diff options
| -rw-r--r-- | textproc/py-martel/Makefile | 37 | ||||
| -rw-r--r-- | textproc/py-martel/distinfo | 2 | ||||
| -rw-r--r-- | textproc/py-martel/files/patch-Generate.py | 29 | ||||
| -rw-r--r-- | textproc/py-martel/pkg-plist | 55 |
4 files changed, 106 insertions, 17 deletions
diff --git a/textproc/py-martel/Makefile b/textproc/py-martel/Makefile index 8c3fbb8a669d..496998d884c9 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 726f84441c80..01b4d1a11d03 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 caafeaaebc6b..045356cec66e 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 2d28c8d99a52..b5934810dbcf 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 |