Add test for ipynb as toctree

[chrisjsewell]

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[codecov]

Codecov Report

Merging #141 into master will not change coverage by %.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #141   +/-   ##
=======================================
  Coverage   83.85%   83.85%           
=======================================
  Files           9        9           
  Lines         805      805           
=======================================
  Hits          675      675           
  Misses        130      130           

Flag	Coverage Δ
#pytests	83.85% <100.00%> (ø)

Impacted Files	Coverage Δ
myst_nb/parser.py	91.15% <100.00%> (ø)

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[chrisjsewell]

@AakashGfude @mmcky In this PR I added a test for including a toctree in a notebook, and don't find any issues?

You need to modify this test to reproduce the issue you are having.
FYI, if you uncomment the following line, with a suitable path on your machine:

https://github.com/ExecutableBookProject/MyST-NB/blob/2cf7e6467eae1c64daf124d4020a29b1b47412da/tests/test_parser.py#L49

Then run pytest -k test_toctree_in_ipynb,
it will output the full test build there for you to look at (rather than in the default temporary directory)

[chrisjsewell]

The main thing here is that we need a minimal working example of the problem, to identify the issue

[mmcky]

@chrisjsewell here is a pretty minimal example

https://github.com/ExecutableBookProject/myst-nb.example-project/tree/minimal

It contains:

1. conf.py
2. 1 x document with a single markdown and code cell
3. 1 x index

Note: this will build. But the pdf contains no content and sphinx throws a warning that ar1_processes cannot be referenced.

[mmcky]

So the issue comes about when a notebook contains a code block. As soon as I delete the code cell from ar1_processes document in the above minimal example. The pdf will compile as expected without the sphinx warning that the ar1_processes document is missing.

[chrisjsewell]

From b541b73, this is only an issue for latex (and possibly other non-html) builds.
The initial doctrees are created correctly created, but for some reason other.doctree is not included in the build process in later phases, evidenced by the post-transform CellOutputsToNodes never being called on it.

[mmcky]

@chrisjsewell I suspect this will be an issue for:

1. texinfo
2. manpage
3. latex
4. singlehtml

not that we plan to support manpage and texinfo

It seems to be an issue with inlining the toctree elements with an exception being triggered during the recursive parsing when copying the toctree (#128 (comment)). As that fails I suspect the document doesn't progress to the next phase in sphinx

[mmcky]

Ok I think the offending line in docutils is:

obj = self.__class__(rawsource=self.rawsource, **self.attributes)

for error

*** TypeError: __init__() got multiple values for argument 'outputs'

when it tries to unpack **attributes there are two outputs in the method call as **attributes includes {'ids': [], 'classes': [], 'names': [], 'dupnames': [], 'backrefs': [], 'outputs': 0}

and the method has an outputs argument

class CellOutputBundleNode(nodes.container):
    """Represent a MimeBundle in the Sphinx AST, to be transformed later."""

    def __init__(self, outputs, rawsource="", *children, **attributes):
        self.outputs = outputs
        attributes["outputs"] = len(outputs)
        super().__init__("", **attributes)

[chrisjsewell]

Thanks @mmcky, this should be fixed in ebd9363

[chrisjsewell]

Here I now skip the creation of the CellOutputNode if the code cell has no outputs. @choldgraf any reason you can think of why this should not be done?

[choldgraf]

Nah that sounds like a good idea to me

[chrisjsewell]

👍

[mmcky]

perfect thanks @chrisjsewell just got the pdf building by changing the count variable name.