# pylimer-tools
[](https://github.com/GenieTim/pylimer-tools/actions/workflows/run-tests.yml)
[](https://github.com/GenieTim/pylimer-tools/actions/workflows/run-tests.yml)
[](https://github.com/GenieTim/pylimer-tools/actions/workflows/run-tests.yml)
[](https://codecov.io/gh/GenieTim/pylimer-tools)
[](https://github.com/GenieTim/pylimer-tools/actions/workflows/publish-documentation-html.yml)
[](https://pypi.org/project/pylimer-tools/)
[](https://pypi.org/project/pylimer-tools/)
[](LICENSE)
Pronunciation: "pylimer” like "pü-limer”, with the "py” as in the German word "müde” (IPA: /ˈpyːlɪmɚ/).
`pylimer-tools` is a toolkit for simulation, analysis, and data handling of bead–spring polymer systems in Python and C++. It combines high-level Python utilities with performant C++ extensions for common tasks in computational polymer science.
## Table of Contents
- [pylimer-tools](#pylimer-tools)
- [Table of Contents](#table-of-contents)
- [1. Features](#1-features)
- [2. Installation](#2-installation)
- [Requirements](#requirements)
- [Stable Release](#stable-release)
- [Build from Source](#build-from-source)
- [Requirements](#requirements-1)
- [Build](#build)
- [3. Test Installation](#3-test-installation)
- [4. CLI Tools](#4-cli-tools)
- [5. Documentation](#5-documentation)
- [6. Development \& Testing](#6-development--testing)
- [Adding Features](#adding-features)
- [7. Citing](#7-citing)
- [8. Contributing](#8-contributing)
- [9. Code of Conduct](#9-code-of-conduct)
- [10. Acknowledgements](#10-acknowledgements)
- [11. License](#11-license)
- [Pronunciation Note](#pronunciation-note)
## 1. Features
A selection of features includes:
- Monte Carlo structure (network "universe”) generation
- Dissipative Particle Dynamics (DPD) simulation with slip-springs
- Maximum Entropy Homogenization Procedure (MEHP) with and without slip-links
- LAMMPS output readers: data, dump, thermodynamic outputs
- Network analysis: loops, chain reconstruction, degree statistics
- Structural metrics: radius of gyration, end-to-end distance, distributions
- Normal mode analysis for stress autocorrelation, loss and storage modulus
- Command line interfaces for batch workflows
## 2. Installation
### Requirements
Python >= 3.9.
### Stable Release
Stable release from PyPI:
```
pip install pylimer-tools
```
### Build from Source
#### Requirements
Build requires CMake, a C++17 compiler, and (optionally) Ninja for faster builds.
Additionally, the system packages `flex` and `bison` are required (`winflexbison` on Windows using `choco`) to build the dependency `igraph`.
#### Build
To build from source (compiles C++ extension):
```
git clone https://github.com/GenieTim/pylimer-tools.git
cd pylimer-tools
pip install -e .
```
Optional: Use provided helper scripts in `./bin` (e.g. `./bin/build-wheel.sh`, `./bin/build-tests.sh`).
## 3. Test Installation
```python
import pylimer_tools
import pylimer_tools_cpp
print("Installed version: {} == {}".format(
pylimer_tools.__version__,
pylimer_tools_cpp.__version__
))
```
More examples: see the [examples in the documentation](https://genietim.github.io/pylimer-tools/auto_examples/index.html) and [their code in `examples/`](examples/).
Additionally, the [tests](tests/) and the [CLI Tools](src/pylimer_tools/) may serve as examples.
## 4. CLI Tools
Installed console scripts:
- `pylimer-generate-network` – generate random bead-spring networks using our MC generation procedure
- `pylimer-analyse-networks` – batch analysis / statistics given LAMMPS data (structure) files
- `pylimer-basic-lammps-stats` – quick structural stats from LAMMPS data (structure) file
- `pylimer-displace-randomly` – random displacement utility
Run any with `--help` for usage.
## 5. Documentation
Full documentation (API reference, tutorials, examples):
[https://genietim.github.io/pylimer-tools](https://genietim.github.io/pylimer-tools)
## 6. Development & Testing
Clone and install in editable mode (see Installation). Then:
```
./bin/run-tests.sh # full test suite (Python + C++), includes benchmarks & tests that may fail
./bin/run-tests-short.sh # quicker subset, generates coverage, is what's run in the CI
./bin/format-code.sh # apply formatting & style (run before PR)
```
Generate docs:
```
./bin/make-stubs.sh # builds the stubs for the C++ module
./bin/make-docs.sh # build Sphinx HTML docs
```
### Adding Features
- Add tests in `tests/` (unit or integration). New functionality without tests may be deferred.
- Keep public APIs documented in docstrings so they surface in Sphinx.
- If a change alters behavior, update existing tests rather than deleting them. Explain rationale in the PR.
## 7. Citing
If you use `pylimer-tools` in published work, please cite it. A minimal BibTeX example:
```bibtex
@software{pylimer-tools,
title = {pylimer-tools},
author = {Bernhard, Tim},
url = {https://github.com/GenieTim/pylimer-tools},
year = {2025},
note = {See CITATION.cff for full metadata and related method references}
}
```
Also cite the specific theoretical / methodological papers corresponding to the components you use (listed in `CITATION.cff`).
## 8. Contributing
We welcome contributions on GitHub via Issues and Pull Requests.
1. Discuss larger ideas in an Issue first (helps align scope).
2. Fork, branch, implement, add tests & docs.
3. Run formatting and tests locally.
4. Submit PR referencing the Issue (if any).
See also: [Code of Conduct](CODE_OF_CONDUCT.md).
## 9. Code of Conduct
We strive for an inclusive, respectful environment.
By participating you agree to uphold the [Code of Conduct](CODE_OF_CONDUCT.md).
Report concerns to the maintainer email specified there.
## 10. Acknowledgements
The authors gratefully acknowledge financial support from the Swiss National Science Foundation (SNSF project 200021_204196).
## 11. License
GPL-3.0-or-later. See [LICENSE](LICENSE).
## Pronunciation Note
"pylimer” resembles "polymer”; the playful spelling emphasizes Python integration.
Raw data
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"description": "# pylimer-tools\n\n[](https://github.com/GenieTim/pylimer-tools/actions/workflows/run-tests.yml)\n[](https://github.com/GenieTim/pylimer-tools/actions/workflows/run-tests.yml)\n[](https://github.com/GenieTim/pylimer-tools/actions/workflows/run-tests.yml)\n[](https://codecov.io/gh/GenieTim/pylimer-tools)\n[](https://github.com/GenieTim/pylimer-tools/actions/workflows/publish-documentation-html.yml)\n[](https://pypi.org/project/pylimer-tools/)\n[](https://pypi.org/project/pylimer-tools/)\n[](LICENSE)\n\nPronunciation: \"pylimer\u201d like \"p\u00fc-limer\u201d, with the \"py\u201d as in the German word \"m\u00fcde\u201d (IPA: /\u02c8py\u02d0l\u026am\u025a/).\n\n`pylimer-tools` is a toolkit for simulation, analysis, and data handling of bead\u2013spring polymer systems in Python and C++. It combines high-level Python utilities with performant C++ extensions for common tasks in computational polymer science.\n\n## Table of Contents\n\n- [pylimer-tools](#pylimer-tools)\n - [Table of Contents](#table-of-contents)\n - [1. Features](#1-features)\n - [2. Installation](#2-installation)\n - [Requirements](#requirements)\n - [Stable Release](#stable-release)\n - [Build from Source](#build-from-source)\n - [Requirements](#requirements-1)\n - [Build](#build)\n - [3. Test Installation](#3-test-installation)\n - [4. CLI Tools](#4-cli-tools)\n - [5. Documentation](#5-documentation)\n - [6. Development \\& Testing](#6-development--testing)\n - [Adding Features](#adding-features)\n - [7. Citing](#7-citing)\n - [8. Contributing](#8-contributing)\n - [9. Code of Conduct](#9-code-of-conduct)\n - [10. Acknowledgements](#10-acknowledgements)\n - [11. License](#11-license)\n - [Pronunciation Note](#pronunciation-note)\n\n## 1. Features\n\nA selection of features includes:\n\n- Monte Carlo structure (network \"universe\u201d) generation\n- Dissipative Particle Dynamics (DPD) simulation with slip-springs\n- Maximum Entropy Homogenization Procedure (MEHP) with and without slip-links\n- LAMMPS output readers: data, dump, thermodynamic outputs\n- Network analysis: loops, chain reconstruction, degree statistics\n- Structural metrics: radius of gyration, end-to-end distance, distributions\n- Normal mode analysis for stress autocorrelation, loss and storage modulus\n- Command line interfaces for batch workflows\n\n## 2. Installation\n\n### Requirements\n\nPython >= 3.9.\n\n### Stable Release\n\nStable release from PyPI:\n\n```\npip install pylimer-tools\n```\n\n### Build from Source\n\n#### Requirements\n\nBuild requires CMake, a C++17 compiler, and (optionally) Ninja for faster builds.\n\nAdditionally, the system packages `flex` and `bison` are required (`winflexbison` on Windows using `choco`) to build the dependency `igraph`.\n\n#### Build\n\nTo build from source (compiles C++ extension):\n\n```\ngit clone https://github.com/GenieTim/pylimer-tools.git\ncd pylimer-tools\npip install -e .\n```\n\nOptional: Use provided helper scripts in `./bin` (e.g. `./bin/build-wheel.sh`, `./bin/build-tests.sh`).\n\n## 3. Test Installation\n\n```python\nimport pylimer_tools\nimport pylimer_tools_cpp\n\nprint(\"Installed version: {} == {}\".format(\n pylimer_tools.__version__,\n pylimer_tools_cpp.__version__\n))\n\n```\n\nMore examples: see the [examples in the documentation](https://genietim.github.io/pylimer-tools/auto_examples/index.html) and [their code in `examples/`](examples/).\nAdditionally, the [tests](tests/) and the [CLI Tools](src/pylimer_tools/) may serve as examples.\n\n## 4. CLI Tools\n\nInstalled console scripts:\n\n- `pylimer-generate-network` \u2013 generate random bead-spring networks using our MC generation procedure\n- `pylimer-analyse-networks` \u2013 batch analysis / statistics given LAMMPS data (structure) files\n- `pylimer-basic-lammps-stats` \u2013 quick structural stats from LAMMPS data (structure) file\n- `pylimer-displace-randomly` \u2013 random displacement utility\n\nRun any with `--help` for usage.\n\n## 5. Documentation\n\nFull documentation (API reference, tutorials, examples):\n[https://genietim.github.io/pylimer-tools](https://genietim.github.io/pylimer-tools)\n\n## 6. Development & Testing\n\nClone and install in editable mode (see Installation). Then:\n\n```\n./bin/run-tests.sh # full test suite (Python + C++), includes benchmarks & tests that may fail\n./bin/run-tests-short.sh # quicker subset, generates coverage, is what's run in the CI\n./bin/format-code.sh # apply formatting & style (run before PR)\n```\n\nGenerate docs:\n\n```\n./bin/make-stubs.sh # builds the stubs for the C++ module\n./bin/make-docs.sh # build Sphinx HTML docs\n```\n\n### Adding Features\n\n- Add tests in `tests/` (unit or integration). New functionality without tests may be deferred.\n- Keep public APIs documented in docstrings so they surface in Sphinx.\n- If a change alters behavior, update existing tests rather than deleting them. Explain rationale in the PR.\n\n## 7. Citing\n\nIf you use `pylimer-tools` in published work, please cite it. A minimal BibTeX example:\n\n```bibtex\n@software{pylimer-tools,\n\ttitle = {pylimer-tools},\n\tauthor = {Bernhard, Tim},\n\turl = {https://github.com/GenieTim/pylimer-tools},\n\tyear = {2025},\n\tnote = {See CITATION.cff for full metadata and related method references}\n}\n```\n\nAlso cite the specific theoretical / methodological papers corresponding to the components you use (listed in `CITATION.cff`).\n\n## 8. Contributing\n\nWe welcome contributions on GitHub via Issues and Pull Requests.\n\n1. Discuss larger ideas in an Issue first (helps align scope).\n2. Fork, branch, implement, add tests & docs.\n3. Run formatting and tests locally.\n4. Submit PR referencing the Issue (if any).\n\nSee also: [Code of Conduct](CODE_OF_CONDUCT.md).\n\n## 9. Code of Conduct\n\nWe strive for an inclusive, respectful environment. \nBy participating you agree to uphold the [Code of Conduct](CODE_OF_CONDUCT.md). \nReport concerns to the maintainer email specified there.\n\n## 10. Acknowledgements\n\nThe authors gratefully acknowledge financial support from the Swiss National Science Foundation (SNSF project 200021_204196).\n\n## 11. License\n\nGPL-3.0-or-later. See [LICENSE](LICENSE).\n\n## Pronunciation Note\n\n\"pylimer\u201d resembles \"polymer\u201d; the playful spelling emphasizes Python integration.\n",
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