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25 changes: 13 additions & 12 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# pyvoro2

[![CI](https://github.com/IvanChernyshov/pyvoro2/actions/workflows/ci.yml/badge.svg)](https://github.com/IvanChernyshov/pyvoro2/actions/workflows/ci.yml) [![Docs](https://github.com/IvanChernyshov/pyvoro2/actions/workflows/docs.yml/badge.svg)](https://github.com/IvanChernyshov/pyvoro2/actions/workflows/docs.yml) [![PyPI](https://img.shields.io/pypi/v/pyvoro2.svg)](https://pypi.org/project/pyvoro2/) [![Python Versions](https://img.shields.io/pypi/pyversions/pyvoro2.svg)](https://pypi.org/project/pyvoro2/) [![License](https://img.shields.io/pypi/l/pyvoro2.svg)](https://github.com/IvanChernyshov/pyvoro2/blob/main/LICENSE)
**Documentation:** https://IvanChernyshov.github.io/pyvoro2/
[![CI](https://github.com/DeloneCommons/pyvoro2/actions/workflows/ci.yml/badge.svg)](https://github.com/DeloneCommons/pyvoro2/actions/workflows/ci.yml) [![Docs](https://github.com/DeloneCommons/pyvoro2/actions/workflows/docs.yml/badge.svg)](https://github.com/DeloneCommons/pyvoro2/actions/workflows/docs.yml) [![PyPI](https://img.shields.io/pypi/v/pyvoro2.svg)](https://pypi.org/project/pyvoro2/) [![Python Versions](https://img.shields.io/pypi/pyversions/pyvoro2.svg)](https://pypi.org/project/pyvoro2/) [![License](https://img.shields.io/pypi/l/pyvoro2.svg)](https://github.com/DeloneCommons/pyvoro2/blob/main/LICENSE)

**Documentation:** https://delonecommons.github.io/pyvoro2/


---
Expand Down Expand Up @@ -43,7 +44,7 @@ view_tessellation(
)
```

<img src="https://raw.githubusercontent.com/IvanChernyshov/pyvoro2/main/docs/assets/quickstart_box.png" width="50%" alt="Voronoi tessellation in a box" />
<img src="https://raw.githubusercontent.com/DeloneCommons/pyvoro2/main/docs/assets/quickstart_box.png" width="50%" alt="Voronoi tessellation in a box" />

### 2) Power/Laguerre tessellation (weighted Voronoi)

Expand Down Expand Up @@ -127,14 +128,14 @@ implementation-oriented details.

| Section | What it contains |
|---|---|
| [Concepts](https://IvanChernyshov.github.io/pyvoro2/guide/concepts/) | What Voronoi and power/Laguerre tessellations are, and what you can expect from them. |
| [Domains](https://IvanChernyshov.github.io/pyvoro2/guide/domains/) | Which containers exist (`Box`, `OrthorhombicCell`, `PeriodicCell`) and how to choose between them. |
| [Operations](https://IvanChernyshov.github.io/pyvoro2/guide/operations/) | How to compute tessellations, assign query points, and compute probe (ghost) cells. |
| [Topology and graphs](https://IvanChernyshov.github.io/pyvoro2/guide/topology/) | How to build a neighbor graph that respects periodic images, and how normalization helps. |
| [Inverse fitting](https://IvanChernyshov.github.io/pyvoro2/guide/inverse/) | Fit power/Laguerre radii from desired pairwise plane positions (with optional constraints/penalties). |
| [Visualization](https://IvanChernyshov.github.io/pyvoro2/guide/visualization/) | Optional py3Dmol helpers for debugging and exploratory analysis. |
| [Examples (notebooks)](https://IvanChernyshov.github.io/pyvoro2/notebooks/01_basic_compute/) | End-to-end examples that combine the pieces above. |
| [API reference](https://IvanChernyshov.github.io/pyvoro2/reference/api/) | The full reference (docstrings). |
| [Concepts](https://delonecommons.github.io/pyvoro2/guide/concepts/) | What Voronoi and power/Laguerre tessellations are, and what you can expect from them. |
| [Domains](https://delonecommons.github.io/pyvoro2/guide/domains/) | Which containers exist (`Box`, `OrthorhombicCell`, `PeriodicCell`) and how to choose between them. |
| [Operations](https://delonecommons.github.io/pyvoro2/guide/operations/) | How to compute tessellations, assign query points, and compute probe (ghost) cells. |
| [Topology and graphs](https://delonecommons.github.io/pyvoro2/guide/topology/) | How to build a neighbor graph that respects periodic images, and how normalization helps. |
| [Inverse fitting](https://delonecommons.github.io/pyvoro2/guide/inverse/) | Fit power/Laguerre radii from desired pairwise plane positions (with optional constraints/penalties). |
| [Visualization](https://delonecommons.github.io/pyvoro2/guide/visualization/) | Optional py3Dmol helpers for debugging and exploratory analysis. |
| [Examples (notebooks)](https://delonecommons.github.io/pyvoro2/notebooks/01_basic_compute/) | End-to-end examples that combine the pieces above. |
| [API reference](https://delonecommons.github.io/pyvoro2/reference/api/) | The full reference (docstrings). |

## Installation

Expand Down Expand Up @@ -197,7 +198,7 @@ Some parts of the implementation, tests, and documentation were developed with
AI assistance (OpenAI ChatGPT). The maintainer reviews and integrates changes,
and remains responsible for the resulting code and scientific claims.

Details are documented in the [AI usage](https://IvanChernyshov.github.io/pyvoro2/project/ai/) page.
Details are documented in the [AI usage](https://delonecommons.github.io/pyvoro2/project/ai/) page.

## License

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6 changes: 3 additions & 3 deletions mkdocs.yml
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@@ -1,8 +1,8 @@
site_name: pyvoro2
site_description: Python bindings for Voro++ (3D Voronoi and power/Laguerre tessellations) with periodic and topology utilities.
site_url: https://IvanChernyshov.github.io/pyvoro2/
repo_url: https://github.com/IvanChernyshov/pyvoro2
repo_name: IvanChernyshov/pyvoro2
site_url: https://delonecommons.github.io/pyvoro2/
repo_url: https://github.com/DeloneCommons/pyvoro2
repo_name: DeloneCommons/pyvoro2
edit_uri: edit/main/docs/

theme:
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7 changes: 4 additions & 3 deletions pyproject.toml
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Expand Up @@ -38,9 +38,10 @@ classifiers = [
]

[project.urls]
Homepage = 'https://github.com/IvanChernyshov/pyvoro2'
Repository = 'https://github.com/IvanChernyshov/pyvoro2'
Issues = 'https://github.com/IvanChernyshov/pyvoro2/issues'
Homepage = 'https://github.com/DeloneCommons/pyvoro2'
Documentation = 'https://delonecommons.github.io/pyvoro2/'
Repository = 'https://github.com/DeloneCommons/pyvoro2'
Issues = 'https://github.com/DeloneCommons/pyvoro2/issues'



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2 changes: 1 addition & 1 deletion src/pyvoro2/__about__.py
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Expand Up @@ -5,4 +5,4 @@
"""

# Keep this as a simple assignment so scikit-build-core can extract it via regex.
__version__ = '0.4.2'
__version__ = '0.4.2.post1'
4 changes: 2 additions & 2 deletions tools/gen_readme.py
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Expand Up @@ -35,7 +35,7 @@
from urllib.parse import quote


DEFAULT_GITHUB_REPO = 'IvanChernyshov/pyvoro2'
DEFAULT_GITHUB_REPO = 'DeloneCommons/pyvoro2'
DEFAULT_REPO_REF = 'main'

PROJECT_ROOT = Path(__file__).resolve().parents[1]
Expand Down Expand Up @@ -353,7 +353,7 @@ def main() -> None:

# Header + badges.
parts.append(
f'# {pkg_name}\n\n' + badges + '\n' + f'**Documentation:** {docs_site}\n'
f'# {pkg_name}\n\n' + badges + '\n\n' + f'**Documentation:** {docs_site}\n'
)

# Add pages.
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