[BioPython] Patches to enable Doc building for source and rpm distributions

[Bill Barnard]

I've got some time free to work with Biopython again. I wanted to be
able to easily create an rpm including the Doc directory. I found that
the Makefile in the Doc directory didn't work quite correctly, so I set
out to remedy that.

My set of changes are small, and you may not want to commit all of them.
In particular I added two lines to setup.py to run make in the Doc
directory. There may be some better way to accomplish that task, but I
don't know distutils very well so I'm not a good judge. Also these are
only "needed" to enable the addition of the doc files in the rpm
generated by setup.py bdist_rpm.

I found that generating the pdf & html doc files to be straightforward
except for two things:

1) the hevea.sty file needs to be included in the distribution to allow
the make to complete; that's simply added in the MANIFEST.in file.

2) Generating html from biopdb_faq.tex has a minor failure (resulting in
a missing image file referenced in the html) due to lack of bounding box
information in the .tex file. Since the .tex file is exported (I assume)
from the .lyx file, I thought the "problem" should be fixed there. I did
not figure it out, and didn't want to learn too much more about LyX in
order to do so. Instead I created a patch file for the .tex file that
permits proper html generation by hevea. The patch is applied in the
Makefile.

The Makefile is actually entirely new. The old Makefile didn't have much
in it, and was not very generic. The new one is a bit cleaner and more
generic.

I'm attaching the two patch files to this email. I'll see when it comes
back to me whether anything in my email chain has stripped the patch
files from the email.

I hope this is useful. If it is, then I may visit the subdirectories of
Doc to structure their Makefiles similarly, and set them up to be called
recursively.

Cheers,

Bill
-- 
Bill Barnard <bill at barnard-engineering.com>
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