Always re-execute example notebooks / use myst-nb (#144)

* Current example notebooks are terribly outdated. Run them on every pull request, to stay in sync with the library.
* Use myst-nb instead of nbsphinx (more actively developed, fewer dependency problems)
* Exclude outdated examples for now
* Use m2r2 instead of unmaintained m2r for markdown parsing

Author: dweindl

doc/conf.py

@@ -50,9 +50,8 @@
     'sphinx.ext.autosummary',
     'sphinx.ext.intersphinx',
     'sphinx.ext.viewcode',
-    'myst_parser',
     'sphinx_markdown_tables',
-    'nbsphinx',
+    'myst_nb',
 ]
 
 intersphinx_mapping = {
@@ -73,6 +72,9 @@
     'build/html',
     '**.ipynb_checkpoints',
     'logo/LICENSE.md',
+    # TODO update and un-exclude
+    'example/example_visualization.ipynb',
+    'example/example_visualization_without_visspec.ipynb',
 ]
 
 master_doc = 'index'
@@ -90,10 +92,14 @@
 # For some reason causes sphinx import errors otherwise
 autodoc_mock_imports = ['yaml']
 
+# myst_nb options
+#  https://myst-nb.readthedocs.io/en/latest/configuration.html
+nb_execution_mode = "force"
+
+
 source_suffix = {
     '.rst': 'restructuredtext',
     '.txt': 'restructuredtext',
-    '.md': 'markdown',
 }
 
 # ignore numpy warnings

doc/example.rst

@@ -9,8 +9,6 @@ The following examples should help to get a better idea of how to use the PEtab
    :maxdepth: 1
 
    example/example_petablint.ipynb
-   example/example_visualization.ipynb
-   example/example_visualization_without_visspec.ipynb
    example/example_visualization_with_visspec.ipynb
 
 Examples of systems biology parameter estimation problems specified in PEtab

doc/md2rst.py

@@ -1,4 +1,4 @@
-import m2r
+import m2r2
 import re
 
 
@@ -26,7 +26,7 @@ def absolute_links(txt):
 
 def md2rst(source: str, target: str):
     txt = absolute_links(read(source))
-    txt = m2r.convert(txt)
+    txt = m2r2.convert(txt)
     with open(target, 'w') as f:
         f.write(txt)
 

setup.py

@@ -83,12 +83,9 @@ def absolute_links(txt):
               'sphinxcontrib-napoleon>=0.7',
               'sphinx-markdown-tables>=0.0.15',
               'sphinx-rtd-theme>=0.5.1',
-              'myst-parser>=0.16.1',
-              'nbsphinx>=0.8.2',
-              'm2r>=0.2.1',
+              'm2r2',
+              'myst-nb>=0.14.0',
               'ipython>=7.21.0',
-              # https://github.com/spatialaudio/nbsphinx/issues/641
-              'Jinja2==3.0.3',
           ]
       }
       )