Rendering of math blocks in generated notebooks doesn't display tech

[ChrisRackauckas]

Example: https://github.com/JuliaDiffEq/DiffEqTutorials.jl/blob/master/notebook/introduction/ode_introduction.ipynb . Jupyter seems to treat that as a markdown block.

[mpastell]

This is due to Jupyter using different markdown variant than Weave. In this case the easiest fix is to use $$ for math blocks instead of ````math .

You could also use pandoc2* formats instead of md2* if you need a closer match between weave output and notebooks.

[ChrisRackauckas]

So the fix is on my end to change to using pandoc2* commands? I can go ahead with that, but wanted to double check before editing all of the jmds.

[mpastell]

Can't you can use $$ in both md2html and notebook output? i.e does the below work?

$$\frac{dx}{dt} &= \sigma (y - x)\\
\frac{dy}{dt} &= x (\rho - z) -y\\
\frac{dz}{dt} &= xy - \beta z$$

I personally prefer to use md2* formats so I don't need to use pandoc (you may encounter some new bugs), but if you need features from pandoc that julia markdown doesn't have then it's best to switch the format.

[mpastell]

There seems to be a problem with Weave writer adding \begin{align} to math blocks (see: #142) . Probably that wasn't the best design choice as it makes the documents incompatible with Jupyter now...

I think it might be to remove that feature, but it will break documents that rely on that...

[ChrisRackauckas]

For the notebooks to render correctly, they need to be like:

$$
\begin{align}
\frac{dx}{dt} &= \sigma (y - x)\\
\frac{dy}{dt} &= x (\rho - z) -y\\
\frac{dz}{dt} &= xy - \beta z
\end{align}
$$

Note the newline before the $$. This isn't compatible with the other formats, since we cannot write align in there since it will double up, but also because of the newline handling on the $$ breaks the other formats IIRC. I think you should just leave it up to the user to handle the align command.

[mpastell]

I'll remove the align from output for now. I also think I should be able to extend the Julia markdown parser to handle $$ with newlines, but it may take some time.

FYI: math rendering without the newlines before and after $$ works in Jupyterlab.

[mpastell]

I just remembered why align is added by default: it seemed like the best option to output math that works in both Mathjax and Latex.

@ChrisRackauckas do you have a good suggestion how to ouput math in Latex instead of using aligned? by default (=after removing current weave output formatting) this markdown:

$$\begin{align} \frac{dx}{dt} &= \sigma (y - x)\\\ \frac{dy}{dt} &= x (\rho - z) -y\\\ \frac{dz}{dt} &= xy - \beta z \end{align}$$

becomes the following in tex:

$$\begin{align}
\frac{dx}{dt} &= \sigma (y - x)\\
\frac{dy}{dt} &= x (\rho - z) -y\\
\frac{dz}{dt} &= xy - \beta z
\end{align}$$

Which then gives the following error when running xelatex:

! Package amsmath Error: Erroneous nesting of equation structures;
(amsmath)                trying to recover with `aligned'.

I'm having a hard time coming up with a good fix that would work well.

[ChrisRackauckas]

I'm not sure, I think it needs to not output the $$ when it sees aligns.

[mpastell]

This is probably the best option, to check for align, equation etc. I will not probably remember all that people want to use, but new special cases will be easy to add.

[mpastell]

I ended up extending the markdown parser so that this now also works with Weave:

$$
\begin{align}
\frac{dx}{dt} &= \sigma (y - x)\\
\frac{dy}{dt} &= x (\rho - z) -y\\
\frac{dz}{dt} &= xy - \beta z
\end{align}
$$