- Update to version 0.8, as distributed with Biopython 1.00a4

- This port now installs Martel from the Biopython distribution

textproc/py-martel/Makefile

@@ -6,13 +6,13 @@
 #
 
 PORTNAME=	martel
-PORTVERSION=	0.6
+PORTVERSION=	0.8
 PORTEPOCH=	1
 CATEGORIES=	textproc biology python
-MASTER_SITES=	${MASTER_SITE_LOCAL}
+MASTER_SITES=	http://www.biopython.org/Download/
 MASTER_SITE_SUBDIR=	wjv
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-DISTNAME=	Martel-${PORTVERSION}
+DISTNAME=	biopython-${BIOPYTHON_VERSION}
 
 MAINTAINER=	wjv@FreeBSD.org
 
@@ -20,9 +20,9 @@ BUILD_DEPENDS=	${PYDISTUTILS}
 RUN_DEPENDS=	${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
 
 USE_PYTHON=	yes
-USE_BZIP2=	yes
+WRKSRC=		${WRKDIR}/${DISTNAME}/Martel
+BIOPYTHON_VERSION=	1.00a4
 PYTHON_SETUP=	${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py
-EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
 
 do-build:
 	@ cd ${WRKSRC} && ${PYTHON_SETUP} build
@@ -33,14 +33,4 @@ pre-install:
 do-install:
 	@ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX}
 
-post-install:
-.if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCSDIR}
-.for docfile in README HISTORY doc/*
-	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
-.endfor
-	@ ${MKDIR} ${EXAMPLESDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/examples/* ${EXAMPLESDIR}
-.endif
-
 .include <bsd.port.mk>

textproc/py-martel/distinfo

@@ -1 +1 @@
-MD5 (Martel-0.6.tar.bz2) = f7d720ff6169c75a588ea4e8e2a8542b
+MD5 (biopython-1.00a4.tar.gz) = bca77b4242c9a8495f60c7475b884c5d

textproc/py-martel/files/patch-Generate.py

@@ -1,18 +0,0 @@
-From: "Andrew Dalke" <dalke@acm.org>
-To: <biopython-dev@biopython.org>
-Date: Tue, 16 Jan 2001 18:57:23 -0700
-
-There's a small bug with the debug_level = 2 option
-in Martel.  When the debug position is within the
-first 8 characters it does not show the match text.
-
---- Generate.py.orig	Fri Jan 19 14:50:01 2001
-+++ Generate.py	Fri Jan 19 14:50:06 2001
-@@ -460,7 +460,7 @@
-             s = s[:17] + " ... " + s[-17:]
-         self.msg = s
-     def __call__(self, text, x, end):
--        print "Match %s (x=%d): %s" % (repr(text[x-8:x+8]), x,
-+        print "Match %s (x=%d): %s" % (repr(text[max(0, x-8):x+8]), x,
-                                             repr(self.msg))
-         return x

textproc/py-martel/pkg-plist

@@ -1,11 +1,3 @@
-%%PORTDOCS%%share/doc/martel/HISTORY
-%%PORTDOCS%%share/doc/martel/README
-%%PORTDOCS%%share/doc/martel/intro.txt
-%%PORTDOCS%%share/doc/martel/tech_description.txt
-%%PORTDOCS%%share/doc/martel/writing_a_format.txt
-%%PORTDOCS%%share/examples/martel/sample.comma
-%%PORTDOCS%%share/examples/martel/sample.swissprot
-%%PORTDOCS%%share/examples/martel/sample.tab
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Expression.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Expression.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Expression.pyo
@@ -15,12 +7,18 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/Generate.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Iterator.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Iterator.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Iterator.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/LAX.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/LAX.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/LAX.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Parser.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Parser.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/Parser.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/RecordReader.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/RecordReader.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/RecordReader.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/Time.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/Time.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/Time.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/__init__.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/__init__.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/__init__.pyo
@@ -37,5 +35,3 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/optimize.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/optimize.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/optimize.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel
-%%PORTDOCS%%@dirrm share/examples/martel
-%%PORTDOCS%%@dirrm share/doc/martel