COMP: Fix html build

Author: thewtex

docs/README.md

@@ -12,7 +12,7 @@ Insight Journal using MyST Markdown:
 This template demonstrates how to create reproducible, open science articles using:
 
 - **MyST Markdown** for rich scientific document authoring
-- **Pixi** for dependency management and build automation  
+- **Pixi** for dependency management and build automation
 - **Source code** organization in `src/`
 - **Data** organization in `data/`
 - **Multi-format exports** (PDF, HTML, DOCX, MECA, etc.)
@@ -30,8 +30,7 @@ This template demonstrates how to create reproducible, open science articles usi
 ├── data/                  # Data files and images
 │   └── img1.png          # Sample test image
 ├── myst.yml              # MyST configuration
-├── pixi.toml             # Pixi dependency management
-└── requirements.txt      # Python requirements
+└── pixi.toml             # Pixi dependency management
 ```
 
 ## Quick Start
@@ -106,7 +105,7 @@ This template demonstrates:
 The template is configured to export to:
 
 - **HTML**: Interactive web version
-- **PDF**: 
+- **PDF**:
   - arXiv two-column format
   - Plain LaTeX book format
 - **DOCX**: Microsoft Word format

docs/assets/favicon.ico

@@ -39,7 +39,6 @@ venue:
   url: https://insight-journal.org
 github: InsightSoftwareConsortium/InsightJournalTemplate
 doi: 10.5281/zenodo.1234567
-handle: 1338
 abstract: |
   This document describes a new algorithm implemented using the Insight Toolkit
   ITK (www.itk.org). The code of the algorithm is written following the
@@ -49,10 +48,6 @@ abstract: |
   output data that the authors used for validating the algorithm described in
   this paper. This adheres to the fundamental principle that scientific
   publications must facilitate reproducibility of the reported results.
-math:
-  "\\psi": "\\psi"
-  "\\mathbf": "\\mathbf"
-  "\\xi": "\\xi"
 exports:
   - format: pdf
     template: arxiv_two_column

docs/assets/logo-insight-journal-square-dark.png

@@ -49,7 +49,7 @@ project:
 
   # Bibliography
   bibliography:
-    - doc/references.bib
+    - docs/references.bib
 
   # Export configurations
   exports:
@@ -83,8 +83,7 @@ project:
 # Website configuration
 site:
   title: Insight Journal Template
-  logo: logo.png
-  favicon: favicon.ico
+  favicon: docs/assets/favicon.ico
   nav:
     - title: Article
       url: /index.html
@@ -93,10 +92,7 @@ site:
 
   # Site options
   options:
+    logo: docs/assets/logo-insight-journal-square-light.png
+    logo_dark: docs/assets/logo-insight-journal-square-dark.png
     logo_text: Insight Journal Template
-    hide_title_on_index: true
-
-  # Social media and external links
-  domains:
-    - https://insight-journal.org
-    - https://github.com/InsightSoftwareConsortium/InsightJournalTemplate
+    hide_title_on_index: true

docs/assets/logo-insight-journal-square-light.png

@@ -11,11 +11,11 @@ platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
 
 [dependencies]
 # MyST ecosystem
-mystmd = "*"
+mystmd = ">=1.6.0,<2"
 jupyter-book = "*"
 
 # Python scientific stack
-python = ">=3.9"
+python = ">=3.11"
 numpy = "*"
 matplotlib = "*"
 scipy = "*"