#51 updated packages

environment.yml

@@ -7,14 +7,16 @@ dependencies:
   - python=3.11
   - ipython
   # sphinx
-  - sphinx=5.3.0 # sphinx-design currently requires sphinx[version>=2,<5]
-  - pydata-sphinx-theme=0.13.3 # website theme
-  - myst-parser=0.18.1 # Markdown support
-  - myst-nb=0.17.1 # Jupyter notebook support
-  - sphinx-autobuild=2021.3.14 # live-html support
-  - sphinx-autoapi=2.1.0 # to build docs from source code instead of package import
-  - sphinx-design=0.3.0 # responsive web component support
-  - sphinx-notfound-page=0.8.3 # custom 404 page
-  - graphviz=7.1.0 # for plotting dependency diagrams with sphinx-autoapi
-  - sphinx-favicon=1.0.1 # for custom favicons
-  - sphinx-copybutton=0.5.2 # for copy button on code blocks
+  - sphinx=6.2.1 # sphinx-design currently requires sphinx[version>=2,<5] # https://github.com/sphinx-doc/sphinx/releases
+  # theme and extensions
+  - pydata-sphinx-theme=0.13.3 # website theme # https://github.com/pydata/pydata-sphinx-theme/releases
+  - myst-parser=2.0.0 # Markdown support # https://github.com/executablebooks/MyST-Parser/releases
+  - nbsphinx=0.9.2 # Jupyter notebook support # https://github.com/spatialaudio/nbsphinx/releases
+  - sphinx-autoapi=2.1.0 # to build docs from source code instead of package import # https://github.com/readthedocs/sphinx-autoapi/tags
+  - sphinx-design=0.4.1 # responsive web component support # https://github.com/executablebooks/sphinx-design/releases
+  - sphinx-notfound-page=0.8.3 # custom 404 page # https://github.com/readthedocs/sphinx-notfound-page/tags
+  - graphviz=8.0.5 # for plotting dependency diagrams with sphinx-autoapi # https://anaconda.org/conda-forge/graphviz/files
+  - sphinx-favicon=1.0.1 # for custom favicons # https://github.com/tcmetzger/sphinx-favicon/releases
+  - sphinx-copybutton=0.5.2 # for copy button in code blocks # https://github.com/executablebooks/sphinx-copybutton/releases
+  # build process
+  - sphinx-autobuild=2021.3.14 # live-html support # https://github.com/executablebooks/sphinx-autobuild/releases

sphinx/conf.py

@@ -14,8 +14,6 @@
 
 needs_sphinx = '5.3.0'
 
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
     # native extensions
     'sphinx.ext.autodoc',
@@ -25,14 +23,14 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.extlinks',
     'sphinx.ext.napoleon',
-    'sphinx.ext.inheritance_diagram', # for plotting dependency diagrams with sphinx-autoapi
+    'sphinx.ext.inheritance_diagram',
     # iPython extensions
     'IPython.sphinxext.ipython_directive',
     'IPython.sphinxext.ipython_console_highlighting',
     # Markdown support
-    # 'myst_parser', do not enable separately if using myst_nb, compare https://github.com/executablebooks/MyST-NB/issues/421#issuecomment-1164427544
+    'myst_parser', # do not enable separately if using myst_nb, compare https://github.com/executablebooks/MyST-NB/issues/421#issuecomment-1164427544
     # Jupyter Notebook support
-    'myst_nb',
+    'nbsphinx',
     # API documentation support
     'autoapi',
     # responsive web component support
@@ -123,9 +121,7 @@
 
 source_suffix = {
     '.rst': 'restructuredtext',
-    '.md': 'myst-nb',
-    '.ipynb': 'myst-nb',
-    '.myst': 'myst-nb',
+    '.md': 'markdown'
 }
 
 myst_enable_extensions = [
@@ -136,9 +132,10 @@
     "html_image",
 ]
 
-## myst_nb configuration ################################################
+## nbsphinx configuration ################################################
 
-nb_execution_mode = 'off'
+nbsphinx_execute = 'never'
+nbsphinx_allow_errors = True
 
 ## sphinx-favicon configuration #########################################