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

[Peter Cock]

(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