From owner-svn-ports-all@freebsd.org Sun May 13 22:30:01 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id F145BFD7638; Sun, 13 May 2018 22:30:00 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id A1364797A3; Sun, 13 May 2018 22:30:00 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 830CD13862; Sun, 13 May 2018 22:30:00 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w4DMU0Jv065866; Sun, 13 May 2018 22:30:00 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w4DMU0jP065865; Sun, 13 May 2018 22:30:00 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201805132230.w4DMU0jP065865@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 13 May 2018 22:30:00 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r469835 - head/biology/py-biopython X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/biology/py-biopython X-SVN-Commit-Revision: 469835 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 13 May 2018 22:30:01 -0000 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