Bioperl-guts: 'releaseable system', Makefile.PL issues and documentation

Chris Dagdigian dag@genetics.com
Wed, 23 Sep 1998 11:59:52 -0400


I agree with Ewan...at this point we are really close to
having a 'buildable' distribution off the source tree.

The current main hangup is a functional/robust Makefile.PL
script. I placed my skeletal (ie non-functional) Makefile.PL in
the CVS tree so that others could work on it.

The current script does an inplace edit on
PreSeq.pm and Seq.pm to uncomment "#__END__"
which is necessary for the autoloading
mechanism to work. Of course it now
bombs out with this error:

==================================
[dag@bioperl Bio]$ perl Makefile.PL 
Bioperl module installation
Preparing modules for AUTOLOADing...done.
Checking if your kit is complete...
Looks good
Writing Makefile for Bio
[dag@bioperl Bio]$ make
mkdir ./blib
mkdir ./blib/lib
mkdir ./blib/arch
mkdir ./blib/arch/auto
mkdir ./blib/arch/auto/Bio
mkdir ./blib/lib/auto
mkdir ./blib/lib/auto/Bio
mkdir ./blib/man3
cp SimpleAlign.pm ./blib/lib/SimpleAlign.pm
cp PreSeq.pm ./blib/lib/PreSeq.pm
Package Bio::PreSeq (Bio/PreSeq.pm) does not match filename ./blib/lib/PreSeq.pm at 
/usr/lib/perl5/AutoSplit.pm line 200, <IN> chunk 3631.
make: *** [pm_to_blib] Error 255
[dag@bioperl Bio]$ 
========================================================


The current Makefile.PL also does nothing with
the XS C extensions. I'm wondering what
the Makefile.PL behavior should be...should
it ask the user if the C extensions should
be compiled?

Something like:
====================
%[dag@bioperl Bio]$ perl Makefile.PL 
%Bioperl module installation
%Preparing modules for AUTOLOADing...done.
%Checking if your kit is complete...
%Looks good
%
%  **Some bioperl modules require compiled C extensions,
%  do you wish to compile them at this time? (y/n) [y]
=====================

If we make the README or INSTALL file clear enough I don't
have a problem with having end users invoke a separate
Makefile.PL for the C stuff. That may be an easier solution.


What do people think?


Documentation structure
========================
I'd like to propose the following files:

README    - text file, basic info

INSTALL   - textfile, usual install instructions

DOC-INDEX.pod   - podfile with L<> links to all the other
                 pod2html module translations, useful for
                 web-based documentation
                 
USAGE.pod - podfile, the "cookbook" file that shows
            usage along with example. Can be written
            and edited as USAGE.txt and then one of
            us can POD format it prior to release.
            
                        

  
  

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