* pin docutils < 0.18 (https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/322)

* Prep for v0.15.1

* rework, issue warning rather than force version pin on docutils

* only test html if no warnings

* doc: add entry for citations page

* update changelog

This PR updates `jupyter-book` to enable `myst-nb~=0.17.1` and `sphinx5` support. It also includes new versions of `sphinx-design`, `sphinx-thebe`, and `sphinx-book-theme`

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update version pins for sphinx4 upgrade

* upgrade jupytext to support markdown-it-py required by myst-parser

* update sphinx-book-theme

* upgrade sphinx-jupyterbook-latex to 0.4.3

* remove html_add_permalink as deprecated in sphinx>=3.5

* fix test_build test set

* fix test_sphinx_multitoc_numbering tests with sphinx3,sphinx4

* fix test_tocdirective tests to include sphinx3,sphinx4 fixtures

* mathjax3 is now the default so config needs to use mathjax3_config

* add warning for sphinx>=4 and _config using mathjax_config

* remove myst_url_schemes from default config as set in myst_parser

* Update setup.cfg

include `nb_merge_sreams` in `myst-nb~=0.13.1`

Co-authored-by: Chris Sewell <chrisj_sewell@hotmail.com>

* Revert "add warning for sphinx>=4 and _config using mathjax_config"

This reverts commit 3f9bf18409cf4140dc6c85d882b5286b82ec41be.

* Revert "Revert "add warning for sphinx>=4 and _config using mathjax_config""

This reverts commit d1d74bc5d6c2e59467eae9ddc4bd6c93b5c1acd2.

* Update with warning for mathjax config in sphinxv4 including tests

* change to report stderr to be more useful

* enable tasklist as a myst_enable_extensions default option:

* enable myst_dmath_double_inline=True as a default to mirror jupyter notebook

* TEST: add a test for additional config passthrough

* docs: add section on nb_merge_streams from myst_nb

* Update jupyter_book/config.py

Co-authored-by: Chris Holdgraf <choldgraf@berkeley.edu>

* migrate to intersphinx

* move merge-stdout-stderr to execute docs page

* revert fb180ad and leave myst_url_schemes as a configuration option for jb

* add myst_dmath_double_inline to schema and update test

* add a github issue to remind us to remove this in 0.14

Co-authored-by: Chris Sewell <chrisj_sewell@hotmail.com>
Co-authored-by: Chris Holdgraf <choldgraf@berkeley.edu>

* Update jupyterbook-latex to sphinx-jupyterbook-latex

* docs: update

Co-authored-by: AakashGC <aakashguptachoudhury@gmail.com>

This commit removes all code related to the `_toc.yml`,
which is now implemented in https://github.com/executablebooks/sphinx-external-toc.
This implementation adds a range of new features, including:

- `glob` to specify multiple files with unix-style wildcard
- `toctree` options: `caption`, `hidden`, `maxdepth`, `numbered`, `titlesonly`
- The `toctree` are now added directly to the docutils/sphinx AST
  (rather than appending to the source text),
  which means that its is source format agnostic, i.e. will work for rst, md, ipynb, py, ...
- The `tableofcontents` directive is also handled at the same time as the `toctree` insertion,
  rather than later in a post-transform,
  which avoids having to use any builder specific logic.
- The `jupyter-book toc` CLI is now a plugin of the sphinx-external-toc CLI, and is split into multiple commands
  - The new `jupyter-book toc to-site` command allows a template project to be generated directly from a `toc.yml`

The format of the `_toc.yml` has been changed slightly.
To aide users, the code in `jupyter-book build` will check the format is as expected before calling sphinx,
and point users to the new `jupyter-book toc migrate` command.

This also involved updating `jupyterbook-latex` to `v0.3.0`,
and removes the `nested-lookup` dependency.

Co-authored-by: AakashGC <aakashguptachoudhury@gmail.com>

This PR brings improvements to `PDF` builds via `LaTeX` by incorporating the
[jupyterbook-latex](https://github.com/executablebooks/jupyterbook-latex

) extension.

This initial release:

1. harmonises the document structure for `html` and `latex` outputs, by implementing support for `part`/`chapter` structures in the `_toc.yml` for PDF via LaTeX,
2. brings support for the jupyter-book directive `tableofcontents` to PDF via LaTeX, and
3. adds support for commonly used tags on `code-cell` directives (such as `hide-cell`) to PDF via LaTeX

Co-authored-by: mmcky <mamckay@gmail.com>
Co-authored-by: mmcky <mmcky@users.noreply.github.com>

* suppressing resolve_any_xref issue

* modified fixture files

This commit adds support to build individual `pdf` files for each source document (.md etc) using the generic sphinx `pdflatex` builder. It can be enabled for `builder=pdflatex` using the `cli` option `--individualpages`, for example:

```bash
jb build <project> --builder=pdflatex --individualpages
```

A use case is for lecture sets, where each file is an independent lecture,
and also to support downloadable PDFs for websites. 

Individual `pdf` files can be specified manually in `sphinx` configuration through the [latex_documents](https://www.sphinx-doc.org/en/3.x/usage/configuration.html#confval-latex_documents) tuple configuration. 
This commmit implements an auto-builder that collects the source files and titles and updates the `latex_documents` tuple when calling `sphinx_build`

An example for [myst-nb.example_project](https://github.com/executablebooks/myst-nb.example-project/pull/8/files

) shows how these tuples can be constructed. 

Co-authored-by: Chris Sewell <chrisj_sewell@hotmail.com>

Otherwise the margin directive is not available for LaTeX builds

The sphinx-panels sphinx extension has been added to the base jupyter-book distribution, and its use documented.

Some other minor documetation updates have also been applied

The generation of sphinx config has been consolidated into a single entry point: `jupyter_book.config:get_final_config`, where before it was spread over yaml.py and sphinx.py, making it difficult to determine what the finaly configuration would be.

This now allows for proper testing of the configuration generation, added in tests/test_config.py, which also clarified some bugs identified in #915. These have now been fixed.

Finally this has also allowed for the addition of a `jb config sphinx` command, which generates the a Sphinx conf.py representation of the build configuration.
This should help advanced users/maintainers to understand/debug builds.