+            if not isinstance(key, str):
+                raise TypeError(f"canonical object keys must be strings, got {key!r}")
+            out[key] = _encode(value[key], key)
+        return out
+    raise TypeError(f"value not representable in canonical form: {value!r}")
+
+
+def canonical_bytes(value) -> bytes:
+    """Canonical serialization: JCS structural rules, floats pre-encoded.
+
+    Deterministic byte output for any JSON-compatible value tree whose
+    numeric comparison fields already carry IEEE754 bit-pattern hex strings
+    (see `float_to_bits`). Raises TypeError on raw floats, non-string keys
+    and non-JSON types — those are spec violations, not formatting choices.
+    """
+    encoded = _encode(value, None)
+    text = json.dumps(
+        encoded,
+        ensure_ascii=False,  # UTF-8, minimal escaping per JCS
+        separators=(",", ":"),  # no insignificant whitespace
+        allow_nan=False,
+    )
+    return text.encode("utf-8")

proofroot-0.1.0/src/proofroot/phase.py

@@ -0,0 +1,74 @@
+"""D2 RunPhase + terminal-state decision, D5 evidence tier vocabulary.
+
+Port of EvidenceCore.jl's D2/D5. Per §5.10 discipline 2, the legacy UPPER-CASE
+phase spellings ("COMPLETED"/"FAILED"/…) are deliberately NOT ported — they
+exist to read pre-unification ParaLife run artifacts, whose reason to exist is
+not portable. New artifacts serialize TitleCase.
+"""
+
+from __future__ import annotations
+
+import enum
+
+
+class RunPhase(str, enum.Enum):
+    """The unified 8-value TitleCase run lifecycle phases (D2).
+
+    Only the enum values and terminality are shared semantics; the transition
+    map stays with each host's run lifecycle (Parcells' 6-step and Parworlds'
+    8-step lifecycles were deliberately not unified in the first generation).
+    """
+
+    PLANNED = "Planned"
+    VALIDATED = "Validated"
+    INITIALIZING = "Initializing"
+    RUNNING = "Running"
+    ASSAYING = "Assaying"
+    FINALIZING = "Finalizing"
+    COMPLETED = "Completed"
+    FAILED = "Failed"
+
+
+def is_terminal(phase: RunPhase) -> bool:
+    """A phase is an irreversible terminal state iff it is Completed or Failed."""
+    return phase is RunPhase.COMPLETED or phase is RunPhase.FAILED
+
+
+def parse_phase(name: str) -> RunPhase:
+    """Resolve a phase from its serialized (TitleCase) string form.
+
+    Raises on anything else — including the legacy UPPER-CASE spellings, which
+    are a ParaLife-local compatibility layer and intentionally not accepted
+    here.
+    """
+    try:
+        return RunPhase(name)
+    except ValueError:
+        raise ValueError(f"unknown run phase {name!r}") from None
+
+
+# ── D5: evidence tier vocabulary (cross-program governance, ADR-0016) ────────
+# exploration and unknown may never be cited as evidence; confirmatory must be
+# declared explicitly. The safety direction: a missing field degrades to
+# unknown — never to confirmatory — so "forgot to declare" fails closed.
+
+EVIDENCE_TIER_EXPLORATION = "exploration"
+EVIDENCE_TIER_CONFIRMATORY = "confirmatory"
+EVIDENCE_TIER_UNKNOWN = "unknown"
+EVIDENCE_TIERS = frozenset(
+    {EVIDENCE_TIER_EXPLORATION, EVIDENCE_TIER_CONFIRMATORY, EVIDENCE_TIER_UNKNOWN}
+)
+
+
+def resolve_evidence_tier(declared: str | None) -> str:
+    """Resolve the evidence tier of a run artifact.
+
+    ``None``/missing degrades to ``unknown`` (fail closed). A declared tier
+    must be a member of the vocabulary — a typo must raise, not silently pass
+    as either citable or uncitable.
+    """
+    if declared is None:
+        return EVIDENCE_TIER_UNKNOWN
+    if declared not in EVIDENCE_TIERS:
+        raise ValueError(f"unknown evidence tier: {declared!r}")
+    return declared