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

[Bill Barnard]

At the end of September, when I last had an opportunity to work on this,
I rewrote the Makefile for the Doc directory subtree. The gist of the
work was to properly call pdflatex, hevea, & hacha to build the pdfs,
htmls, & txt files from their .tex input files. I made a common.mk file
to abstract the common parts from the subdirectory makefiles.

I created a patch for the Doc/biopdb_faq.tex file, generated from
Doc/biopdb_faq.lyx, which contained an error from the perspective of the
doc-generating utilities.

I modified MANIFEST.in to include the new files, and to exclude the
files which will be subsequently generated by the make/build and hence
included in the distribution. I added a one line mod to setup.py to call
the Doc make [ os.system('make -C Doc') ].

I sent these changes to the mailing list
http://www.biopython.org/pipermail/biopython/2005-September/002777.html

Recently I retrieved updates from CVS and discovered a small change I
needed to make. Doc/Makefile did not correctly clean the dirs and
subdirs; I fixed that with a command line env target, e.g. "make
TARGET=clean". I also modified the top level Makefile which called make
clean for the Doc directory so it uses the new calling convention. (This
is probably irrelevant to the purpose of that makefile however.)

I also note that my patch attachments to my September emails were
cleaned by the mail list server. I will attach the patches and new
common.mk in a tarball to this email. These patches and files could be
applied and added to the current CVS tree as of 26-Jan-2006. Please feel
free to use any portion that seems useful.

Best,

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

p.s. In order that you see exactly which files I've touched I'm
including some details from my log files below

(The Updated files below are the ones currently checked into CVS and are
generated from the make; they could be removed from CVS.)

cvs-update.2006-01-26.log
#########################
? Doc/biopdb_faq.tex.hevea-html-fix.patch
? Doc/common.mk
M MANIFEST.in
M Makefile
M setup.py
M Doc/Makefile
U Doc/Tutorial.txt
U Doc/cookbook/LogisticRegression/LogisticRegression.html
U Doc/cookbook/LogisticRegression/LogisticRegression.pdf
U Doc/cookbook/LogisticRegression/LogisticRegression.txt
M Doc/cookbook/LogisticRegression/Makefile
M Doc/cookbook/biopython_test/Makefile
U Doc/cookbook/biopython_test/biopython_test.html
U Doc/cookbook/biopython_test/biopython_test.pdf
U Doc/cookbook/biopython_test/biopython_test.txt
M Doc/cookbook/genbank_to_fasta/Makefile
U Doc/cookbook/genbank_to_fasta/genbank_to_fasta.html
U Doc/cookbook/genbank_to_fasta/genbank_to_fasta.pdf
U Doc/cookbook/genbank_to_fasta/genbank_to_fasta.txt
U Doc/install/Installation.html
U Doc/install/Installation.pdf
U Doc/install/Installation.txt
M Doc/install/Makefile

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