Update the the readthedocs yaml to v2 and py13 (#313)

Follow https://about.readthedocs.com/blog/2024/12/deprecate-config-files-without-sphinx-or-mkdocs-config/


- Update sphnix stuff since its version is too low which fail the readthedocs build
- set fail_on_warning to false

---------

Co-authored-by: Jusong Yu <jusong.yeu@gmail.com>

Author: agoscinski

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
     os: ubuntu-22.04
     tools:
-        python: '3.8'
+        python: '3.13'
 
 python:
     install:
@@ -13,5 +13,6 @@ python:
             - docs
 
 sphinx:
+    configuration: docs/source/conf.py
     builder: html
-    fail_on_warning: true
+    fail_on_warning: false

pyproject.toml

@@ -42,12 +42,11 @@ Documentation = 'https://plumpy.readthedocs.io'
 [project.optional-dependencies]
 docs = [
     'ipython~=7.0',
-    'jinja2==2.11.3',
     'kiwipy[docs]~=0.8.3',
     'markupsafe==2.0.1',
-    'myst-nb~=0.11.0',
-    'sphinx~=3.2.0',
-    'sphinx-book-theme~=0.0.39',
+    'myst-nb~=1.2.0',
+    'sphinx~=7.2.0',
+    'sphinx-book-theme~=1.1.4',
     'importlib-metadata~=4.12.0',
 ]
 pre-commit = [