Re: [Biopython] Biopython Tutorial no longer written in LaTeX, but RST

This particular glitch has now been fixed by Wil Tyler in this pull request:

https://github.com/biopython/biopython/pull/4582

Thank you,

Peter

On Thu, Jan 4, 2024 at 10:07 AM Peter Cock <[email protected]> wrote:
>
> As an example, consider this page:
>
> https://biopython.org/docs/dev/Tutorial/chapter_seq_objects.html
>
> The "Edit on GitHub" link takes you to the source page is here:
>
> https://github.com/biopython/biopython/blob/master/Doc/Tutorial/chapter_seq_objects.rst
>
> Note the section links (HTML anchor names) are more friendly now, consider:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial-1.82.html#sec24
>
> vs:
>
> https://biopython.org/docs/dev/Tutorial/chapter_seq_objects.html#transcription
>
> This is an example which still needs tweaking following the conversion.
> The original approach of using a LaTeX table with vertical arrows and
> centered alignment is probably not going to work as nicely in RST.
> Perhaps a figure is better here instead?
>
> Peter
>
> On Thu, Jan 4, 2024 at 10:04 AM Peter Cock <[email protected]> wrote:
> >
> > Hello all,
> >
> > It has taken years, and efforts at several of the BOSC CoFest meetings,
> > but finally the changes to convert the Biopython Tutorial and Cookbook
> > from LaTeX into reStructuredText (RST) are live:
> >
> > https://biopython.org/docs/dev/
> >
> > We had previously standardized all the in-code documentation using
> > Python's docstring system into RST and switched from the obsolete
> > epydoc tool to using Sphinx for for the API documentation:
> >
> > https://biopython.org/docs/dev/api/
> >
> > This change means Sphinx is now also used to build the Tutorial and
> > Cookbook at the same time, giving consistent HTML output. We can
> > in theory also output this in PDF or eBook formats (not done yet).
> >
> > The RST markup language is similar to Markdown, but slightly more
> > powerful for larger documents, and was developed within the Python
> > ecosystem. This change means new contributors won't need to learn
> > LaTeX, but also we don't need the LaTeX tools installed to build the
> > documentation - something which was a barrier to doing this as part
> > of the continuous integration testing.
> >
> > At the time of writing the old URLs do not yet redirect:
> >
> > http://biopython.org/DIST/docs/tutorial/Tutorial.html
> > http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
> >
> > We will keep the historic versions as there are, e.g.
> >
> > http://biopython.org/DIST/docs/tutorial/Tutorial-1.82.html
> > http://biopython.org/DIST/docs/tutorial/Tutorial-1.82.pdf
> >
> > I would encourage all of you to proof read your favorite sections
> > on the new Sphinx output, and if you spot a typo there is an
> > "Edit on GitHub" link top right of each page... many eyes make
> > light work?
> >
> > Thanks all,
> >
> > Peter
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