From 44c5c53d8d5f576767a007467042c997eee239e5 Mon Sep 17 00:00:00 2001
From: Ben Jeffery <ben.jeffery@bdi.ox.ac.uk>
Date: Tue, 26 Aug 2025 01:37:41 +0100
Subject: [PATCH] Doc changes for consistency across tskit-dev
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 docs/_config.yml         |  13 +++++++++----
 docs/favicon.ico         | Bin 0 -> 3902 bytes
 requirements/CI-docs.txt |   2 +-
 3 files changed, 10 insertions(+), 5 deletions(-)
 create mode 100644 docs/favicon.ico

diff --git a/docs/_config.yml b/docs/_config.yml
index 27dd90d..14129a9 100644
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -5,6 +5,7 @@ title: Tszip manual
 author: Tskit Developers
 copyright: "2023"
 only_build_toc_files: true
+favicon: favicon.ico
 
 execute:
   execute_notebooks: cache
@@ -22,22 +23,26 @@ html:
   use_repository_button: true
   use_edit_page_button: true
 
-  # NOTE this gets replaced by the build infrastructure during deployment
-  extra_navbar: __TSZIP_VERSION__
-  extra_footer: __TSZIP_VERSION__
 
 sphinx:
     extra_extensions:
+    - sphinx_copybutton
     - sphinx.ext.autodoc
     - sphinx.ext.viewcode
     - sphinx.ext.intersphinx
     - sphinx_issues
     - sphinxarg.ext
+    - IPython.sphinxext.ipython_console_highlighting
 
     config:
       html_theme: sphinx_book_theme
       html_theme_options:
-         pygment_dark_style: monokai
+         pygments_dark_style: monokai
+         navigation_with_keys: false
+         logo:
+           text: |
+             tszip<br/>
+             version __TSZIP_VERSION__
       myst_enable_extensions:
       - colon_fence
       - deflist
diff --git a/docs/favicon.ico b/docs/favicon.ico
new file mode 100644
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diff --git a/requirements/CI-docs.txt b/requirements/CI-docs.txt
index a4e8f0e..c58f62b 100644
--- a/requirements/CI-docs.txt
+++ b/requirements/CI-docs.txt
@@ -1,5 +1,5 @@
 humanize==4.10.0
-jupyter-book==1.0.2
+jupyter-book==1.0.4.post1
 numcodecs==0.12.1
 sphinx-issues==4.1.0
 sphinx-argparse==0.4.0