Files not included in TOC tree with .rst files are used as index / header

Describe the bug Hi all, I am building a jupyter-book but some of my files are not included in the toc tree.

To Reproduce Steps to reproduce the behavior:

1. Go to ‘https://github.com/lhoupert/from-python-to-numpy/tree/jb-version’, clone the directory and cd jb-version
2. Build the jupyter-book jupyter-book build .

Expected behavior

My _toc.yml file is:

- file: 00-book

- header: Get started
- file: 01-preface
- file: 02-introduction
- file: 03-anatomy

- header: Vectorization
- file: 04-code-vectorization
- file: 05-problem-vectorization
- file: 06-custom-vectorization
- file: 07-beyond-numpy

- header: Conclusion
- file: 08-conclusion

- header: References
- file: 09-quick-reference
- file: 10-bibliography

but when the html is built a few sections are missing:

You can see the whole website here

This is consistent with the warnings I got when building the website:

/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/00-book.rst:81: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/00-book.rst:91: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/00-book.rst:110: WARNING: Explicit markup ends without a blank line; unexpected unindent.

checking consistency... /Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/02-introduction.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/03-anatomy.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/05-problem-vectorization.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/06-custom-vectorization.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/07-beyond-numpy.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_useful/from-python-to-numpy/jb-version/10-bibliography.rst: WARNING: document isn't included in any toctree

Interestingly, when I didnt put any header entries in the _toc.yml file, the html rendering only display the first two from my TOC.

You will also notice something strange happening on the first page of the website, the name of the files which were not included in the toc are listed:

Another problem with the warning errors below. They don’t make sense as my file 00-book.rst has only 74 lines…

from-python-to-numpy/jb-version/00-book.rst:81: WARNING: Explicit markup ends without a blank line; unexpected unindent.
from-python-to-numpy/jb-version/00-book.rst:91: WARNING: Explicit markup ends without a blank line; unexpected unindent.
from-python-to-numpy/jb-version/00-book.rst:110: WARNING: Explicit markup ends without a blank line; unexpected unindent.

Thank you for the help! Environment (please complete the following information):

• Python Version [Python 3.7.4]
• Output of Jupyter Book: 0.7.1

Additional context Add any other context about the problem here.

[lhoupert]

It seems that it is fixed now! thanks to https://github.com/executablebooks/jupyter-book/pull/1293 .

The only thing I add to do was to migrate my pre-existing toc to the new format (I just had to follow the instructions in my terminal after trying to build with the last version of master).

[lhoupert]

Thank you @AakashGfude for having a look. I updated a minimal example here: https://github.com/lhoupert/jupyter-book/tree/test-rst-toc/tests/books/toc/test_rst

The _toc.yml file is:

- file: content0

- part: Part1
  chapters:
  - file: content3
  - file: content3a

- part: Part2
  chapters:
  - file: content3b
  - file: content3c
  - file: content3d

When running jupyter-build in this directory. I don’t have the warning WARNING: Explicit markup ends without a blank line; unexpected unindent but I got these error messages:

checking consistency... /Users/locupe/Dropbox/Work/Python/Repos_fork/jupyter-book/tests/books/toc/test_rst/content3a.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_fork/jupyter-book/tests/books/toc/test_rst/content3c.rst: WARNING: document isn't included in any toctree
/Users/locupe/Dropbox/Work/Python/Repos_fork/jupyter-book/tests/books/toc/test_rst/content3d.rst: WARNING: document isn't included in any toctree