bio-logic-compiler 0.1.0__tar.gz

bio_logic_compiler-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: bio-logic-compiler
+Version: 0.1.0
+Summary: A Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates from biological connectivity.
+Author: Your Name
+Author-email: Your Name <your.email@example.com>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: networkx
+Requires-Dist: matplotlib
+Dynamic: author
+Dynamic: requires-python
+
+# Bio-Logic Compiler
+
+This project provides a Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates (AND, OR, NOT, NAND, NOR, etc) from biological connectivity.
+
+## Features
+- Model neurons as nodes and synapses as weighted edges (networkx)
+- Add synapses manually or ingest from JSON/CSV files
+- Extract logic gates from neuron thresholds and synaptic weights
+- Detects AND, OR, NOT, NAND, NOR, direct pass-through, and complex motifs
+- Visualize neural circuits with matplotlib
+- Comprehensive unit tests
+
+## Usage
+
+1. **Install dependencies**
+   ```sh
+   pip install -r requirements.txt
+   ```
+
+2. **Run Example**
+   ```sh
+   python bio_compiler.py
+   ```
+
+   ```sh
+   python -m unittest test_bio_compiler.py
+   ```
+
+   ```sh
+   python test_visualization.py
+   ```
+
+
+## File Structure
+- `bio_compiler.py` — Main class and logic extraction
+- `app.py` — Dash web app (main UI)
+- `sample_circuit.json` / `sample_circuit.csv` — Example data
+- `requirements.txt` — Dependencies
+- `pyproject.toml`, `setup.py` — Packaging
+
+## Logic Extraction Principle
+A neuron fires if:
+
+$$
+\sum (I_n \cdot w_n) \geq \theta
+$$
+
+Where $I$ is the input (0 or 1), $w$ is the synaptic weight, and $\theta$ is the threshold.
+
+- **AND**: All excitatory inputs must be active (threshold = sum of weights)
+- **OR**: Any excitatory input triggers firing (threshold <= min weight)
+- **NOT**: Inhibitory input vetoes firing
+- **NAND/NOR**: Mixed motifs with both excitatory and inhibitory inputs
+
+## Extending
+- Add support for temporal summation and motif discovery
+- Integrate with real connectome data (e.g., FlyWire)
+- Enhance visualization and reporting
+
+## Advanced Features
+- FlyWire connectome data ingestion (JSON/CSV)
+- Temporal modeling (simulate time steps)
+- Motif discovery (logic motif extraction)
+
+## Packaging
+- `pyproject.toml` and `setup.py` for pip/Poetry installation
+- `requirements.txt` for quick dependency install
+
+## License
+MIT

bio_logic_compiler-0.1.0/README.md

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+# Bio-Logic Compiler
+
+This project provides a Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates (AND, OR, NOT, NAND, NOR, etc) from biological connectivity.
+
+## Features
+- Model neurons as nodes and synapses as weighted edges (networkx)
+- Add synapses manually or ingest from JSON/CSV files
+- Extract logic gates from neuron thresholds and synaptic weights
+- Detects AND, OR, NOT, NAND, NOR, direct pass-through, and complex motifs
+- Visualize neural circuits with matplotlib
+- Comprehensive unit tests
+
+## Usage
+
+1. **Install dependencies**
+   ```sh
+   pip install -r requirements.txt
+   ```
+
+2. **Run Example**
+   ```sh
+   python bio_compiler.py
+   ```
+
+   ```sh
+   python -m unittest test_bio_compiler.py
+   ```
+
+   ```sh
+   python test_visualization.py
+   ```
+
+
+## File Structure
+- `bio_compiler.py` — Main class and logic extraction
+- `app.py` — Dash web app (main UI)
+- `sample_circuit.json` / `sample_circuit.csv` — Example data
+- `requirements.txt` — Dependencies
+- `pyproject.toml`, `setup.py` — Packaging
+
+## Logic Extraction Principle
+A neuron fires if:
+
+$$
+\sum (I_n \cdot w_n) \geq \theta
+$$
+
+Where $I$ is the input (0 or 1), $w$ is the synaptic weight, and $\theta$ is the threshold.
+
+- **AND**: All excitatory inputs must be active (threshold = sum of weights)
+- **OR**: Any excitatory input triggers firing (threshold <= min weight)
+- **NOT**: Inhibitory input vetoes firing
+- **NAND/NOR**: Mixed motifs with both excitatory and inhibitory inputs
+
+## Extending
+- Add support for temporal summation and motif discovery
+- Integrate with real connectome data (e.g., FlyWire)
+- Enhance visualization and reporting
+
+## Advanced Features
+- FlyWire connectome data ingestion (JSON/CSV)
+- Temporal modeling (simulate time steps)
+- Motif discovery (logic motif extraction)
+
+## Packaging
+- `pyproject.toml` and `setup.py` for pip/Poetry installation
+- `requirements.txt` for quick dependency install
+
+## License
+MIT

bio_logic_compiler-0.1.0/bio_logic_compiler.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: bio-logic-compiler
+Version: 0.1.0
+Summary: A Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates from biological connectivity.
+Author: Your Name
+Author-email: Your Name <your.email@example.com>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: networkx
+Requires-Dist: matplotlib
+Dynamic: author
+Dynamic: requires-python
+
+# Bio-Logic Compiler
+
+This project provides a Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates (AND, OR, NOT, NAND, NOR, etc) from biological connectivity.
+
+## Features
+- Model neurons as nodes and synapses as weighted edges (networkx)
+- Add synapses manually or ingest from JSON/CSV files
+- Extract logic gates from neuron thresholds and synaptic weights
+- Detects AND, OR, NOT, NAND, NOR, direct pass-through, and complex motifs
+- Visualize neural circuits with matplotlib
+- Comprehensive unit tests
+
+## Usage
+
+1. **Install dependencies**
+   ```sh
+   pip install -r requirements.txt
+   ```
+
+2. **Run Example**
+   ```sh
+   python bio_compiler.py
+   ```
+
+   ```sh
+   python -m unittest test_bio_compiler.py
+   ```
+
+   ```sh
+   python test_visualization.py
+   ```
+
+
+## File Structure
+- `bio_compiler.py` — Main class and logic extraction
+- `app.py` — Dash web app (main UI)
+- `sample_circuit.json` / `sample_circuit.csv` — Example data
+- `requirements.txt` — Dependencies
+- `pyproject.toml`, `setup.py` — Packaging
+
+## Logic Extraction Principle
+A neuron fires if:
+
+$$
+\sum (I_n \cdot w_n) \geq \theta
+$$
+
+Where $I$ is the input (0 or 1), $w$ is the synaptic weight, and $\theta$ is the threshold.
+
+- **AND**: All excitatory inputs must be active (threshold = sum of weights)
+- **OR**: Any excitatory input triggers firing (threshold <= min weight)
+- **NOT**: Inhibitory input vetoes firing
+- **NAND/NOR**: Mixed motifs with both excitatory and inhibitory inputs
+
+## Extending
+- Add support for temporal summation and motif discovery
+- Integrate with real connectome data (e.g., FlyWire)
+- Enhance visualization and reporting
+
+## Advanced Features
+- FlyWire connectome data ingestion (JSON/CSV)
+- Temporal modeling (simulate time steps)
+- Motif discovery (logic motif extraction)
+
+## Packaging
+- `pyproject.toml` and `setup.py` for pip/Poetry installation
+- `requirements.txt` for quick dependency install
+
+## License
+MIT

bio_logic_compiler-0.1.0/bio_logic_compiler.egg-info/SOURCES.txt

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+README.md
+cli.py
+pyproject.toml
+setup.py
+bio_logic_compiler.egg-info/PKG-INFO
+bio_logic_compiler.egg-info/SOURCES.txt
+bio_logic_compiler.egg-info/dependency_links.txt
+bio_logic_compiler.egg-info/entry_points.txt
+bio_logic_compiler.egg-info/requires.txt
+bio_logic_compiler.egg-info/top_level.txt

bio_logic_compiler-0.1.0/bio_logic_compiler.egg-info/dependency_links.txt

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+

bio_logic_compiler-0.1.0/bio_logic_compiler.egg-info/entry_points.txt

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+[console_scripts]
+bio-logic-compiler = bio_compiler:BioCompiler

bio_logic_compiler-0.1.0/bio_logic_compiler.egg-info/requires.txt

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+networkx
+matplotlib

bio_logic_compiler-0.1.0/bio_logic_compiler.egg-info/top_level.txt

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+cli

bio_logic_compiler-0.1.0/cli.py

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+import argparse
+import subprocess
+import sys
+import os
+
+def run_module(module):
+    # Run a Python module in a subprocess
+    python = sys.executable
+    subprocess.run([python, module])
+
+def main():
+    parser = argparse.ArgumentParser(description="Bio-Logic Compiler CLI")
+    subparsers = parser.add_subparsers(dest="command")
+
+    subparsers.add_parser("start-api", help="Start the FastAPI server (api.py)")
+    subparsers.add_parser("start-ui", help="Start the Dash UI (app.py)")
+    subparsers.add_parser("run-sim", help="Run the CartPole environment (environment.py)")
+
+    args = parser.parse_args()
+
+    if args.command == "start-api":
+        run_module("api.py")
+    elif args.command == "start-ui":
+        run_module("app.py")
+    elif args.command == "run-sim":
+        run_module("environment.py")
+    else:
+        parser.print_help()
+
+if __name__ == "__main__":
+    main()

bio_logic_compiler-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "bio-logic-compiler"
+version = "0.1.0"
+description = "A Python MVP for a Bio-Logic Compiler that models neural circuits as graphs, analyzes neuron firing thresholds, and reverse-engineers Boolean logic gates from biological connectivity."
+authors = [
+    { name = "Your Name", email = "your.email@example.com" }
+]
+readme = "README.md"
+requires-python = ">=3.8"
+dependencies = [
+    "networkx",
+    "matplotlib"
+]
+
+[project.scripts]
+bio-logic-compiler = "bio_compiler:BioCompiler"

bio_logic_compiler-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

bio_logic_compiler-0.1.0/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name="bio-logic-compiler",
+    version="1.0.0",
+    description="Unified CLI for the Bio-Logic synthetic brain ecosystem",
+    author="Your Name",
+    author_email="your.email@example.com",
+    packages=find_packages(),
+    py_modules=["cli"],
+    install_requires=[
+        "networkx",
+        "matplotlib"
+    ],
+    python_requires=">=3.8",
+    include_package_data=True,
+    long_description=open("README.md").read(),
+    long_description_content_type="text/markdown",
+    entry_points={
+        "console_scripts": [
+            "biologic=cli:main"
+        ]
+    },
+)