boolforge 1.0.0__tar.gz

boolforge-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Claus Kadelka
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

boolforge-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: boolforge
+Version: 1.0.0
+Summary: Methods to generate and analyze random Boolean functions and Boolean networks, with a focus on canalization.
+Author-email: Claus Kadelka <ckadelka@iastate.edu>, Benjamin Coberly <ckadelka@iastate.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://ckadelka.github.io/BoolForge/
+Project-URL: Documentation, https://ckadelka.github.io/BoolForge/
+Project-URL: Repository, https://github.com/ckadelka/BoolForge
+Project-URL: Issues, https://github.com/ckadelka/BoolForge/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: networkx
+Requires-Dist: pandas
+Provides-Extra: cana
+Requires-Dist: cana; extra == "cana"
+Provides-Extra: bio
+Requires-Dist: requests; extra == "bio"
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == "plot"
+Provides-Extra: speed
+Requires-Dist: numba; extra == "speed"
+Provides-Extra: symbolic
+Requires-Dist: pyeda; extra == "symbolic"
+Provides-Extra: dev
+Requires-Dist: jupytext; extra == "dev"
+Requires-Dist: jupyterlab; extra == "dev"
+Requires-Dist: cana; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: requests; extra == "dev"
+Provides-Extra: all
+Requires-Dist: cana; extra == "all"
+Requires-Dist: requests; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Requires-Dist: numba; extra == "all"
+Requires-Dist: pyeda; extra == "all"
+Dynamic: license-file
+
+# BoolForge
+
+**BoolForge** is a Python toolbox for generating, sampling, and analyzing
+Boolean functions and Boolean networks, with a particular emphasis on
+**canalization** and the uniform random generation of functions with prescribed structure.
+
+While many existing tools focus on simulation and dynamical analysis,
+BoolForge emphasizes **controlled generation and analysis**
+of Boolean functions and networks, enabling systematic studies of
+canalization, robustness, and ensemble properties.
+
+The package provides tools for:
+
+- random sampling of Boolean functions with prescribed canalizing structure,
+- generation of Boolean networks with controlled update rules and wiring diagrams,
+- analysis of canalization, activity, sensitivity, and related structural measures,
+- interoperability with other Boolean network software and model formats.
+
+BoolForge is designed for researchers working with regulatory networks,
+discrete dynamical systems, and random Boolean network ensembles in
+systems biology and network science.
+
+---
+
+## Installation
+
+### Stable release (recommended)
+
+Install the latest stable version from PyPI:
+
+```bash
+pip install boolforge
+```
+
+BoolForge requires **Python 3.10 or later**.
+
+---
+
+### Development version
+
+To install the latest development version directly from GitHub:
+
+```bash
+pip install git+https://github.com/ckadelka/BoolForge
+```
+
+---
+
+## Optional dependencies (extended functionality)
+
+BoolForge is fully usable with its core dependencies, but some features rely on
+optional packages that can be installed via *extras*.
+
+### Performance acceleration
+
+Some internal routines are automatically accelerated if
+[numba](https://numba.pydata.org/) is available.
+
+To enable numba acceleration:
+
+```bash
+pip install boolforge[speed]
+```
+
+When numba is not installed, BoolForge transparently falls back to
+pure-Python implementations.
+
+---
+
+### Plotting and visualization
+
+Plotting of wiring diagrams and network structure requires
+[matplotlib](https://matplotlib.org/).
+
+To enable plotting:
+
+```bash
+pip install boolforge[plot]
+```
+
+---
+
+### CANA integration
+
+Some methods interface with the
+[CANA](https://github.com/CASCI-lab/CANA) package for advanced canalization
+measures.
+
+To enable CANA-based functionality:
+
+```bash
+pip install boolforge[cana]
+```
+
+---
+
+### Symbolic logic and expression minimization
+
+Symbolic representations and logical expression minimization rely on
+[PyEDA](https://pyeda.readthedocs.io/).
+
+To enable symbolic functionality:
+
+```bash
+pip install boolforge[symbolic]
+```
+
+---
+
+### Biological model retrieval
+
+The retrival and loading of hundreds of published biological Boolean
+network models relies on the
+[requests](https://requests.readthedocs.io/en/latest/) package for web access.
+
+To enable biological model retrieval:
+
+```bash
+pip install boolforge[bio]
+```
+
+---
+
+### All optional features
+
+To install BoolForge with **all optional dependencies**:
+
+```bash
+pip install boolforge[all]
+```
+
+---
+
+## Compatibility and interoperability
+
+BoolForge supports import and export of Boolean network representations used by
+other software packages.
+
+In particular, BoolForge supports the **BNet format** commonly used by
+[pyboolnet](https://github.com/hklarner/pyboolnet), without requiring pyboolnet
+itself to be installed.
+
+BoolForge also supports conversion to and from the format used by
+ [CANA](https://github.com/CASCI-lab/CANA).
+ 
+---
+
+## Documentation
+
+Full documentation, including tutorials and API reference, is available at:
+
+https://ckadelka.github.io/BoolForge/
+
+---
+
+## Citation
+
+If you use BoolForge in your research, please cite the accompanying
+application note:
+
+Kadelka, C., & Coberly, B. (2025).  
+*BoolForge: A Python toolbox for Boolean functions and Boolean networks*.  
+arXiv:2509.02496.  
+https://arxiv.org/abs/2509.02496
+
+A machine-readable citation file (`CITATION.cff`) is included in the repository
+and can be used directly by GitHub, Zenodo, and reference managers.
+
+---
+
+## License
+
+BoolForge is released under the MIT License.

boolforge-1.0.0/README.md

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+# BoolForge
+
+**BoolForge** is a Python toolbox for generating, sampling, and analyzing
+Boolean functions and Boolean networks, with a particular emphasis on
+**canalization** and the uniform random generation of functions with prescribed structure.
+
+While many existing tools focus on simulation and dynamical analysis,
+BoolForge emphasizes **controlled generation and analysis**
+of Boolean functions and networks, enabling systematic studies of
+canalization, robustness, and ensemble properties.
+
+The package provides tools for:
+
+- random sampling of Boolean functions with prescribed canalizing structure,
+- generation of Boolean networks with controlled update rules and wiring diagrams,
+- analysis of canalization, activity, sensitivity, and related structural measures,
+- interoperability with other Boolean network software and model formats.
+
+BoolForge is designed for researchers working with regulatory networks,
+discrete dynamical systems, and random Boolean network ensembles in
+systems biology and network science.
+
+---
+
+## Installation
+
+### Stable release (recommended)
+
+Install the latest stable version from PyPI:
+
+```bash
+pip install boolforge
+```
+
+BoolForge requires **Python 3.10 or later**.
+
+---
+
+### Development version
+
+To install the latest development version directly from GitHub:
+
+```bash
+pip install git+https://github.com/ckadelka/BoolForge
+```
+
+---
+
+## Optional dependencies (extended functionality)
+
+BoolForge is fully usable with its core dependencies, but some features rely on
+optional packages that can be installed via *extras*.
+
+### Performance acceleration
+
+Some internal routines are automatically accelerated if
+[numba](https://numba.pydata.org/) is available.
+
+To enable numba acceleration:
+
+```bash
+pip install boolforge[speed]
+```
+
+When numba is not installed, BoolForge transparently falls back to
+pure-Python implementations.
+
+---
+
+### Plotting and visualization
+
+Plotting of wiring diagrams and network structure requires
+[matplotlib](https://matplotlib.org/).
+
+To enable plotting:
+
+```bash
+pip install boolforge[plot]
+```
+
+---
+
+### CANA integration
+
+Some methods interface with the
+[CANA](https://github.com/CASCI-lab/CANA) package for advanced canalization
+measures.
+
+To enable CANA-based functionality:
+
+```bash
+pip install boolforge[cana]
+```
+
+---
+
+### Symbolic logic and expression minimization
+
+Symbolic representations and logical expression minimization rely on
+[PyEDA](https://pyeda.readthedocs.io/).
+
+To enable symbolic functionality:
+
+```bash
+pip install boolforge[symbolic]
+```
+
+---
+
+### Biological model retrieval
+
+The retrival and loading of hundreds of published biological Boolean
+network models relies on the
+[requests](https://requests.readthedocs.io/en/latest/) package for web access.
+
+To enable biological model retrieval:
+
+```bash
+pip install boolforge[bio]
+```
+
+---
+
+### All optional features
+
+To install BoolForge with **all optional dependencies**:
+
+```bash
+pip install boolforge[all]
+```
+
+---
+
+## Compatibility and interoperability
+
+BoolForge supports import and export of Boolean network representations used by
+other software packages.
+
+In particular, BoolForge supports the **BNet format** commonly used by
+[pyboolnet](https://github.com/hklarner/pyboolnet), without requiring pyboolnet
+itself to be installed.
+
+BoolForge also supports conversion to and from the format used by
+ [CANA](https://github.com/CASCI-lab/CANA).
+ 
+---
+
+## Documentation
+
+Full documentation, including tutorials and API reference, is available at:
+
+https://ckadelka.github.io/BoolForge/
+
+---
+
+## Citation
+
+If you use BoolForge in your research, please cite the accompanying
+application note:
+
+Kadelka, C., & Coberly, B. (2025).  
+*BoolForge: A Python toolbox for Boolean functions and Boolean networks*.  
+arXiv:2509.02496.  
+https://arxiv.org/abs/2509.02496
+
+A machine-readable citation file (`CITATION.cff`) is included in the repository
+and can be used directly by GitHub, Zenodo, and reference managers.
+
+---
+
+## License
+
+BoolForge is released under the MIT License.

boolforge-1.0.0/boolforge/__init__.py

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+# Core public classes
+from .boolean_function import (
+    BooleanFunction, 
+    display_truth_table,
+    get_layer_structure_from_canalized_outputs
+)
+from .boolean_network import (
+    BooleanNetwork, 
+    get_entropy_of_basin_size_distribution
+)
+from .wiring_diagram import WiringDiagram
+
+# Canonical public generators
+from .generate import (
+    random_function,
+    random_NCF,
+    random_k_canalizing_function,
+    random_wiring_diagram,
+    random_network,
+    random_null_model,
+)
+
+from .utils import (
+    bin2dec,
+    dec2bin,
+    get_left_side_of_truth_table,
+    hamming_weight_to_ncf_layer_structure,
+)
+
+from .modularity import (
+    compress_trajectories,
+    product_of_trajectories,
+    plot_trajectory,
+)
+
+from .bio_models import get_bio_models_from_repository
+
+# Version
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ = "unknown"
+
+__all__ = [
+    "bin2dec",
+    "dec2bin",
+    "get_left_side_of_truth_table",
+    "hamming_weight_to_ncf_layer_structure",
+    "BooleanFunction",
+    "display_truth_table",
+    "get_layer_structure_from_canalized_outputs",
+    "BooleanNetwork",
+    "get_entropy_of_basin_size_distribution",
+    "WiringDiagram",
+    "random_function",
+    "random_NCF",
+    "random_k_canalizing_function",
+    "random_wiring_diagram",
+    "random_network",
+    "random_null_model",
+    "get_bio_models_from_repository",
+    "__version__",
+    
+    "compress_trajectories",
+    "product_of_trajectories",
+    "plot_trajectory"
+]

boolforge-1.0.0/boolforge/_version.py

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+__version__ = '1.0.0'