fibernet 1.24.0__tar.gz

fibernet-1.24.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.18.0] - 2026-07-05
+
+### Added
+- **Mesh export module** (`fibernet/io/mesh_export.py`)
+  - Export to STL (ASCII and binary)
+  - Export to Wavefront OBJ
+  - Export to Stanford PLY
+  - Cylindrical mesh generation for fibers
+  - Configurable polygon approximation (n_sides)
+
+### Tests
+- 9 new tests in `tests/test_mesh_export.py`
+- Total: 752 passing, 6 skipped
+
+## [1.17.0] - 2026-07-05
+
+### Added
+- **Network comparison module** (`fibernet/analysis/comparison.py`)
+  - `NetworkFingerprint`: structural fingerprint computation
+  - `NetworkComparator`: pairwise distances, clustering, similarity search
+  - `compare_networks()`: compare multiple networks
+  - `network_similarity()`: pairwise similarity score
+- Example 14: advanced structural analysis workflow
+
+### Tests
+- 14 new tests in `tests/test_comparison.py`
+- Total: 743 passing, 6 skipped
+
+## [1.16.0] - 2026-07-05
+
+### Added
+- **Homogenization module** (`fibernet/analysis/homogenization.py`)
+  - `EffectiveElasticProperties`: E, nu, G computation (2D/3D)
+  - `EffectiveThermalProperties`: thermal conductivity, CTE
+  - `EffectiveElectricalProperties`: electrical conductivity
+  - `compute_effective_properties()`: comprehensive analysis
+
+### Tests
+- 13 new tests in `tests/test_homogenization.py`
+- Total: 729 passing, 6 skipped
+
+## [1.15.0] - 2026-07-05
+
+### Added
+- **Spatial statistics module** (`fibernet/analysis/spatial.py`)
+  - `SpatialStatistics`: Ripley's K, pair correlation, nearest neighbor
+  - `OrientationAnalysis`: nematic order, orientation histograms
+  - `LengthAnalysis`: length distributions, statistics, fitting
+  - `ConnectivityAnalysis`: degree distribution, mean connectivity
+  - `AnisotropyAnalysis`: fabric tensor, anisotropy index
+  - `compute_spatial_statistics()`: comprehensive analysis
+
+### Tests
+- 22 new tests in `tests/test_advanced_statistics.py`
+- Total: 716 passing, 6 skipped
+
+## [1.14.0] - 2026-07-05
+
+### Added
+- **Material database** (`fibernet/materials.py`)
+  - 29 pre-defined materials (polymers, metals, ceramics, biological, carbon)
+  - `get_material()`: quick material lookup
+  - `list_materials()`: list all available materials
+  - `compare_materials()`: material selection tool
+  - `m()`: shortcut for get_material
+- **Unit conversion utilities** (`fibernet/units.py`)
+  - Length: m, mm, um, nm, cm, km, in, ft
+  - Force: N, kN, mN, µN, nN, lbf, dyne
+  - Pressure: Pa, kPa, MPa, GPa, TPa, bar, atm, psi, ksi
+  - Temperature: K, C, F, R
+  - Energy: J, kJ, mJ, cal, kcal, eV, BTU, kWh
+
+### Tests
+- 33 new tests in `tests/test_materials.py` and `tests/test_units.py`
+- Total: 694 passing, 6 skipped
+
+## [1.13.0] - 2026-07-05
+
+### Added
+- **Fractal network generators** (`fibernet/gen/fractal.py`)
+  - Sierpinski triangle
+  - Koch curve
+  - Fractal tree
+  - Hilbert curve
+- **Gradient network generators** (`fibernet/gen/gradient.py`)
+  - Density gradient (linear, exponential, sinusoidal)
+  - Property gradient (material properties varying spatially)
+  - Multi-zone networks (custom regions with different properties)
+- Example 13: publication-ready research workflow
+
+### Tests
+- 29 new tests in `tests/test_fractal.py` and `tests/test_gradient.py`
+- Total: 687 passing, 6 skipped
+
+## [1.12.0] - 2026-07-04
+
+### Added
+- Network topology analysis module
+- Comprehensive topology metrics
+
+### Tests
+- Total: 658 passing
+
+## [1.11.0] - 2026-07-04
+
+### Added
+- Visualization module (2D/3D plotting)
+- Design of Experiments (DOE) module
+  - Grid search
+  - Latin hypercube sampling
+  - Random sampling
+  - Sensitivity analysis
+
+### Tests
+- Total: 635 passing
+
+## [1.10.0] - 2026-07-04
+
+### Added
+- Fatigue analysis module
+- Creep analysis module
+- Diffusion/transport module
+
+### Tests
+- Total: 607 passing
+
+## [1.9.0] - 2026-07-03
+
+### Added
+- Benchmark suite for performance testing
+- Enhanced multiscale testing
+
+### Tests
+- Total: 585 passing
+
+## [1.8.0] - 2026-07-03
+
+### Added
+- Electromagnetic analysis
+- Molecular dynamics integration
+- Open-source tool integrations
+- Research case study examples
+
+### Tests
+- Total: 575 passing
+
+## [1.7.0] - 2026-07-02
+
+### Added
+- Graph neural network (GNN) module
+- Permeability analysis
+- Uncertainty quantification (UQ)
+- Coefficient of thermal expansion (CTE)
+
+### Tests
+- Total: 544 passing
+
+## [1.6.0] - 2026-07-02
+
+### Added
+- Incremental FEM solver
+- Buckling analysis module
+
+### Tests
+- Total: 477 passing
+
+## [1.5.0] - 2026-07-01
+
+### Added
+- Nonlinear mechanics module
+- Damage mechanics
+- Viscoelasticity
+
+### Tests
+- Total: 448 passing
+
+## [1.4.0] - 2026-07-01
+
+### Added
+- Periodic boundary conditions (PBC)
+- Transforms module
+- Advanced generators (chiral, woven, hierarchical)
+
+### Tests
+- Total: 410 passing
+
+## [1.3.0] - 2026-06-30
+
+### Added
+- Machine learning module
+  - Property prediction
+  - Feature engineering
+- Percolation analysis
+- Integration tests
+
+### Tests
+- Total: 370 passing
+
+## [1.2.0] - 2026-06-30
+
+### Added
+- Taichi-accelerated FEM solver
+- I/O modules (VTK, LAMMPS, GMSH, PDB, XYZ)
+- Pandas integration
+
+### Tests
+- Total: 320 passing
+
+## [1.1.0] - 2026-06-29
+
+### Added
+- Simulation modules (thermal, fracture, etc.)
+- Core data structures
+- Basic generators
+
+### Tests
+- Total: 250 passing
+
+## [1.0.0] - 2026-06-28
+
+### Added
+- Initial release
+- Core fiber network data structures
+- Basic random network generators
+- Simple FEM solver
+- Sphinx documentation framework
+- GitHub Actions CI/CD
+- pyproject.toml for pip installation
+
+### Tests
+- Total: 180 passing
+

fibernet-1.24.0/CONTRIBUTING.md

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+# Contributing to FiberNet
+
+We love contributions! This document provides guidelines for contributing to FiberNet.
+
+## Code of Conduct
+
+This project adheres to the [Contributor Covenant](https://www.contributor-covenant.org/) code of conduct.
+
+## How Can I Contribute?
+
+### Reporting Bugs
+
+1. **Check existing issues** first
+2. **Use the latest version**
+3. **Create a detailed report** with:
+   - Clear description
+   - Steps to reproduce
+   - Expected vs actual behavior
+   - Environment details (Python, OS, dependencies)
+   - Minimal reproducible example
+
+### Suggesting Features
+
+1. **Check existing issues and PRs**
+2. **Describe the use case** clearly
+3. **Propose an implementation** if possible
+
+### Submitting Code
+
+1. Fork the repository
+2. Create a feature branch: `git checkout -b feature/my-feature`
+3. Make your changes
+4. Add tests for new functionality
+5. Ensure all tests pass: `pytest tests/ -v`
+6. Format code: `black fibernet tests`
+7. Commit with clear messages
+8. Push and submit a Pull Request
+
+## Development Setup
+
+```bash
+# Clone your fork
+git clone https://github.com/YOUR_USERNAME/fibernet.git
+cd fibernet
+
+# Install in development mode
+pip install -e ".[dev]"
+
+# Run tests
+pytest tests/ -v
+
+# Build documentation
+cd docs && make html
+```
+
+## Code Style
+
+- Follow PEP 8
+- Use `black` for formatting
+- Use type hints where helpful
+- Write docstrings in NumPy format
+- Keep functions focused and small
+- Add tests for new functionality
+
+## Testing
+
+All new features must include tests:
+
+```bash
+# Run all tests
+pytest tests/ -v
+
+# Run with coverage
+pytest tests/ --cov=fibernet --cov-report=html
+
+# Run specific test file
+pytest tests/test_core.py -v
+```
+
+## Documentation
+
+Update documentation when adding features:
+
+- Add API reference to `docs/api/`
+- Update tutorials in `tutorials/`
+- Update `CHANGELOG.md`
+
+Build docs locally:
+```bash
+cd docs
+make html
+open _build/html/index.html
+```
+
+## Pull Request Process
+
+1. Update `CHANGELOG.md` with details of your change
+2. Update `README.md` if necessary
+3. Ensure CI passes (tests, docs build)
+4. Request review from maintainers
+5. Address review comments
+
+## Optional Dependencies
+
+FiberNet is designed to work with only `numpy` and `scipy`. When adding features that require optional dependencies:
+
+- Make imports conditional with try/except
+- Provide clear error messages when dependencies are missing
+- Document the optional dependency in docstrings
+
+Example:
+```python
+try:
+    import networkx as nx
+    HAS_NETWORKX = True
+except ImportError:
+    HAS_NETWORKX = False
+    nx = None
+
+def my_function():
+    if not HAS_NETWORKX:
+        raise ImportError("networkx required. Install with: pip install fibernet[graph]")
+    # ... use networkx
+```
+
+## Questions?
+
+- Open a GitHub on GitHub
+- Email the ML-BioMat lab
+
+Thank you for contributing!

fibernet-1.24.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 FiberNet Contributors
+
+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.

fibernet-1.24.0/MANIFEST.in

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+include LICENSE
+include README.md
+include CHANGELOG.md
+include CONTRIBUTING.md
+include requirements.txt
+include requirements-dev.txt
+recursive-include fibernet *.py
+recursive-include tests *.py
+recursive-include examples *.py
+recursive-include docs *.rst *.py
+global-exclude __pycache__
+global-exclude *.py[cod]
+global-exclude .DS_Store
+prune docs/_build
+prune build
+prune dist
+prune *.egg-info