biomorphx 1.0.0__py3-none-any.whl

biomorphx/__init__.py

@@ -0,0 +1,79 @@
+"""
+BioMorphX (v1.0.0) — Unified Cross-Scale Mechano-Genomic, Biomaterial, Nanofabrication
+& Life-Critical Biomedical Engineering Python SDK.
+"""
+from types import SimpleNamespace
+from .core import (
+    __version__,
+    __author__,
+    ClinicalBoundsError,
+    LifeCriticalSafetyWarning,
+    SafetyCertificate,
+    verify_bounds,
+    conformal_safety_interval,
+    AA_MECH_TABLE,
+    SANTALUCIA_NN,
+    HUMAN_CODON_TABLE,
+    NATIVE_TISSUE_ATLAS,
+    PKPD_DRUG_ATLAS,
+    SNIPPET_REGISTRY,
+    analyze_mechano_protein,
+    design_crispr_mechano_guide,
+    optimize_mrna_construct,
+    design_chrono_hydrogel,
+    simulate_scaffold_degradation,
+    generate_auxetic_gcode_and_stl,
+    simulate_lnp_nanocarrier,
+    mbsp_filter_and_quantify,
+    audit_icu_hemodynamics_ventilation,
+    optimize_renal_pkpd_dosing,
+    list_snippets,
+    get_snippet,
+    run_snippet,
+    self_test,
+)
+
+safety = SimpleNamespace(
+    ClinicalBoundsError=ClinicalBoundsError,
+    LifeCriticalSafetyWarning=LifeCriticalSafetyWarning,
+    SafetyCertificate=SafetyCertificate,
+    verify_bounds=verify_bounds,
+    conformal_safety_interval=conformal_safety_interval,
+)
+
+seqmech = SimpleNamespace(
+    AA_MECH_TABLE=AA_MECH_TABLE,
+    SANTALUCIA_NN=SANTALUCIA_NN,
+    HUMAN_CODON_TABLE=HUMAN_CODON_TABLE,
+    analyze_mechano_protein=analyze_mechano_protein,
+    design_crispr_mechano_guide=design_crispr_mechano_guide,
+    optimize_mrna_construct=optimize_mrna_construct,
+)
+
+biomaterials = SimpleNamespace(
+    NATIVE_TISSUE_ATLAS=NATIVE_TISSUE_ATLAS,
+    design_chrono_hydrogel=design_chrono_hydrogel,
+    simulate_scaffold_degradation=simulate_scaffold_degradation,
+)
+
+nanofab = SimpleNamespace(
+    generate_auxetic_gcode_and_stl=generate_auxetic_gcode_and_stl,
+    simulate_lnp_nanocarrier=simulate_lnp_nanocarrier,
+)
+
+imaging = SimpleNamespace(
+    mbsp_filter_and_quantify=mbsp_filter_and_quantify,
+)
+
+clinical = SimpleNamespace(
+    PKPD_DRUG_ATLAS=PKPD_DRUG_ATLAS,
+    audit_icu_hemodynamics_ventilation=audit_icu_hemodynamics_ventilation,
+    optimize_renal_pkpd_dosing=optimize_renal_pkpd_dosing,
+)
+
+snippets = SimpleNamespace(
+    SNIPPET_REGISTRY=SNIPPET_REGISTRY,
+    list_snippets=list_snippets,
+    get_snippet=get_snippet,
+    run_snippet=run_snippet,
+)

biomorphx/cli.py

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+"""Command-Line Interface for BioMorphX."""
+import argparse
+import json
+from .core import __version__, list_snippets, get_snippet, run_snippet, self_test
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="biomorphx",
+        description="BioMorphX v1.0.0 — Cross-Scale Mechano-Genomic, Biomaterial, Nanofab & Clinical SDK",
+    )
+    parser.add_argument("--version", action="version", version=f"biomorphx {__version__}")
+    sub = parser.add_subparsers(dest="cmd")
+
+    sub.add_parser("list-snippets", help="List all 12 built-in one-liner biomedical snippets")
+    p_show = sub.add_parser("show-snippet", help="Print Python code for a specific snippet")
+    p_show.add_argument("name", help="Snippet ID (e.g. 01_protein_mechano_unfolding)")
+
+    p_run = sub.add_parser("run-snippet", help="Execute a built-in snippet and print JSON output")
+    p_run.add_argument("name", help="Snippet ID")
+
+    sub.add_parser("self-test", help="Run deterministic self-test across all 12 pipelines")
+
+    args = parser.parse_args()
+    if args.cmd == "list-snippets":
+        print(json.dumps(list_snippets(), indent=2))
+    elif args.cmd == "show-snippet":
+        print(get_snippet(args.name))
+    elif args.cmd == "run-snippet":
+        out = run_snippet(args.name)
+        print(json.dumps(out, indent=2, default=str))
+    else:
+        print(json.dumps(self_test(), indent=2))
+
+
+if __name__ == "__main__":
+    main()