Digital Drosophila Archive
57 lines
3.4 KiB
Python
57 lines
3.4 KiB
Python
"""Predeclare and verify old inputs before executing any alternative dynamics."""
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import ast
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from datetime import datetime, timezone
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import importlib.metadata
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import json
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import platform
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from pathlib import Path
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import shutil
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import subprocess
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import sys
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from context import CFG,ROOT,EXP,MODEL,AC,digest,save,source_hashes
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def frozen_integrity():
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sys.path.insert(0,str(ROOT/CFG['prior_model']))
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import audit_semantics as old
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result=old.integrity()
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for p in (ROOT/CFG['prior_model'],AC,ROOT/'registry/feedback-context-review-20260930'):
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result[str(p.relative_to(ROOT))]=old.manifest_check(p,digest)
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assert all(x['pass'] for x in result.values())
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return result
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def main():
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assert (MODEL/'oracle_runner.py').is_file()
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assert not (EXP/'protocol').exists(),'Refusing reused experiment protocol'
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for d in ('protocol','external-resources','inputs','components','oracle','regression','audit','performance'):(EXP/d).mkdir()
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source=AC/'external-resources/model.py'
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assert digest(source)=='fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e'
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tree=ast.parse(source.read_text())
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assert all(isinstance(x,(ast.Import,ast.ImportFrom,ast.Assign,ast.FunctionDef,ast.Expr)) for x in tree.body)
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inputs=[source,AC/'external-resources/LICENSE',AC/'external-resources/environment_full.yml',
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AC/'audit/selected-real-edges.csv',AC/'audit/selected-metadata.parquet',ROOT/CFG['prior_model']/'math_reference.py']
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for name in CFG['motifs']:
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inputs.extend([AC/'motifs'/f'{name}-edges.csv',AC/'motifs'/f'{name}-events.parquet',AC/'motifs'/f'{name}-state.npz'])
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save(EXP/'protocol/preregistered.json',dict(config=CFG,timestamp_utc=datetime.now(timezone.utc).isoformat(),
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source_hashes=source_hashes(),input_hashes=[dict(path=str(p.relative_to(ROOT)),sha256=digest(p),bytes=p.stat().st_size) for p in inputs],
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parent_commit=subprocess.check_output(['git','-C',str(ROOT),'rev-parse','HEAD'],text=True).strip(),
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pre_model_execution=True))
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save(EXP/'regression/old-integrity-before.json',frozen_integrity())
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for name in ('model.py','LICENSE','environment_full.yml'):
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dst=EXP/'external-resources'/name
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with (AC/'external-resources'/name).open('rb') as src,dst.open('xb') as out:shutil.copyfileobj(src,out)
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assert digest(dst)==digest(AC/'external-resources'/name)
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versions={n:importlib.metadata.version(n) for n in ('numpy','pandas','pyarrow','torch','scipy')}
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save(EXP/'environment/frozen-scientific-environment.json',dict(python=sys.version,executable=sys.executable,
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platform=platform.platform(),package_versions=versions))
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save(EXP/'environment/bootstrap-notes.json',dict(isolated_venv_only=True,existing_environments_modified=False,
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initial_install_failure='New venv pip22.0.2 lacks --report; upgraded ONLY new venv pip to author-pinned23.0.1 before installing',
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MarkupSafe='Author-pinned1.1.1 used PyPI source distribution and legacy setup.py because no CPython3.10 wheel; other requested core packages used wheels',
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author_environment='Windows conda CPython3.10.11',actual_environment='Linux CPython3.10.12; not binary-identical',
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package_download_provenance='install-report.json contains HTTPS PyPI archive URLs and SHA256 for packages'))
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print('PREPARED: old integrity PASS; independent model hypotheses preregistered',flush=True)
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if __name__=='__main__':main()
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