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

[Peter Cock]

Working from https://github.com/biopython/biopython/pull/4573
the PDF Tutorial from Sphinx is looking OK now. The title page
is specific to the PDF, and does not seem to have an equivalent
in the HTML output.

I can also tweak the copyright footer (HTML specific) as suggested.

So, I am thinking we'll build the PDF as part of future releases,
and include this in the source code zip/tar-ball releases.

Peter

On Fri, Jan 5, 2024 at 6:34 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> (We were talking about using ctrl+f or similar to search a single
> file Tutorial.html or Tutorial.pdf being very useful.)
>
> On Fri, Jan 5, 2024 at 3:26 PM Iddo Friedberg <idoerg at gmail.com> wrote:
> > On Fri, Jan 5, 2024 at 4:51 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >> On Thu, Jan 4, 2024 at 9:09 PM Iddo Friedberg <idoerg at gmail.com> wrote:
> >> > On Thu, Jan 4, 2024 at 2:44 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
> >> >> I too used to search it that way. Not sure how well Sphinx's search
> >> >> box works in comparison - but that was a benefit of the single HTML
> >> >> file vs multiple files.
> >> >
> >> > Or the HTML :)  Perhaps a one-page HTML document can be
> >> > generated from the RST pages? Or would there be an indexing
> >> > mechanism (less desirable).
> >>
> >> The multi-page HTML has a search function.
> >
> > It does, but it looks like it does not' limit itself to a specific document
> > subtree: looks like the search is not confined to the, say, cookbook &
> > tutorial only.
>
> Currently I integrated the two into a single Sphinx document. This
> will make some things easier like cross-referencing between the
> tutorial and API documentation.
>
> However, we could probably decouple them again if there was a
> compelling reason to do so. Certainly each is 400~500 pages as PDF,
> making a combined file nearly 1000 pages, which is a bit unwieldy.
>
> >> >> As to the authorship, that crossed my mind too. The Sphinx author
> >> >> field gets used in the footer so short and sweet as it stands seems
> >> >> fine: "© Copyright 1999-2024, The Biopython Contributors."
> >> >>
> >> >> Rather on this page between the title and the table of contents
> >> >> might work nicely? https://biopython.org/docs/dev/Tutorial/index.html
> >> >
> >> > Yes, I think a named author section would be nice there. And I'm not
> >> > jsut saying that becuase I'm on there ;) but also to preserve some
> >> > sense fo history.
> >>
> >> Grin.
>
> Added in https://github.com/biopython/biopython/pull/4573 - comments?
>
> >> > We might want to revise the copyright to CC-BY though?
> >>
> >> That would have been a good call in hindsight when we started the
> >> BSD dual licensing process.
> >>
> >> The tutorial is part of the main repository and thus under our
> >> Biopython specific license. We may be able to apply the BSD as
> >> well with all the history contributor agreements (I haven't checked).
> >
> > So we can write that the docs are also under the Dual Biopython /
> > BSD license, it's good enough, for most practical purposes (reuse
> > & accreditation).  The copyright without additions  implies no reuse
> > / redistribution.  But you can add instead "Copyright 1999-2024,
> > The Biopython Contributors, may be reused under the Biopython
> > License (linked)."
>
> Good point, we should look at tweaking the Sphinx footer to mention
> the license there.
>
> Peter