BiomedicalAISystem 2026.5.0__tar.gz

biomedicalaisystem-2026.5.0/.gitignore

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+# =============================================================================
+# Universal Biomedical Skills - Git Ignore
+# =============================================================================
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual Environments
+venv/
+ENV/
+env/
+.venv/
+test_demonstration/venv/
+
+# Environment Variables
+.env
+.env.local
+*.env
+
+# Jupyter Notebooks
+.ipynb_checkpoints/
+*.ipynb_checkpoints
+
+# IDEs and Editors
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+.project
+.pydevproject
+.settings/
+
+# OS Files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# =============================================================================
+# Data Files (Large/Generated)
+# =============================================================================
+*.h5ad
+*.h5
+*.mtx
+*.mtx.gz
+*.tsv.gz
+*.csv.gz
+
+# Test Data Directories
+scRNAsedata/
+analyzed_data/
+qc_results/
+qc_results_demo/
+
+# =============================================================================
+# Archive (External References & Old Versions)
+# =============================================================================
+archive/
+
+# =============================================================================
+# Sensitive Files
+# =============================================================================
+token.txt
+*.token
+credentials.json
+secrets.yaml
+*.pem
+*.key
+
+# =============================================================================
+# Temporary Files
+# =============================================================================
+*.tmp
+*.temp
+*.log
+*.bak
+.~lock.*
+
+# =============================================================================
+# Build Outputs
+# =============================================================================
+platform/build/
+platform/output/
+platform/reports/
+
+# =============================================================================
+# Claude Code
+# =============================================================================
+.claude/

biomedicalaisystem-2026.5.0/BiomedicalAISystem/__init__.py

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+# BiomedicalAISystem — Universal Life-Science & Clinical AI Skills Platform
+# Copyright (c) 2026 MD Babu Mia, PhD <md.babu.mia@mssm.edu>
+# Icahn School of Medicine at Mount Sinai.
+# Released under the MIT License (see LICENSE).
+
+"""
+BiomedicalAISystem
+==================
+
+A research-grade, agentic AI platform for orchestrating biomedical *skills*
+across multiple LLM providers (Anthropic, OpenAI, Google, local models).
+
+``BiomedicalAISystem`` is the distribution name; the runtime engine is the
+``biokernel`` package. This top-level module re-exports the public API of
+``biokernel`` so either import path works::
+
+    import BiomedicalAISystem as bas
+    print(bas.__version__)
+
+    # equivalent, lower-level entry point
+    import biokernel
+
+Key capabilities
+----------------
+- Universal Skill Description Language (USDL) — write-once, deploy-anywhere skills
+- Semantic routing for intelligent skill matching
+- DAG-based workflow engine for multi-agent orchestration
+- Cross-platform evaluation with biomedical-domain rubrics
+- MCP (Model Context Protocol) server for tool integration
+
+Bundled data
+------------
+The curated skills catalog is shipped with the package and can be located via
+:func:`catalog_path`.
+"""
+
+from __future__ import annotations
+
+from importlib import import_module
+from pathlib import Path
+from typing import Any
+
+# Re-export everything the runtime engine exposes.
+import biokernel as _biokernel
+
+try:  # Prefer the installed distribution version, fall back to the engine's.
+    from importlib.metadata import PackageNotFoundError, version as _dist_version
+
+    try:
+        __version__ = _dist_version("BiomedicalAISystem")
+    except PackageNotFoundError:  # running from a source checkout
+        __version__ = _biokernel.__version__
+except Exception:  # pragma: no cover - extremely old Pythons
+    __version__ = _biokernel.__version__
+__author__ = _biokernel.__author__
+__email__ = _biokernel.__email__
+__institution__ = getattr(_biokernel, "__institution__", "")
+
+# Make the engine importable as an attribute, e.g. BiomedicalAISystem.biokernel
+biokernel = _biokernel
+
+_DATA_DIR = Path(__file__).resolve().parent
+
+
+def catalog_path() -> Path:
+    """Return the filesystem path to the bundled ``skills_catalog.json``."""
+    return _DATA_DIR / "skills_catalog.json"
+
+
+def load_catalog() -> Any:
+    """Load and return the bundled skills catalog as a Python object."""
+    import json
+
+    with catalog_path().open("r", encoding="utf-8") as fh:
+        return json.load(fh)
+
+
+def cli() -> None:
+    """Entry point shim for the ``biomedical-ai`` console script."""
+    from biokernel.cli import main as _main
+
+    _main()
+
+
+def __getattr__(name: str) -> Any:
+    """Transparently proxy attribute access to the ``biokernel`` package."""
+    try:
+        return getattr(_biokernel, name)
+    except AttributeError:
+        # Allow access to biokernel submodules, e.g. BiomedicalAISystem.schema
+        try:
+            return import_module(f"biokernel.{name}")
+        except ModuleNotFoundError as exc:  # pragma: no cover
+            raise AttributeError(
+                f"module 'BiomedicalAISystem' has no attribute {name!r}"
+            ) from exc
+
+
+__all__ = [
+    "__version__",
+    "__author__",
+    "__email__",
+    "__institution__",
+    "biokernel",
+    "catalog_path",
+    "load_catalog",
+    "cli",
+]