Upgrade to 0.5

PR: 24184
Submitted by: MAINTAINER

4 files changed, 106 insertions, 17 deletions

diff --git a/textproc/py-martel/Makefile b/textproc/py-martel/Makefile
index 8c3fbb8a669..496998d884c 100644
--- a/textproc/py-martel/Makefile
+++ b/textproc/py-martel/Makefile
@@ -6,42 +6,49 @@
 #
 
 PORTNAME=	martel
-PORTVERSION=	0.4
-PORTREVISION=	1
+PORTVERSION=	0.5
 PORTEPOCH=	1
 CATEGORIES=	textproc biology python
 MASTER_SITES=	http://www.biopython.org/~dalke/Martel/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-DISTNAME=	Martel-0.4
+DISTNAME=	Martel-${PORTVERSION}
 
 MAINTAINER=	johann@egenetics.com
 
 RUN_DEPENDS=	${PYTHON_SITELIBDIR}/TextTools/__init__.py:${PORTSDIR}/textproc/py-mxTextTools
 
 PYTHON_VERSION=	python2.0
+PLIST=		${WRKDIR}/PLIST
+PKG_PLIST=	${PKGDIR}/pkg-plist
 
 MARTEL_DIR=	${PYTHON_SITELIBDIR}/Martel
-MARTEL_EXAMPLEDIR=${PREFIX}/share/examples/martel
+MARTEL_EGDIR=	${PREFIX}/share/examples/martel
 MARTEL_DOCDIR=	${PREFIX}/share/doc/martel
+MARTEL_DOCS=	README HISTORY doc/intro.txt doc/tech_description.txt \
+		doc/writing_a_format.txt
 
 do-build:
 	@ ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${WRKSRC}
 	@ ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${WRKSRC}
 
-do-install:
-	@ ${MKDIR} ${MARTEL_DIR}
-	@ (cd ${WRKSRC} && find *.py *.pyc *.pyo formats test \
-	  | cpio --quiet -pdum -R ${BINOWN}:${BINGRP} ${MARTEL_DIR})
-	@ ${MKDIR} ${MARTEL_EXAMPLEDIR}/builders
-	@ ${INSTALL_DATA} ${WRKSRC}/examples/* ${MARTEL_EXAMPLEDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/builders/* ${MARTEL_EXAMPLEDIR}/builders
-
-post-install:
+pre-install:
+	@ ${CAT} ${PKG_PLIST} > ${PLIST}
 .if !defined(NOPORTDOCS)
 	@ ${MKDIR} ${MARTEL_DOCDIR}
-.for docfile in README HISTORY doc/*
-	@ ${INSTALL_MAN} ${WRKSRC}/${docfile} ${MARTEL_DOCDIR}
+.for docfile in ${MARTEL_DOCS}
+	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${MARTEL_DOCDIR}/ && \
+	  ${ECHO} ${MARTEL_DOCDIR:S|^${PREFIX}/||}/${docfile:S|^doc/||} \
+	  >> ${PLIST}
 .endfor
+	@ ${ECHO} @dirrm ${MARTEL_DOCDIR:S|^${PREFIX}/||} >> ${PLIST}
 .endif
 
+do-install:
+	@ ${MKDIR} ${MARTEL_DIR}
+	@ (cd ${WRKSRC} && find *.py *.pyc *.pyo formats test \
+	  | cpio --quiet -pdum -R ${BINOWN}:${BINGRP} ${MARTEL_DIR})
+	@ ${MKDIR} ${MARTEL_EGDIR}/builders
+	@ ${INSTALL_DATA} ${WRKSRC}/examples/* ${MARTEL_EGDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/builders/* ${MARTEL_EGDIR}/builders
+
 .include <bsd.port.mk>
diff --git a/textproc/py-martel/distinfo b/textproc/py-martel/distinfo
index 726f84441c8..01b4d1a11d0 100644
--- a/textproc/py-martel/distinfo
+++ b/textproc/py-martel/distinfo
@@ -1 +1 @@
-MD5 (Martel-0.4.tar.gz) = 3f54a121b70b69f6167dd61343c73cc0
+MD5 (Martel-0.5.tar.gz) = 97f78433f8b6bfbedcf99d7ca1bc887d
diff --git a/textproc/py-martel/files/patch-Generate.py b/textproc/py-martel/files/patch-Generate.py
index caafeaaebc6..045356cec66 100644
--- a/textproc/py-martel/files/patch-Generate.py
+++ b/textproc/py-martel/files/patch-Generate.py
@@ -1,3 +1,32 @@
+From: "Andrew Dalke" <dalke@acm.org>
+To: <biopython-dev@biopython.org>
+Date: Wed, 6 Dec 2000 01:12:29 -0700
+
+There's a bug in Martel-0.4 and earlier versions.
+
+Suppose you have  ([<>][ABC])+[<>]?
+and want to match it against
+
+   <A<B<
+
+The "<A" matches the first [<>][ABC].  The "<B" matches
+the second [<>][ABC].  The parser tries to match the final
+"<" against [<>][ABC] and should fail then try to match
+the "<" against [<>]? .
+
+The bug was that it would match the "<" against the [<>] in
+[<>][ABC] and fail at that point.  It gives an assertion error
+about "l" being greater than "r".
+
+Here's the patch.  The only consequence should be a small hit
+in performance.
+
+                    Andrew
+
+[ Note from port maintainer:
+  This patch was somehow not incorporated into Martel 0.5 ]
+
+
 --- Generate.py.orig	Wed Nov 22 09:26:48 2000
 +++ Generate.py	Thu Dec  7 12:27:09 2000
 @@ -268,11 +268,11 @@
diff --git a/textproc/py-martel/pkg-plist b/textproc/py-martel/pkg-plist
index 2d28c8d99a5..b5934810dbc 100644
--- a/textproc/py-martel/pkg-plist
+++ b/textproc/py-martel/pkg-plist
@@ -19,6 +19,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/convert_re.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/convert_re.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/convert_re.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/GenBank.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/GenBank.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/GenBank.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/MDL_10_1996.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/MDL_10_1996.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/MDL_10_1996.pyo
@@ -34,12 +37,36 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/__init__.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blastall_2_0_10.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blastall_2_0_10.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blastall_2_0_10.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocks_12.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocks_12.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocks_12.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocksplus.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocksplus.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/blocksplus.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/embl65.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/embl65.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/embl65.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/enzyme26.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/enzyme26.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/enzyme26.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/primers.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/primers.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/primers.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prodoc16.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prodoc16.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prodoc16.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prosite16.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prosite16.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/prosite16.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/swissprot38.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/swissprot38.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/swissprot38.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/taxonomy.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/taxonomy.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/taxonomy.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/trembl14.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/trembl14.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/trembl14.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/optimize.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/optimize.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/optimize.pyo
@@ -58,6 +85,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/test/support.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Expression.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Expression.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Expression.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_GenBank.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_GenBank.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_GenBank.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Generate.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Generate.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Generate.pyo
@@ -88,18 +118,42 @@ lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_RecordReader2.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blastall_2_0_10.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blastall_2_0_10.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blastall_2_0_10.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blocks_12.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blocks_12.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blocks_12.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blocksplus.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blocksplus.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_blocksplus.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_convert_re.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_convert_re.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_convert_re.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_embl65.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_embl65.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_embl65.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_enzyme26.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_enzyme26.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_enzyme26.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_optimize.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_optimize.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_optimize.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_primers.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_primers.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_primers.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prodoc16.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prodoc16.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prodoc16.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prosite16.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prosite16.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_prosite16.pyo
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_swissprot38.py
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_swissprot38.pyc
 lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_swissprot38.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_taxonomy.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_taxonomy.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_taxonomy.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_trembl14.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_trembl14.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_trembl14.pyo
 share/examples/martel/README
 share/examples/martel/builders/SwissProtBuilder.py
 share/examples/martel/builders/SwissProtBuilder.pyc
@@ -118,4 +172,3 @@ share/examples/martel/toxml.pyo
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel/test
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel/formats
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel
-@unexec rm -rf %D/share/doc/martel 2>/dev/null || true