Date: Sun, 13 May 2018 22:30:00 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r469835 - head/biology/py-biopython Message-ID: <201805132230.w4DMU0jP065865@repo.freebsd.org>
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Author: yuri Date: Sun May 13 22:30:00 2018 New Revision: 469835 URL: https://svnweb.freebsd.org/changeset/ports/469835 Log: biology/py-biopython: Unbreak on python3; Add license Two items prevented python3 compatibility: * Breakage of ASCII codec due to non-ascii characters in README: https://github.com/biopython/biopython/issues/1649 * The outdated dependency: print/py-reportlab1 instead of the modern version 3.X print/py-reportlab Port changes: * USES=python:2.7 -> USES=python * Add pre-configure that clears the README file * Add LICENSE/LICENSE_FILE Testing: * Ran the tutorial testcase http://biopython.org/DIST/docs/tutorial/Tutorial.html, particularly pdf writing through print/py-reportlab worked fine. Asked the upstream to clarify the acceptable dependency version: https://github.com/biopython/biopython/issues/1650 Approved by: portmgr blanket (unbreak for python3; add license) Modified: head/biology/py-biopython/Makefile Modified: head/biology/py-biopython/Makefile ============================================================================== --- head/biology/py-biopython/Makefile Sun May 13 21:46:05 2018 (r469834) +++ head/biology/py-biopython/Makefile Sun May 13 22:30:00 2018 (r469835) @@ -3,6 +3,7 @@ PORTNAME= biopython PORTVERSION= 1.71 +PORTREVISION= 1 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -10,16 +11,22 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= mauricio@arareko.net COMMENT= Collection of Python modules for bioinformatics +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE.rst + BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} -USES= python:2.7 +USES= python USE_PYTHON= distutils autoplist OPTIONS_DEFINE= REPORTLAB OPTIONS_DEFAULT= REPORTLAB REPORTLAB_DESC= PDF support in Bio.Graphics module -REPORTLAB_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}reportlab1>0:print/py-reportlab1@${FLAVOR} +REPORTLAB_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}reportlab>0:print/py-reportlab@${FLAVOR} + +pre-configure: # unbreak for python3: README.rst can't be decoded with the ascii codec: https://github.com/biopython/biopython/issues/1649 + @truncate -s 0 ${WRKSRC}/README.rst .include <bsd.port.mk>
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