From 7132c95360d1ada1e2770bd6bd1ee774bc6b6be7 Mon Sep 17 00:00:00 2001
From: Boris MUZELLEC <boris.muzellec@owkin.com>
Date: Tue, 28 Oct 2025 15:38:15 +0100
Subject: [PATCH 1/5] docs: update .readthedocs.yaml to handle installation
 through uv

---
 .readthedocs.yaml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 0e0a8fa5..63bd7931 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,17 +1,18 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Build from the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
-# Explicitly set the version of Python and its requirements
+# Use uv to install dependencies from pyproject.toml
 python:
   install:
-    - requirements: docs/requirements.txt
-    - method: pip
+    - method: uv
       path: .
+      extra_requirements:
+        - doc

From 2babcee66704e5e16dfc5a6736d560263508b926 Mon Sep 17 00:00:00 2001
From: Boris MUZELLEC <boris.muzellec@owkin.com>
Date: Tue, 28 Oct 2025 15:46:15 +0100
Subject: [PATCH 2/5] docs: update .readthedocs.yaml to handle installation
 through uv

---
 .readthedocs.yaml | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 63bd7931..7032b7db 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,18 +1,18 @@
 version: 2
 
-build:
-  os: "ubuntu-22.04"
-  tools:
-    python: "3.11"
-
-# Build from the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/source/conf.py
+   configuration: docs/source/conf.py
 
-# Use uv to install dependencies from pyproject.toml
-python:
-  install:
-    - method: uv
-      path: .
-      extra_requirements:
-        - doc
+build:
+   os: ubuntu-24.04
+   tools:
+      python: "3.13"
+   jobs:
+      pre_create_environment:
+         - asdf plugin add uv
+         - asdf install uv latest
+         - asdf global uv latest
+      create_environment:
+         - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+      install:
+         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group doc

From 106a6b4dc30eb5945b90614deed6c9443bbb8ce0 Mon Sep 17 00:00:00 2001
From: Boris MUZELLEC <boris.muzellec@owkin.com>
Date: Tue, 28 Oct 2025 15:48:41 +0100
Subject: [PATCH 3/5] docs: update .readthedocs.yaml to handle installation
 through uv

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 7032b7db..da2b88cf 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -15,4 +15,4 @@ build:
       create_environment:
          - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
       install:
-         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group doc
+         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --group doc

From d4894f5d45692009c2e072325ba439e1ec9acc0b Mon Sep 17 00:00:00 2001
From: Boris MUZELLEC <boris.muzellec@owkin.com>
Date: Tue, 28 Oct 2025 15:51:32 +0100
Subject: [PATCH 4/5] docs: update .readthedocs.yaml to handle installation
 through uv

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index da2b88cf..afb0deef 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -15,4 +15,4 @@ build:
       create_environment:
          - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
       install:
-         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --group doc
+         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --extra doc

From b6f8a74b083486dc33992719ab921d42c15e2997 Mon Sep 17 00:00:00 2001
From: Boris MUZELLEC <boris.muzellec@owkin.com>
Date: Tue, 28 Oct 2025 15:56:05 +0100
Subject: [PATCH 5/5] docs: remove binder

---
 docs/source/conf.py | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index f31fb9af..a9fa9905 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -12,7 +12,6 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 from datetime import date
-from pathlib import Path
 
 import git
 
@@ -257,14 +256,4 @@
 sphinx_gallery_conf = {
     "examples_dirs": "../../examples",  # path to your example scripts
     "gallery_dirs": "auto_examples",  # path to where to save gallery generated output
-    "binder": {
-        "org": "Owkin",
-        "repo": "PyDESeq2",
-        "branch": current_commit,  # Can be any branch, tag, or commit hash.
-        # Use a branch that hosts your docs.
-        "binderhub_url": "https://mybinder.org",  # public binderhub url
-        "dependencies": str(Path(__file__).parents[2] / "requirements.txt"),
-        "notebooks_dir": "jupyter_notebooks",
-        "use_jupyter_lab": True,
-    },
 }