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neurolibre / template

Template repository for NeuroLibre preprint submissions.
GNU General Public License v3.0
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error jb build #1

Open pbellec opened 2 years ago

pbellec commented 2 years ago

I tried to compile the book with a recent jupyter book and got the following error message:

The Table of Contents file is malformed: toc is not a mapping: <class 'list'>
You may need to migrate from the old format, using:

    jupyter-book toc migrate /home/pbellec/git/high_confidence_ad/content/_toc.yml -o /home/pbellec/git/high_confidence_ad/content/_toc.yml
pbellec commented 2 years ago

after applying the suggested fix I still get a bunch of errors: 

/home/pbellec/git/high_confidence_ad/content/00-simple_markdown.md:1: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
/home/pbellec/git/high_confidence_ad/content/00-simple_markdown.md:8: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
/home/pbellec/git/high_confidence_ad/content/00-simple_markdown.md:: WARNING: toctree contains reference to nonexisting document '02-simple_myst' [etoc.ref]
WARNING: Execution Failed with traceback saved in /home/pbellec/git/high_confidence_ad/content/_build/html/reports/01-simple_notebook.log
/home/pbellec/git/high_confidence_ad/content/01-simple_notebook.ipynb:10002: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
/home/pbellec/git/high_confidence_ad/content/01-simple_notebook.ipynb:30002: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
WARNING: Execution Failed with traceback saved in /home/pbellec/git/high_confidence_ad/content/_build/html/reports/02-simple-myst.log
/home/pbellec/git/high_confidence_ad/content/02-simple-myst.md:12: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
/home/pbellec/git/high_confidence_ad/content/02-simple-myst.md:18: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
/home/pbellec/git/high_confidence_ad/content/02-simple-myst.md:39: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
mathieuboudreau commented 2 years ago

My book was built with Jupyter Book 10.0 and my Dockerfile froze the book at that version.

Newer versions of Jupyter Book use a different Table of Contents format.

mathieuboudreau commented 2 years ago

Ooops I just noticed this is not in the PR for my book. Still, the comment might apply; if the Jupyter Book version isn't frozen, the ever-continuing changes in their new versions might break the build (e.g. changes in the Table of Contents format)