Double-check case sensitivity of anchor links

[jpfeuffer]

Because the case sensitivity might be different between RST and ipynb (stricter).

E.g. (Peptide identification section)[#peptideidentification] to (Peptide identification section)[#PeptideIdentification]

[timosachsenberg]

might need to be added to PR template

[jpfeuffer]

Or "mass-defect" vs "Mass-Defect"

[poshul]

These are all done except for wrap_classes, which was causing me issues.

[jpfeuffer]

What do you mean? Can you post an example reference to the problematic link(s)?

[jpfeuffer]

And thanks!

[poshul]

for example the links to simpleexample and complex example on line 62 don't work in Jupyter. I was still fighting with the syntax to get them to work on Friday, but haven't had a chance to finish up that work, and likely wont in the next couple of days.

[jpfeuffer]

Ah I see. Those are special RST style links SimpleExample_. They point to an additional HTML span element created with e.g. .. _SimpleExample.
I don't think this (empty) span is converted into markdown of the ipynb.
It is probably better if we use "normal" links to headers that are always present:

`simple example <#A-simple-example>`_

or something like this.

[tapaswenipathak]

@greengypsy: can you check if there is existing documentation for this? If not, add and close?

[matteopilz]

The class & function references are also not working now, how should we do this?

[jpfeuffer]

You mean in ipynb? It never worked. ipynb has no knowledge about the API documentation. We could only link back to the readthedocs page. Could be done with another custom pandoc "plugin" that looks for :py:class: roles during conversion and treats them specially.

[matteopilz]

Yes, in ipynb. It probably wasn't mentioned before, because we only had a few of them. I will look into pandoc and try to find out if we can write a conversion script / plugin.

[jpfeuffer]

Here is a filter with which we change the links:
https://github.com/OpenMS/pyopenms-docs/blob/master/docs/pandoc_filters/transformlinks_pandocfilter.py