doc: update user guide & Pages deploy

.github/workflows/doc.yml

@@ -20,22 +20,21 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: recursive
-      # Need to refine this by specifying components required for doc
+      # Deps
       - uses: dtolnay/rust-toolchain@nightly
       - uses: peaceiris/actions-mdbook@v2
         with:
           mdbook-version: "0.4.36"
-      # Generate user guide first because it removes all existing files
-      # from the target directory
-      - name: Generate User Guide
-        run: mdbook build -d ../target/doc/ user-guide/
-      - name: Generate Rust Docs
-        run: cargo +nightly doc --all --no-deps --all-features
-
+      # Generate / using sudo before I'm forced to retry this 83491 times due to CI constraints
+      - name: Generate documentation
+        run: |
+          sudo chmod +x docs/build.sh
+          sudo ./docs/build.sh
+      # Deploy
       - name: Deploy Docs
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_branch: gh-pages
           publish_dir: ./target/doc
-          force_orphan: true
+          force_orphan: true

docs/build.sh

@@ -0,0 +1,11 @@
+# Generate docs
+
+cargo +nightly doc --all --no-deps --all-features
+mdbook build user-guide/
+
+# Add stuff to the deployed folder
+
+mv user-guide/book target/doc/user-guide
+cp docs/index.html target/doc
+cp docs/index.css target/doc
+cp docs/theme.js target/doc

docs/index.css

@@ -0,0 +1,124 @@
+:root {
+    /* Light mode colors */
+    --background-color: #f5f5f5;
+    --body-background: white;
+    --text-color: #34495e;
+    --heading-color: #2c3e50;
+    --link-color: #3498db;
+    --border-color: #eee;
+    --box-shadow: 0 2px 8px rgba(0, 0, 0, 0.1);
+}
+
+/* Dark mode colors */
+.dark-mode {
+    --background-color: #1a1a1a;
+    --body-background: #121212;
+    --text-color: #c0c0c0;
+    --heading-color: #e0e0e0;
+    --link-color: #4da6ff;
+    --border-color: #333;
+    --box-shadow: 0 2px 8px rgba(255, 255, 255, 0.05);
+}
+
+html {
+    background-color: var(--background-color);
+    height: 100%;
+    transition: background-color 0.3s;
+}
+
+body {
+    max-width: 65ch;
+    margin: 1rem auto;
+    padding: 1.5rem;
+    line-height: 1.6;
+    background-color: var(--body-background);
+    height: auto;
+    box-shadow: var(--box-shadow);
+    border-radius: 8px;
+    color: var(--text-color);
+    transition: background-color 0.3s, color 0.3s;
+    position: relative; /* Added to help with positioning */
+}
+
+h1, h2, h3 {
+    font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
+    color: var(--heading-color);
+    margin-bottom: 1rem;
+    transition: color 0.3s;
+}
+
+h1 {
+    font-size: 2rem;
+    border-bottom: 2px solid var(--border-color);
+    margin-top: 0.1rem;
+    padding-bottom: 0.5rem;
+    transition: border-color 0.3s;
+    position: relative; /* Added to help with positioning */
+}
+
+h2 {
+    font-size: 1.5rem;
+    margin-top: 1rem;
+}
+
+p, li {
+    font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, sans-serif;
+    color: var(--text-color);
+    margin-bottom: 1rem;
+    transition: color 0.3s;
+}
+
+a:link, a:visited {
+    color: var(--link-color);
+    text-decoration: none;
+    border-bottom: 1px solid transparent;
+    transition: border-color 0.2s ease, color 0.3s;
+}
+
+a:hover {
+    border-bottom-color: var(--link-color);
+}
+
+/* Theme toggle styles */
+.theme-switch {
+    position: absolute;
+    top: 0.5rem;
+    right: 0.5rem;
+    display: flex;
+    align-items: center;
+}
+
+.theme-switch input {
+    display: none;
+}
+
+.theme-switch-label {
+    cursor: pointer;
+    display: inline-block;
+    width: 50px;
+    height: 24px;
+    background-color: var(--border-color);
+    border-radius: 12px;
+    position: relative;
+    transition: background-color 0.3s;
+}
+
+.theme-switch-label::after {
+    content: '';
+    position: absolute;
+    width: 20px;
+    height: 20px;
+    border-radius: 50%;
+    background-color: var(--text-color);
+    top: 2px;
+    left: 2px;
+    transition: transform 0.3s;
+}
+
+.theme-switch input:checked + .theme-switch-label {
+    background-color: var(--link-color);
+}
+
+.theme-switch input:checked + .theme-switch-label::after {
+    transform: translateX(26px);
+}

docs/index.html

@@ -0,0 +1,34 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Honeycomb</title>
+    <link rel="stylesheet" href="index.css">
+</head>
+<body>
+    <div class="theme-switch">
+        <input type="checkbox" id="theme-toggle">
+        <label for="theme-toggle" class="theme-switch-label"></label>
+    </div>
+
+    <h1>Honeycomb 🐝</h1>
+
+    <h2>Scope of the project</h2>
+
+    <p>Honeycomb aims to provide a safe, efficient and scalable implementation
+    of combinatorial maps for meshing applications. More specifically, the
+    goal is to converge towards a (or multiple) structure(s) adapted to
+    algorithms exploiting GPUs and many-core architectures.</p>
+
+    <h2>Links</h2>
+
+    <ul>
+        <li><a href="https://github.com/LIHPC-Computational-Geometry/honeycomb">repository</a></li>
+        <li><a href="https://crates.io/crates/integraal">crates dot io</a></li>
+        <li><a href="honeycomb">master branch documentation</a></li>
+        <li><a href="user-guide">user guide</a></li>
+    </ul>
+    <script src="theme.js"></script>
+</body>
+</html>

docs/theme.js

@@ -0,0 +1,16 @@
+document.getElementById('theme-toggle').addEventListener('change', function() {
+    document.documentElement.classList.toggle('dark-mode', this.checked);
+    // Optional: Persist theme preference in localStorage
+    localStorage.setItem('theme', this.checked ? 'dark' : 'light');
+});
+
+// Check for saved theme preference or system preference on page load
+document.addEventListener('DOMContentLoaded', () => {
+    const savedTheme = localStorage.getItem('theme');
+    const themeToggle = document.getElementById('theme-toggle');
+
+    if (savedTheme === 'dark') {
+        document.documentElement.classList.add('dark-mode');
+        themeToggle.checked = true;
+    }
+});

user-guide/src/SUMMARY.md

@@ -9,11 +9,13 @@
 - [Other content](./project-structure/others.md)
     - [Benchmarks](./project-structure/honeycomb-benches.md)
     - [Examples](./project-structure/honeycomb-examples.md)
-    - [User guide](./project-structure/honeycomb-guide.md)
 
 # Kernels
 
+- [DVR](./kernels/dvr.md)
 - [Grisubal](./kernels/grisubal.md)
+- [Polygon triangulation](./kernels/triangulations.md)
+- [Splits](./kernels/splits.md)
 
 # Definitions
 
@@ -27,5 +29,4 @@
     - [Add / Remove a dimension](./definitions/changeNdim.md)
     - [Add / Remove a free dart](./definitions/changeNdart.md)
     - [Sewing / Unsewing operation](./definitions/sew.md)
-- [Advanced Operations](./definitions/advancedops.md)
 

user-guide/src/definitions/embedding.md

@@ -10,10 +10,9 @@ dedicated sections.
 
 ## Implementation
 
-Because embedding is defined per-application or per-needs, our combinatorial map
-implementation uses a generic system to handle this; The storage follows our
-own specific logic, which is detailed in [this](../honeycomb_core/struct.CMap2.html#note-on-cell-identifiers)
-documentation entry.
+Because embedding is defined per-application or per-needs, our combinatorial map implementation uses
+a generic system to handle this; The storage follows our own specific logic, which is detailed in
+[this](../../honeycomb_core/cmap/struct.CMap2.html#note-on-cell-identifiers) documentation entry.
 
 ## Examples
 

user-guide/src/definitions/sew.md

@@ -35,9 +35,9 @@ Exact properties of the link operation directly depends on the property of the m
 
 The *i-sew* operation corresponds to an *i-link* operation, coupled with an update of the affected attributes. *How*
 the attributes are updated is defined through trait implementation in the Rust crate (see
-[AttributeUpdate](../honeycomb_core/trait.AttributeUpdate.html),
-[AttributeBind](../honeycomb_core/trait.AttributeBind.html)). *Which* attributes are updated can be deduced from the
-dimension *i* of the sewing operation. This is summarized in the following table:
+[AttributeUpdate](../../honeycomb_core/attributes/trait.AttributeUpdate.html),
+[AttributeBind](../../honeycomb_core/attributes/trait.AttributeBind.html)). *Which* attributes are updated can be
+deduced from the dimension *i* of the sewing operation. This is summarized in the following table:
 
 | Dimension | Geometrical operation | 0-cell / Vertex Attributes | 1-cell / Edge Attributes | 2-cell / Face Attributes | 3-cell / Volume Attributes |
 |-----------|-----------------------|----------------------------|--------------------------|--------------------------|----------------------------|
@@ -49,4 +49,4 @@ dimension *i* of the sewing operation. This is summarized in the following table
 
 The unsew operation is the complementary to the sew operation. It behaves according to similar properties, but is used
 to remove links between darts. It does so by replacing values of the beta functions by the null dart. Geometrical
-updates are handled and defined in the same way as for the sew operation.
+updates are handled and defined in the same way as for the sew operation.

user-guide/src/index.md

@@ -20,8 +20,9 @@ The current objective is to
 - ~improve the structure without having to deal with data races and similar issues, thanks to the Rust's guarantees~
 - ~implement basic meshing algorithms to evaluate the viability of the implementation & improve our structure using
   Rust's framework to streamline the refactoring and parallelization process~
+- ~Benchmark and/or profile and/or parallelize our first algorithm, **grisubal**~
 - Ship a first stable version of the library (see this [issue](https://github.com/LIHPC-Computational-Geometry/honeycomb/issues/150))
-- Benchmark and/or profile and/or parallelize our first algorithm, **grisubal**
+- Work on efficient parallelism
 
 ### Core Requirements
 
@@ -53,28 +54,16 @@ version, and use the GitHub Pages documentation instead of the one hosted on doc
 
 ## Documentation
 
-Published crates:
-
-- [honeycomb](honeycomb/) *Main crate*
-- [honeycomb-core](honeycomb_core/) *Core definitions and tools*
-- [honeycomb-kernels](honeycomb_kernels/) *Meshing kernel implementations*
-- [honeycomb-render](honeycomb_render/) *Visualization tool*
-
-Others:
-
-- [honeycomb-benches](honeycomb_benches/) *Rust code benchmarks*
-- [honeycomb-examples](honeycomb_examples/) *Rust code examples*
-
-You can also generate this documentation locally using **mdbook** and **cargo doc**:
+You can generate this book and the Rust documentation locally using respectively **mdbook** and **cargo doc**:
 
 ```shell
-# Serve the doc on a local server
-mdbook serve --open -d ../target/doc/ user-guide/ &
+mdbook serve --open user-guide/
+```
+```shell
 cargo +nightly doc --all --all-features --no-deps
 ```
 
-Note that generating the doc using a stable toolchain is possible,
-the features just won't be documented as clearly.
+Note that generating the doc using a stable toolchain is possible, the features just won't be documented as clearly.
 
 ## Contributing
 
@@ -109,7 +98,7 @@ defined in the Apache-2.0 license, shall be dual licensed as above, without any
 
 ### Combinatorial Maps
 
-- Damiand, Guillaume, and Pascal Lienhardt. *Combinatorial Maps: Efficient Data Structures for Computer Graphics and
+- Damiand and Lienhardt. *Combinatorial Maps: Efficient Data Structures for Computer Graphics and
   Image Processing*. Chapman&Hall/CRC, 2015.
     - Provides an in-depth presentation of the structure and its variants
     - [Link](https://hal.science/hal-01090890v1)
@@ -118,6 +107,15 @@ defined in the Apache-2.0 license, shall be dual licensed as above, without any
       implementation uses a different approach than ours, & support N-dimensionnal map.
     - [Link](https://doc.cgal.org/latest/Combinatorial_map/)
 
+### Algorithms
+
+- Staten, Noble, and Wilson. *Constructing Tetrahedral Meshes No Matter How Ugly*. SIAM, 2024
+    - Describes the logic behind an overlay grid algorithm.
+    - [Link](https://internationalmeshingroundtable.com/assets/research-notes/imr32/2011.pdf)
+- Rangarajan and Lew. *Provably Robust Directional Vertex Relaxation for geometric mesh optimization*. SIAM, 2017
+    - usage TBD
+    - [Link](https://epubs.siam.org/doi/abs/10.1137/16M1089101)
+
 ### Integration
 
 - The repository structure and workspace system is heavily inspired by

user-guide/src/kernels/dvr.md

@@ -0,0 +1,5 @@
+# Directional Vertices Relaxation
+
+---
+
+WIP: https://github.com/LIHPC-Computational-Geometry/honeycomb/pull/212