Date: Tue, 09 Jan 2001 16:46:35 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/24184: Port update: textproc/py-martel (MAINTAINER) Message-ID: <E14G02l-000KBC-00@fling.sanbi.ac.za>
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>Number: 24184
>Category: ports
>Synopsis: Port update: textproc/py-martel (MAINTAINER)
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Tue Jan 09 06:50:01 PST 2001
>Closed-Date:
>Last-Modified:
>Originator: Johann Visagie
>Release: FreeBSD 5.0-CURRENT i386
>Organization:
Electric Genetics
>Environment:
>Description:
- Update Martel (textproc/py-martel) from 0.4 to 0.5
- Changes in new version comprise (mostly) the addition of numerous new
formats. This is to be considered a development release.
- ${PLIST} is now generated dynamically. This allows for (a) a clean
deinstall after a -DNOPORTDOCS install, whilst (b) still including the docs
should the port be built as a package. (Is there no easier way to do
this?) Based on original py-xml Makefile by Jacques Vidrine
<nectar@FreeBSD.org>.
>How-To-Repeat:
>Fix:
diff -ruN py-martel.bak/Makefile py-martel/Makefile
--- py-martel.bak/Makefile Tue Jan 9 16:34:46 2001
+++ py-martel/Makefile Tue Jan 9 16:27:47 2001
@@ -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 -ruN py-martel.bak/distinfo py-martel/distinfo
--- py-martel.bak/distinfo Tue Jan 9 16:34:46 2001
+++ py-martel/distinfo Tue Jan 9 15:08:02 2001
@@ -1 +1 @@
-MD5 (Martel-0.4.tar.gz) = 3f54a121b70b69f6167dd61343c73cc0
+MD5 (Martel-0.5.tar.gz) = 97f78433f8b6bfbedcf99d7ca1bc887d
diff -ruN py-martel.bak/files/patch-Generate.py py-martel/files/patch-Generate.py
--- py-martel.bak/files/patch-Generate.py Tue Jan 9 16:34:46 2001
+++ py-martel/files/patch-Generate.py Tue Jan 9 16:33:44 2001
@@ -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 -ruN py-martel.bak/pkg-plist py-martel/pkg-plist
--- py-martel.bak/pkg-plist Tue Jan 9 16:34:46 2001
+++ py-martel/pkg-plist Tue Jan 9 16:18:30 2001
@@ -19,6 +19,9 @@
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/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/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_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 @@
@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
>Release-Note:
>Audit-Trail:
>Unformatted:
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