ports/171115: [Update]biology/py-biopython:update to 1.60

[Mauricio Herrera Cuadra]

The patch is still wonky, please review the output:

[root at freebsd9-vm] /usr/ports/biology/py-biopython # patch < biopython-1.60.diff.txt 
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|Index: Makefile
|===================================================================
|--- Makefile    (revision 304395)
|+++ Makefile    (working copy)
--------------------------
Patching file Makefile using Plan A...
Hunk #1 failed at 1.
1 out of 1 hunks failed--saving rejects to Makefile.rej
Hmm...  The next patch looks like a unified diff to me...
The text leading up to this was:
--------------------------
|Index: pkg-descr
|===================================================================
|--- pkg-descr    (revision 304395)
|+++ pkg-descr    (working copy)
--------------------------
Patching file pkg-descr using Plan A...
Hunk #1 succeeded at 12.
Hmm...  The next patch looks like a unified diff to me...
The text leading up to this was:
--------------------------
|Index: distinfo
|===================================================================
|--- distinfo    (revision 304395)
|+++ distinfo    (working copy)
--------------------------
Patching file distinfo using Plan A...
Hunk #1 succeeded at 1.
Hmm...  The next patch looks like a unified diff to me...
The text leading up to this was:
--------------------------
|Index: pkg-plist
|===================================================================
|--- pkg-plist    (revision 304395)
|+++ pkg-plist    (working copy)
--------------------------
Patching file pkg-plist using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 103.
Hunk #3 succeeded at 358.
Hunk #4 succeeded at 451.
Hunk #5 succeeded at 482.
Hunk #6 succeeded at 509.
Hunk #7 succeeded at 570.
Hunk #8 succeeded at 658.
Hunk #9 succeeded at 686.
Hunk #10 succeeded at 707.
Hunk #11 succeeded at 861.
Hunk #12 succeeded at 1017.
Hunk #13 succeeded at 1033.
Hunk #14 succeeded at 1055.
done


[root at freebsd9-vm] /usr/ports/biology/py-biopython # cat Makefile.rej 
***************
*** 1,29 ****
- # New ports collection makefile for:    py-biopython
- # Date created:        28 July 2000
- # Whom:            Johann Visagie <johann at egenetics.com>
- #
  # $FreeBSD$
- #
  
  PORTNAME=    biopython
- PORTVERSION=    1.59
  CATEGORIES=    biology python
  MASTER_SITES=    http://www.biopython.org/DIST/
  PKGNAMEPREFIX=    ${PYTHON_PKGNAMEPREFIX}
  
  MAINTAINER=    mauricio at arareko.net
- COMMENT=    A collection of Python modules for bioinformatics
  
  BUILD_DEPENDS=    ${PYNUMPY}
  RUN_DEPENDS=    ${PYNUMPY}
  
- USE_PYTHON=        2.5-2.7
  USE_PYDISTUTILS=    easy_install
  PYEASYINSTALL_ARCHDEP=    yes
  
  .if !defined(WITHOUT_REPORTLAB)
- BUILD_DEPENDS+=    ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
- RUN_DEPENDS+=    ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
  .endif
  
  .include <bsd.port.mk>
--- 1,23 ----
  # $FreeBSD$
  
  PORTNAME=    biopython
+ PORTVERSION=    1.60
  CATEGORIES=    biology python
  MASTER_SITES=    http://www.biopython.org/DIST/
  PKGNAMEPREFIX=    ${PYTHON_PKGNAMEPREFIX}
  
  MAINTAINER=    mauricio at arareko.net
+ COMMENT=    Collection of Python modules for bioinformatics
  
  BUILD_DEPENDS=    ${PYNUMPY}
  RUN_DEPENDS=    ${PYNUMPY}
  
+ USE_PYTHON=        -2.7
  USE_PYDISTUTILS=    easy_install
  PYEASYINSTALL_ARCHDEP=    yes
  
  .if !defined(WITHOUT_REPORTLAB)
+ RUN_DEPENDS+=    ${PYTHON_PKGNAMEPREFIX}reportlab>0:${PORTSDIR}/print/py-reportlab
  .endif
  
  .include <bsd.port.mk>





________________________________
 From: "rm at FreeBSD.org" <rm at FreeBSD.org>
To: mauricio at arareko.net; rm at FreeBSD.org; freebsd-python at FreeBSD.org; rm at FreeBSD.org 
Sent: Monday, September 17, 2012 7:30 AM
Subject: Re: ports/171115: [Update]biology/py-biopython:update to 1.60
 
Synopsis: [Update]biology/py-biopython:update to 1.60

Responsible-Changed-From-To: freebsd-python->rm
Responsible-Changed-By: rm
Responsible-Changed-When: Mon Sep 17 12:30:45 UTC 2012
Responsible-Changed-Why: 
Take. Hi Mauricio. Here is 'assembled' patch (that was mangled by gnats)
from Wen plus some of my changes: 1. trim Makefile header 2. remove
undefined article from COMMENT 3. change USE_PYTHON to just -2.7 4.
remove reportlab from BUILD_DEPENDS 5. remove deprecated Authors: field
from pkg-descr 6. tab -> space change in pkg-descr:WWW. Here is the
patch: http://people.freebsd.org/~rm/biopython-1.60.diff.txt and here is
the buildlog: http://people.freebsd.org/~rm/py27-biopython-1.60.log.
Would you approve?

http://www.freebsd.org/cgi/query-pr.cgi?pr=171115