- Updat to version 0.6

- Since Martel is currently only maintained as part of the Biopython
  distribution, switch to a using locally maintained distfile culled from the
  Biopython CVS repo, including the "doc" subdirectory from Martel 0.5

4 files changed, 24 insertions, 168 deletions

diff --git a/textproc/py-martel/Makefile b/textproc/py-martel/Makefile
index ce089c0ed05d..f5e63657c2e3 100644
--- a/textproc/py-martel/Makefile
+++ b/textproc/py-martel/Makefile
@@ -6,34 +6,32 @@
 #
 
 PORTNAME=	martel
-PORTVERSION=	0.5
-PORTREVISION=	4
+PORTVERSION=	0.6
 PORTEPOCH=	1
 CATEGORIES=	textproc biology python
-MASTER_SITES=	http://www.biopython.org/~dalke/Martel/
+MASTER_SITES=	${MASTER_SITE_LOCAL}
+MASTER_SITE_SUBDIR=	wjv
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 DISTNAME=	Martel-${PORTVERSION}
 
 MAINTAINER=	wjv@FreeBSD.org
 
+BUILD_DEPENDS=	${PYDISTUTILS}
 RUN_DEPENDS=	${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
 
 USE_PYTHON=	yes
-
-MARTEL_DIR=	${PREFIX}/lib/${PYTHON_VERSION}/site-packages/Martel
-EXAMPLESDIR=	${PREFIX}/share/examples/martel
+USE_BZIP2=	yes
+PYTHON_SETUP=	${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py
+EXAMPLESDIR=	${PREFIX}/share/examples/${PORTNAME}
 
 do-build:
-	@ ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${WRKSRC}
-	@ ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${WRKSRC}
+	@ cd ${WRKSRC} && ${PYTHON_SETUP} build
 
 pre-install:
 	@ ${SH} ${PKGREQ} INSTALL
 
 do-install:
-	@ ${MKDIR} ${MARTEL_DIR}
-	@ (cd ${WRKSRC} && find *.py *.pyc *.pyo formats test \
-	  | cpio --quiet -pdum -R ${BINOWN}:${BINGRP} ${MARTEL_DIR})
+	@ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX}
 
 post-install:
 .if !defined(NOPORTDOCS)
@@ -41,9 +39,8 @@ post-install:
 .for docfile in README HISTORY doc/*
 	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
 .endfor
-	@ ${MKDIR} ${EXAMPLESDIR}/builders
+	@ ${MKDIR} ${EXAMPLESDIR}
 	@ ${INSTALL_DATA} ${WRKSRC}/examples/* ${EXAMPLESDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/builders/* ${EXAMPLESDIR}/builders
 .endif
 
 .include <bsd.port.mk>
diff --git a/textproc/py-martel/distinfo b/textproc/py-martel/distinfo
index 01b4d1a11d03..d45bf3171ca0 100644
--- a/textproc/py-martel/distinfo
+++ b/textproc/py-martel/distinfo
@@ -1 +1 @@
-MD5 (Martel-0.5.tar.gz) = 97f78433f8b6bfbedcf99d7ca1bc887d
+MD5 (Martel-0.6.tar.bz2) = f7d720ff6169c75a588ea4e8e2a8542b
diff --git a/textproc/py-martel/pkg-descr b/textproc/py-martel/pkg-descr
index 6a3e6639643f..4005d54710bc 100644
--- a/textproc/py-martel/pkg-descr
+++ b/textproc/py-martel/pkg-descr
@@ -10,10 +10,8 @@ Biopython - http://www.biopython.org/) where there is often a need to parse
 flat and semi-structured legacy file formats.  However, it is generally
 applicable to the parsing of such files in all fields of endeavour.
 
-More information on Martel may be found in this conference poster:
-http://www.biopython.org/~dalke/Martel/BOSC2000.poster/
-
-Author: Andrew Dalke <dalke@acm.org>
-WWW:    http://www.biopython.org/~dalke/Martel/
+Author:   Andrew Dalke <dalke@dalkescientific.com>
+WWW:	  http://www.dalkescientific.com/Martel/
+See also: http://www.biopython.org/~dalke/Martel/
 
 -- Johann Visagie <wjv@FreeBSD.org>
diff --git a/textproc/py-martel/pkg-plist b/textproc/py-martel/pkg-plist
index f4c8d1d84886..79d57c139a63 100644
--- a/textproc/py-martel/pkg-plist
+++ b/textproc/py-martel/pkg-plist
@@ -3,6 +3,9 @@
 %%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
@@ -24,157 +27,15 @@ 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
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PDB_2_1.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PDB_2_1.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PDB_2_1.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PIR_3_0.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PIR_3_0.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/PIR_3_0.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/__init__.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/formats/__init__.pyc
-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/msre_constants.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_constants.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_constants.pyo
+lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_parse.py
+lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_parse.pyc
+lib/%%PYTHON_VERSION%%/site-packages/Martel/msre_parse.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
-lib/%%PYTHON_VERSION%%/site-packages/Martel/sre_constants.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/sre_constants.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/sre_constants.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/sre_parse.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/sre_parse.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/sre_parse.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/__init__.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/__init__.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/__init__.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/support.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/support.pyc
-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
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Iterator.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Iterator.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Iterator.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_MDL_10_1996.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_MDL_10_1996.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_MDL_10_1996.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_PDB_2_1.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_PDB_2_1.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_PDB_2_1.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_PIR_3_0.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_PIR_3_0.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_PIR_3_0.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_ParseRecords.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_ParseRecords.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_ParseRecords.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Parser.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Parser.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_Parser.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_RecordReader.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_RecordReader.pyc
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_RecordReader.pyo
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_RecordReader2.py
-lib/%%PYTHON_VERSION%%/site-packages/Martel/test/test_RecordReader2.pyc
-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
-share/examples/martel/builders/SwissProtBuilder.pyo
-share/examples/martel/pdb1plm.ent
-share/examples/martel/sample.swissprot
-share/examples/martel/swissprot2html.py
-share/examples/martel/swissprot2html.pyc
-share/examples/martel/swissprot2html.pyo
-share/examples/martel/test.mol
-share/examples/martel/toxml.py
-share/examples/martel/toxml.pyc
-share/examples/martel/toxml.pyo
-@dirrm share/examples/martel/builders
-@dirrm share/examples/martel
-@dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel/test
-@dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel/formats
 @dirrm lib/%%PYTHON_VERSION%%/site-packages/Martel
+%%PORTDOCS%%@dirrm share/examples/martel
 %%PORTDOCS%%@dirrm share/doc/martel