From owner-svn-ports-all@freebsd.org Mon May 14 00:15:33 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 A822AFDC1F7; Mon, 14 May 2018 00:15:33 +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 59AE773DF4; Mon, 14 May 2018 00:15:33 +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 3AC4D14AAA; Mon, 14 May 2018 00:15:33 +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 w4E0FXUq023479; Mon, 14 May 2018 00:15:33 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w4E0FWL9023474; Mon, 14 May 2018 00:15:32 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201805140015.w4E0FWL9023474@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 14 May 2018 00:15:32 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r469841 - in head/science: . py-MDAnalysis py-MDAnalysis/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/science: . py-MDAnalysis py-MDAnalysis/files X-SVN-Commit-Revision: 469841 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: Mon, 14 May 2018 00:15:33 -0000 Author: yuri Date: Mon May 14 00:15:31 2018 New Revision: 469841 URL: https://svnweb.freebsd.org/changeset/ports/469841 Log: New port: science/py-MDAnalysis: Python library to analyze molecular dynamics trajectories Added: head/science/py-MDAnalysis/ head/science/py-MDAnalysis/Makefile (contents, props changed) head/science/py-MDAnalysis/distinfo (contents, props changed) head/science/py-MDAnalysis/files/ head/science/py-MDAnalysis/files/patch-setup.py (contents, props changed) head/science/py-MDAnalysis/pkg-descr (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Mon May 14 00:08:08 2018 (r469840) +++ head/science/Makefile Mon May 14 00:15:31 2018 (r469841) @@ -165,6 +165,7 @@ SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy + SUBDIR += py-MDAnalysis SUBDIR += py-OpenFermion SUBDIR += py-cdo SUBDIR += py-coards Added: head/science/py-MDAnalysis/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-MDAnalysis/Makefile Mon May 14 00:15:31 2018 (r469841) @@ -0,0 +1,31 @@ +# $FreeBSD$ + +PORTNAME= MDAnalysis +DISTVERSION= 0.18.0 +CATEGORIES= science python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Python library to analyze molecular dynamics trajectories + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYNUMPY} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}biopython>=1.59:biology/py-biopython@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}duecredit>0:textproc/py-duecredit@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}GridDataFormats>=0.4.0:math/py-GridDataFormats@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}gsd>=1.4.0:science/py-gsd@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}joblib>0:devel/py-joblib@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.5.1:math/py-matplotlib@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}mmtf-python>=1.0.0:science/py-mmtf-python@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}networkx>=1.0:math/py-networkx@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}six>=1.4.0:devel/py-six@${FLAVOR} + +USES= python +USE_PYTHON= distutils autoplist + +.include Added: head/science/py-MDAnalysis/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-MDAnalysis/distinfo Mon May 14 00:15:31 2018 (r469841) @@ -0,0 +1,3 @@ +TIMESTAMP = 1526244200 +SHA256 (MDAnalysis-0.18.0.tar.gz) = a08acea1755112411e7db55e3f282e164b47a59e15794b38744cce6c596f252a +SIZE (MDAnalysis-0.18.0.tar.gz) = 11085390 Added: head/science/py-MDAnalysis/files/patch-setup.py ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-MDAnalysis/files/patch-setup.py Mon May 14 00:15:31 2018 (r469841) @@ -0,0 +1,11 @@ +--- setup.py.orig 2018-05-13 20:38:06 UTC ++++ setup.py +@@ -253,7 +253,7 @@ def extensions(config): + use_cython = config.get('use_cython', default=not is_release) + use_openmp = config.get('use_openmp', default=True) + +- extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops'] ++ extra_compile_args = ['-std=c99', '-ffast-math', '-funroll-loops'] + define_macros = [] + if config.get('debug_cflags', default=False): + extra_compile_args.extend(['-Wall', '-pedantic']) Added: head/science/py-MDAnalysis/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/py-MDAnalysis/pkg-descr Mon May 14 00:15:31 2018 (r469841) @@ -0,0 +1,6 @@ +MDAnalysis is an object-oriented Python library to analyze trajectories from +molecular dynamics (MD) simulations in many popular formats. It can write most +of these formats, too, together with atom selections suitable for visualization +or native analysis tools. + +WWW: https://www.mdanalysis.org