Fix and update docs

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the OS, Python version and other tools you might need
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CONTRIBUTING.md

@@ -30,7 +30,7 @@ As in the main code, docstrings and comments should be added to clarify the inte
 
 ## Coding style
 
-We aim to be [PEP8](https://www.python.org/dev/peps/pep-0008/) compliant, with a slightly more relaxed attitude towards line length. Lines up to 100 chars are allowed if it means better readability.
+We aim to be [PEP8](https://www.python.org/dev/peps/pep-0008/) compliant, with a slightly more relaxed attitude towards line length. Lines up to 120 chars are allowed if it means better readability.
 
 ### flake8
 
@@ -53,18 +53,18 @@ This will stop the commit from happening if flake8 checks do not pass.
 
 ### isort
 
-`isort` keeps imports in the [PEP8 recommended order](https://www.python.org/dev/peps/pep-0008/#id23) (flake8 / pep8 tools don't handle this). It can be run manually by typing in `isort -rc .` in `cellmlmanip/` and this should generate no errors.
+`isort` keeps imports in the [PEP8 recommended order](https://www.python.org/dev/peps/pep-0008/#id23) (flake8 / pep8 tools don't handle this). It can be run manually by typing in `isort .` in `cellmlmanip/` and this should generate no errors.
 
 There is a git pre-commit hook for this too, the process is a little more manual than for flake8:
 
-https://github.com/timothycrosley/isort#git-hook
+https://github.com/PyCQA/isort#git-hook
 
 
 ## Documentation
 
 Documentation is generated from the docstrings in the code, and files in the ``docs`` directory.
-Both are written using [reStructuredText](http://docutils.sourceforge.net/docs/user/rst/quickref.html).
-This is then compiled into HTML (or other formats) using [Sphinx](http://www.sphinx-doc.org/en/stable/).
+Both are written using [reStructuredText](https://docutils.sourceforge.io/docs/user/rst/quickref.html).
+This is then compiled into HTML (or other formats) using [Sphinx](https://www.sphinx-doc.org/en/stable/).
 We use [readthedocs.org](https://readthedocs.org) to do this automatically, with the result visible at [https://cellmlmanip.readthedocs.io](https://cellmlmanip.readthedocs.io).
 
 ### Building the documentation locally

README.md

@@ -1,4 +1,4 @@
-![Build status](https://github.com/ModellingWebLab/cellmlmanip/actions/workflows/unit-test.yml/badge.svg) [![Documentation Status](https://readthedocs.org/projects/cellmlmanip/badge/?version=latest)](https://cellmlmanip.readthedocs.io/en/latest/?badge=latest) [![Coverage Status](https://codecov.io/gh/ModellingWebLab/cellmlmanip/branch/develop/graph/badge.svg)](https://codecov.io/gh/ModellingWebLab/cellmlmanip/)
+![Build status](https://github.com/ModellingWebLab/cellmlmanip/actions/workflows/unit-test.yml/badge.svg) [![Documentation Status](https://readthedocs.org/projects/cellmlmanip/badge/?version=latest)](https://cellmlmanip.readthedocs.io/en/latest/?badge=latest) [![Coverage Status](https://codecov.io/gh/ModellingWebLab/cellmlmanip/branch/master/graph/badge.svg)](https://codecov.io/gh/ModellingWebLab/cellmlmanip/)
 
 # cellmlmanip
 CellML loading and model equation manipulation library
@@ -12,7 +12,7 @@ Users install `cellmlmanip` using pip.
 pip install cellmlmanip
 ```
 
-Cellmlmanip is tested and developed on Python 3.9 and higher.
+Cellmlmanip is tested and developed on Python 3.10 and higher.
 
 ## Release notes
 For release notes see [RELEASE.md](./RELEASE.md)

docs/source/conf.py

@@ -28,7 +28,7 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = '2.0'
+needs_sphinx = '7.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -52,7 +52,7 @@
 
 # Where to find documentation for projects we use
 intersphinx_mapping = {
-    'networkx': ('https://networkx.github.io/documentation/stable/', None),
+    'networkx': ('https://networkx.org/documentation/stable/', None),
     'rdflib': ('https://rdflib.readthedocs.io/en/stable/', None),
     'sympy': ('https://docs.sympy.org/latest/', None),
     'pint': ('https://pint.readthedocs.io/en/stable/', None),

pyproject.toml

@@ -35,7 +35,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 docs = [
-    "sphinx>=2.0",
+    "sphinx>=7.0",
 ]
 test = [
     "flake8",