Date: Wed, 17 Oct 2018 01:04:42 +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: r482266 - in head/science: . avogadro2 avogadro2/files Message-ID: <201810170104.w9H14gsZ065119@repo.freebsd.org>
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Author: yuri Date: Wed Oct 17 01:04:41 2018 New Revision: 482266 URL: https://svnweb.freebsd.org/changeset/ports/482266 Log: New port: science/avogadro2: Chemical editor and visualization application Added: head/science/avogadro2/ - copied from r482264, head/science/avogadro/ Deleted: head/science/avogadro2/files/ head/science/avogadro2/pkg-plist Modified: head/science/Makefile head/science/avogadro2/Makefile head/science/avogadro2/distinfo head/science/avogadro2/pkg-descr Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Wed Oct 17 01:02:16 2018 (r482265) +++ head/science/Makefile Wed Oct 17 01:04:41 2018 (r482266) @@ -29,6 +29,7 @@ SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro + SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += bagel SUBDIR += bddsolve Modified: head/science/avogadro2/Makefile ============================================================================== --- head/science/avogadro/Makefile Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadro2/Makefile Wed Oct 17 01:04:41 2018 (r482266) @@ -1,66 +1,32 @@ -# Created by: Troels Kofoed Jacobsen <tkjacobsen@gmail.com> # $FreeBSD$ -PORTNAME= avogadro -PORTVERSION= 1.1.1 -PORTREVISION= 16 +PORTNAME= avogadro2 +DISTVERSION= 1.91.0 CATEGORIES= science -MASTER_SITES= SF -MAINTAINER= kde@FreeBSD.org -COMMENT= Advanced molecular editor and viewer +MAINTAINER= yuri@FreeBSD.org +COMMENT= Chemical editor and visualization application -LICENSE= GPLv2+ -LICENSE_FILE= ${WRKSRC}/COPYING +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_armv6= fails to compile: eigen2/Eigen/src/Core/Assign.h: you mixed different numeric types in 'Eigen::ei_static_assert<false>' -BROKEN_armv7= fails to compile: eigen2/Eigen/src/Core/Assign.h: you mixed different numeric types in 'Eigen::ei_static_assert<false>' +BUILD_DEPENDS= hdf5>0:science/hdf5 +LIB_DEPENDS= libAvogadroCore.so:science/avogadrolibs \ + libMoleQueueClient.so:misc/molequeue -LIB_DEPENDS= libopenbabel.so:science/openbabel - -# We need to add a RUN_DEPENDS on eigen2, as the cmake file shiped with -# avogadro to use it, contains 'find_package(Eigen2 REQUIRED)'. -USES= cmake desktop-file-utils eigen:2,build,run pkgconfig qt:4 tar:bzip2 -USE_GL= glu gl -USE_QT= gui network opengl \ - linguisttools_build moc_build qmake_build rcc_build uic_build -CMAKE_ARGS= -DENABLE_GLSL=OFF \ - -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs +USES= cmake:outsource compiler:c++11-lang desktop-file-utils gl libarchive qt:5 +USE_GITHUB= yes +GH_ACCOUNT= OpenChemistry +GH_PROJECT= avogadroapp +USE_QT= core concurrent gui network widgets buildtools_build qmake_build +USE_GL= gl glew glu USE_LDCONFIG= yes -CFLAGS+= -idirafter ${LOCALBASE}/include/eigen2 \ - -idirafter ${LOCALBASE}/include \ - -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib +PLIST_FILES= bin/avogadro2 \ + share/applications/avogadro2.desktop \ + share/pixmaps/avogadro2.png -OPTIONS_DEFINE= PYTHON -OPTIONS_DEFAULT=PYTHON -OPTIONS_SUB= yes - -PYTHON_USES= python:2.7 -PYTHON_BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}sip>0:devel/py-sip@${PY_FLAVOR} -PYTHON_LIB_DEPENDS= ${PY_BOOST} -PYTHON_RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}sip>0:devel/py-sip@${PY_FLAVOR} -PYTHON_CMAKE_ON= -DENABLE_PYTHON=ON \ - -DPYTHON_INCLUDE_DIR:PATH=${WRKDIR}/include/${PYTHON_VERSION} -PYTHON_CMAKE_OFF= -DENABLE_PYTHON=OFF - -post-patch: - @${REINPLACE_CMD} -e \ - '/FLAGS_RELEASE/s|^|#| ; \ - /PC_FILES/s|$${LIB_INSTALL_DIR}|libdata|' ${WRKSRC}/CMakeLists.txt - @${REINPLACE_CMD} -e \ - 's|share/man|man|' ${WRKSRC}/doc/CMakeLists.txt - -pre-configure-PYTHON-on: - @${MKDIR} ${WRKDIR}/include/${PYTHON_VERSION} - @${FIND} ${PYTHON_INCLUDEDIR} ! -name "pyport.h" -type f \ - -maxdepth 1 | ${XARGS} -J % ${LN} -sf % \ - ${WRKDIR}/include/${PYTHON_VERSION} - @${SED} -e 's|^#ifdef _PY_PORT_CTYPE_UTF8_ISSUE|#if 0|' \ - ${PYTHON_INCLUDEDIR}/pyport.h > \ - ${WRKDIR}/include/${PYTHON_VERSION}/pyport.h +post-install: + @${RM} -r ${STAGEDIR}${PREFIX}/share/doc .include <bsd.port.mk> Modified: head/science/avogadro2/distinfo ============================================================================== --- head/science/avogadro/distinfo Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadro2/distinfo Wed Oct 17 01:04:41 2018 (r482266) @@ -1,2 +1,3 @@ -SHA256 (avogadro-1.1.1.tar.bz2) = fe6f7bdea17a27a20be25b70d975145999aae9d90ef320217af2bc4d6e7a0a14 -SIZE (avogadro-1.1.1.tar.bz2) = 11118046 +TIMESTAMP = 1539734244 +SHA256 (OpenChemistry-avogadroapp-1.91.0_GH0.tar.gz) = 3bbe130027a75116de1d5c48dd7e97ff0fa8a785a96c500767bd4965f52e20df +SIZE (OpenChemistry-avogadroapp-1.91.0_GH0.tar.gz) = 2904864 Modified: head/science/avogadro2/pkg-descr ============================================================================== --- head/science/avogadro/pkg-descr Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadro2/pkg-descr Wed Oct 17 01:04:41 2018 (r482266) @@ -1,6 +1,22 @@ -Avogadro is an advanced molecular editor designed for cross-platform use in -computational chemistry, molecular modeling, bioinformatics, materials science, -and related areas. It offers flexible rendering and a powerful plugin -architecture. +Avogadro 2 is a chemical editor and visualization application, it is also a set +of reusable software libraries written in C++ using principles of modularity for +maximum reuse. The development of the first generation Avogadro application and +library is documented in our paper, and this remains the preferred method of +citation at present. The motivation for rewriting Avogadro, along with +improvements and changes made in Avogadro 2 are summarized in our Source +article. We provide a set of permissively licensed, open source, cross platform +software components in the Avogadro 2 libraries, along with an end-user +application with full source code, and binaries. -WWW: http://avogadro.cc/ +The library features updated and improved rendering, where we built upon the +abstraction provided by previous API, but implemented a simple scene graph. This +makes use of features such as impostor sphere rendering, resulting in +significant rendering speed improvements while improving the quality of the +visualization. The core is built for scalability, looking to enable the analysis +of larger chemical structures and simulations being produced by computational +chemistry codes today. Emphasis has also been placed on making it even easier to +extend, using simple Python scripts to add simulation input capabilities, and +data input/output along with access to full-blown C++ plugin APIs where more +control is required. + +WWW: https://www.openchemistry.org/projects/avogadro2/
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