MyST-NB
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executablebooks
Dollar math in markdown cells is incorrectly rendered
Describe the bug
context I am using MyST-NB to write some of the SciPy documentation pages in Markdown and execute them as notebooks.
When I use the {math} role for displaying math, everything works as expected. Using the dollarmath myst extension, however, results in \( syntax showing in the displayed html file, instead of the dollar signs. The generated .ipynb file correctly displays dollar signs for math.
I have experimented with
nb_render_markdown_format = "myst"
render_markdown_format = "myst"
but it doesn't change anything for this case.
expectation I expected math expressions to be correctly rendered as math in the html output.
bug
But instead I see the following output: (note, for example, \(F^{-1}\))
As I mentioned, the generated notebook is correct:
problem
This is a problem because I'd like the notebooks to be downloadable, and having dollar sign syntax instead of the {math} role syntax is more user-friendly in that case.
Reproduce the bug
- Write a jupytext markdown file with dollar math expressions
- Include it in a sphinx documentation set up with the myst_nb extension enabled
- Build the documentation site and look at the outputs.
I know this is not the best reproducible set up but I can point to a branch where I have this set up: https://github.com/scipy/scipy/pull/20303
And the corresponding output: https://output.circle-artifacts.com/output/job/f515f0f8-09d2-495c-a5bc-782826ff51e8/artifacts/0/html/tutorial/stats/sampling.html
List your environment
docutils 0.20.1 py311h38be061_3 conda-forge
jupytext 1.16.1 pyhd8ed1ab_0 conda-forge
myst-nb 1.0.0 pyhd8ed1ab_0 conda-forge
myst-parser 2.0.0 pyhd8ed1ab_0 conda-forge
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.3 pyhd8ed1ab_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
sphinx 7.2.6 pyhd8ed1ab_0 conda-forge
Full environment
List of packages in environment: "/home/melissa/micromamba/envs/scipy-dev"
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
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accessible-pygments 0.0.4 pyhd8ed1ab_0 conda-forge
alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
anyio 4.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py311h459d7ec_4 conda-forge
array-api-strict 1.1.1 pyhd8ed1ab_0 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
asv 0.6.3 py311hb755f60_0 conda-forge
asv_runner 0.2.1 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
backports.zoneinfo 0.2.1 py311h38be061_8 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
beniget 0.4.1 pyhd8ed1ab_0 conda-forge
binutils 2.40 hdd6e379_0 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
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c-compiler 1.7.0 hd590300_0 conda-forge
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ld_impl_linux-64 2.40 h41732ed_0 conda-forge
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xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
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zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
I believe me and @agriyakhetarpal have pinpointed this to the MathJax distribution being hardcoded in MyST-NB. Since SciPy (the target project for these changes) uses a custom MathJax package, MyST-NB does not find it and can't render the math nodes.
Would it be acceptable to propose a feature to customize the MathJax distribution used by MyST-NB?
Thanks!
It is to be noted that this issue, when a custom MathJax distribution is used, is fixed[^1] by adding the following line in conf.py:
myst_update_mathjax = False
I hope this is helpful towards isolating the cause of the bug and narrowing it down to a specific configuration value. We would be happy to make a contribution to MyST-NB by proposing this as a feature, as mentioned by @melissawm above.
xref: https://github.com/scipy/scipy/pull/20518
[^1]: This is as noted in https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#mathjax-and-math-parsing
