Sectioning is not working for a certain notebook

[rclUPC]

Hi,
I am creating an educational book with Jupyter Notebooks for Fluid Mechanics. You can check it here.
As you can see, there are (or ther should be) 6 sections, according to the toc file:

format: jb-book
root: README
chapters:
- file: 0-Intro/IntroPython
  sections:
  - file: 0-Intro/Assignment0
- file: 1-microFlows/Microflows
  sections:
  - file: 1-microFlows/Assignment1
- file: 2-Rheology/rheology
  sections:
  - file: 2-Rheology/FDMViscoelastic
  - file: 2-Rheology/Assignment2
- file: 3-Turbulence/turbulence
  sections:
  - file: 3-Turbulence/ExperimentalMeasurements
  - file: 3-Turbulence/Assignment3
- file: 4-BoundaryLayer/BoundaryLayer
  sections:
  - file: 4-BoundaryLayer/Assignment4
- file: 5-CompressibleFlow/CompressibleFlow
  sections:
  - file: 5-CompressibleFlow/Assignment5

But the section 2 is not being sectioned.

I have no idea what is wrong with this Notebook. I don't know if it a bug, or there is something I am doing wrong.
Hope anyone can see the issue.
Kind regards
Robert

[choldgraf]

Hmm, does your book build produce any error messages or warnings?

[rclUPC]

Nope. This is the output:

Running Sphinx v3.2.1
[etoc] Changing master_doc to 'README'
loading pickled environment... done
myst v0.15.2: MdParserConfig(renderer='sphinx', commonmark_only=False, enable_extensions=['dollarmath', 'colon_fence'], dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, heading_slug_func=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200)
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
no targets are out of date.
build succeeded.

[choldgraf]

Try deleting everything in your build folder first and re-build. It's not detecting changes to any pages so isn't parsing any of the notebooks. Deleting them will restart the process

[rclUPC]

Ok. Done. It doesn't seems to shown anything related with that:

Running Sphinx v3.2.1
making output directory... done
[etoc] Changing master_doc to 'README'
myst v0.15.2: MdParserConfig(renderer='sphinx', commonmark_only=False, enable_extensions=['dollarmath', 'colon_fence'], dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, heading_slug_func=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200)
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 17 source files that are out of date
updating environment: [new config] 17 added, 0 changed, 0 removed
Executing: 0-Intro/Assignment0 in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/0-Intro                                                                        
Executing: 0-Intro/Assignment0-Solution in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/0-Intro                                                               
Executing: 0-Intro/IntroPython in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/0-Intro                                                                        
Executing: 1-microFlows/Assignment1 in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/1-microFlows                                                              
Executing: 1-microFlows/MeniscusBetweenPlates in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/1-microFlows                                                    
 lsoda--  at t (=r1), too much accuracy requested  
       for precision of machine..  see tolsf (=r2) 
      in above,  r1 =  0.5148195504208D+01   r2 =                  NaN
Executing: 1-microFlows/Microflows in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/1-microFlows                                                               
Executing: 2-Rheology/Assignment2 in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/2-Rheology                                                                  
Executing: 2-Rheology/FDMViscoelastic in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/2-Rheology                                                              
Executing: 2-Rheology/rheology in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/2-Rheology                                                                     
Executing: 3-Turbulence/Assignment3 in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/3-Turbulence                                                              
Executing: 3-Turbulence/ExperimentalMeasurements in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/3-Turbulence                                                 
Executing: 3-Turbulence/turbulence in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/3-Turbulence                                                               
Executing: 4-BoundaryLayer/BoundaryLayer in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/4-BoundaryLayer                                                      
Executing: 5-CompressibleFlow/CompressibleFlow in: /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/5-CompressibleFlow                                             
reading sources... [100%] README                                                                                                                                                                       
/home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/0-Intro/Assignment0-Solution.ipynb:10004: WARNING: Document or section may not begin with a transition.
/home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/0-Intro/IntroPython.ipynb:10003: WARNING: Document or section may not begin with a transition.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/0-Intro/Assignment0-Solution.ipynb: WARNING: document isn't included in any toctree
/home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/1-microFlows/MeniscusBetweenPlates.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] README                                                                                                                                                                        
generating indices...  genindexdone
writing additional pages...  searchdone
copying images... [100%] _build/jupyter_execute/5-CompressibleFlow/CompressibleFlow_61_0.png                                                                                                           
copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 4 warnings.

The HTML pages are in _build/html.
[etoc] missing index.html written as redirect to 'README.html'

===============================================================================

Finished generating HTML for book.
Your book's HTML pages are here:
    _build/html/
You can look at your book by opening this file in a browser:
    _build/html/index.html
Or paste this line directly into your browser bar:
    file:///home/robert/GDriveUPC/documents/asignaturas/AdvancedFluidMechanics/JupyterNotebooks/_build/html/index.html            

===============================================================================

and the book looks like before

[rclUPC]

I am sure that there is something wrong in the rheology.ipynb notebook, but I am not able to find it. I have made a test, by replacing this notebook by a markdown file with just a title and some text, and it works fine.

[mmcky]

@rclUPC I built your book using sphinx>=4 and it looks like the sectioning works OK without any changes to your files. Is this the final output you're after?

So this might be an issue when using sphinx==3.2.1. Are you able to upgrade sphinx?

[rclUPC]

@mmcky Yes, that is exactly what I am after. But I am afraid that the solution is other than upgrading sphinx to >= 4. I have upgraded to 4.5.0 (it seems that sphynx 5 is incompatible with present version on jupyter book) and the result, for me, is the same as before:

I have made the build from scratch (deleting previously _build, just in case...) and the same result. Have you changed anything else?
In case it can be useful, this is my output from jupyter-book --version:

Jupyter Book      : 0.12.3
External ToC      : 0.2.4
MyST-Parser       : 0.15.2
MyST-NB           : 0.13.2
Sphinx Book Theme : 0.1.10
Jupyter-Cache     : 0.4.3
NbClient          : 0.5.1

Thank you for your time...

[mmcky]

@rclUPC the only change I made was set execution to off. But that shouldn't change the html output.

-  execute_notebooks: force
+  execute_notebooks: "off"

I am using

Jupyter Book      : 0.12.3
External ToC      : 0.2.4
MyST-Parser       : 0.15.2
MyST-NB           : 0.13.2
Sphinx Book Theme : 0.3.2
Jupyter-Cache     : 0.4.3
NbClient          : 0.5.3

your sphinx-book-theme is quite old. Perhaps try upgrading that too?

I am using sphinx==4.4.0

[rclUPC]

@mmcky Well, actually it seems to do change the html output. I have only changed the execute_notebooks to "off"and it works now.
With respect to the sphinx-book-theme, when I have tried to upgrade it, pip gives this error:

jupyter-book 0.12.3 requires sphinx_book_theme~=0.1.4, but you'll have sphinx-book-theme 0.3.2 which is incompatible.

and, moreover, I think I like more the 0.1.10 version (I don't know if there is any other change besides the easthetic one).

It seems to solve my issue. Thank you very much.

But I have still a question: if the _config file has execute_notebooks:"off", it means that all the notebooks have to be executed before building the book, is it right? It seems that the issue is the executing procedure by python. Is it probably that jupyter book is using a python version different than the one I use when I execute the notebooks? I am using jupyterlab-desktop to execute the notebooks, version 3.8.15, and jupyter book seems to use the one in the anaconda distribution, version 3.8.5 . Could it be the reason of the problem?

[mmcky]

re: theme you're right. The 0.12.3 release does specify that dependency. https://github.com/executablebooks/jupyter-book/blob/60d79c79e1bacda19c4f3e6764b8c879d963480d/pyproject.toml#L47. Sorry should have checked that. There are some improvements coming down the pipeline

[rclUPC]

I have updated anaconda to the new version, with python 3.9.12 and switched back execute_notebooks to force, and it is working. So, it seems that the problem was the python version. For some reason 3.8.5 was giving this problem. I am sorry I cannot help more. I am here at the edge of my programming skills.

[rclUPC]

@mmcky I have still an update on this. My notebooks (and specially the one for Rheology which was failing in sectioning) were not working well with sympy 1.10.1, so I had to downgrade to sympy 1.7.1 (have a look here for details). Now I have realized that with sympy 1.7.1 sectioning of Rheology is not working again, but with sympy 1.10.1, notebooks are not working, but sectioning does. Perhaps you were right with the generation of some markdown generated that is interpreted by sphinx. I don't know.

[mmcky]

thanks for the updates @rclUPC -- does look like there are some interactions with sympy -- with generated output. I will try and take a closer look but my guess is that jupyter-book is treating some output as markdown for some reason.

[mmcky]

using sympy==1.9 I can getting the following execution error:

IndexError: tuple index out of range

so looks like some api changes in sympy? Once you get it building with sympy>=1.7.1 let me know if you still have toc issues.