Date: Sat, 11 May 2019 20:29:57 +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: r501303 - in head/science: . nest nest/files Message-ID: <201905112029.x4BKTvnp070197@repo.freebsd.org>
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Author: yuri Date: Sat May 11 20:29:56 2019 New Revision: 501303 URL: https://svnweb.freebsd.org/changeset/ports/501303 Log: New port: science/nest: Simulator for spiking neural network models Added: head/science/nest/ head/science/nest/Makefile (contents, props changed) head/science/nest/distinfo (contents, props changed) head/science/nest/files/ head/science/nest/files/patch-CMakeLists.txt (contents, props changed) head/science/nest/files/patch-cmake_ProcessOptions.cmake (contents, props changed) head/science/nest/files/patch-extras_nest__vars.sh.in (contents, props changed) head/science/nest/pkg-descr (contents, props changed) head/science/nest/pkg-plist (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Sat May 11 20:27:19 2019 (r501302) +++ head/science/Makefile Sat May 11 20:29:56 2019 (r501303) @@ -161,6 +161,7 @@ SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd + SUBDIR += nest SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran Added: head/science/nest/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/Makefile Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= nest +DISTVERSIONPREFIX= v +DISTVERSION= 2.14.0-2100 +DISTVERSIONSUFFIX= -g788e93e3 +CATEGORIES= science biology # NEST is used in neuroscience + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Simulator for spiking neural network models + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libgsl.so:math/gsl \ + libltdl.so:devel/libltdl \ + libomp.so:devel/openmp + +USES= cmake compiler:c++11-lang ncurses pkgconfig readline +USE_GITHUB= yes +GH_PROJECT= nest-simulator +USE_LDCONFIG= yes + +OPTIONS_DEFINE= PYTHON DOCS +OPTIONS_DEFAULT= PYTHON +OPTIONS_SUB= yes + +PYTHON_CMAKE_BOOL= BUILD_PYTHON +PYTHON_USES= python +PYTHON_CMAKE_ON= -DCYTHON_EXECUTABLE:STRING=${PREFIX}/bin/cython-${PYTHON_VER} +PYTHON_BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cython>0:lang/cython@${PY_FLAVOR} + +PORTDOCS= * + +.include <bsd.port.mk> Added: head/science/nest/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/distinfo Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,3 @@ +TIMESTAMP = 1557603316 +SHA256 (nest-nest-simulator-v2.14.0-2100-g788e93e3_GH0.tar.gz) = 972dcbbe79e3a36bd7e83426dccd12197885537791f70ea9795079226a13aa44 +SIZE (nest-nest-simulator-v2.14.0-2100-g788e93e3_GH0.tar.gz) = 12376006 Added: head/science/nest/files/patch-CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/files/patch-CMakeLists.txt Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,53 @@ +--- CMakeLists.txt.orig 2019-04-23 07:25:32 UTC ++++ CMakeLists.txt +@@ -100,7 +100,7 @@ include( GNUInstallDirs ) + get_filename_component(CMAKE_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX} REALPATH BASE_DIR "${CMAKE_BINARY_DIR}") + # If CMAKE_INSTALL_PREFIX is omitted CMake will set the installation prefix to its default '/usr/local'. + # This is not desired. A subdirectory is allowed, e.g. 'usr/local/nest'. +-if ( "${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local" ) ++if ( FALSE AND "${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr/local" ) + message( FATAL_ERROR "Do not install into '${CMAKE_INSTALL_PREFIX}'. Please set -DCMAKE_INSTALL_PREFIX:PATH=<install prefix>." ) + endif () + +@@ -109,7 +109,7 @@ endif () + ################################################################################ + + # needed for pynest test suite +-if ( ${with-python} STREQUAL "ON" OR ${with-python} STREQUAL "2" OR ${with-python} STREQUAL "3" ) ++if ( BUILD_PYTHON AND (${with-python} STREQUAL "ON" OR ${with-python} STREQUAL "2" OR ${with-python} STREQUAL "3") ) + find_program( NOSETESTS NAMES nosetests ) + endif () + +@@ -198,7 +198,7 @@ enable_testing() + set( TEST_LOGFILE ${PROJECT_BINARY_DIR}/reports/installcheck.log ) + file( MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/reports/ ) + +-if ( HAVE_PYTHON ) ++if ( BUILD_PYTHON AND HAVE_PYTHON ) + add_custom_target( installcheck + COMMAND ${CMAKE_COMMAND} -E env + NEST_PATH="${CMAKE_INSTALL_FULL_BINDIR}" +@@ -225,8 +225,12 @@ endif () + if ( HAVE_LIBNEUROSIM ) + add_subdirectory( conngen ) + endif () +-add_subdirectory( doc ) +-add_subdirectory( examples ) ++if (INSTALL_DOCS) ++ add_subdirectory( doc ) ++endif() ++if (INSTALL_EXAMPLES) ++ add_subdirectory( examples ) ++endif() + add_subdirectory( extras ) + add_subdirectory( lib ) + add_subdirectory( libnestutil ) +@@ -238,7 +242,7 @@ add_subdirectory( nestkernel ) + add_subdirectory( precise ) + add_subdirectory( testsuite ) + add_subdirectory( topology ) +-if ( HAVE_PYTHON ) ++if ( BUILD_PYTHON AND HAVE_PYTHON ) + add_subdirectory( pynest ) + endif () + Added: head/science/nest/files/patch-cmake_ProcessOptions.cmake ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/files/patch-cmake_ProcessOptions.cmake Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,11 @@ +--- cmake/ProcessOptions.cmake.orig 2019-05-11 20:18:03 UTC ++++ cmake/ProcessOptions.cmake +@@ -385,7 +385,7 @@ function( NEST_PROCESS_WITH_PYTHON ) + # confirmed working: 0.19.2+ + # in between unknown + if ( CYTHON_VERSION VERSION_LESS "0.19.2" ) +- message( FATAL_ERROR "Your Cython version is too old. Please install " ++ message( FATAL_ERROR "Your Cython version (" ${CYTHON_VERSION} ") is too old. Please install " + "newer version (0.19.2+)" ) + endif () + Added: head/science/nest/files/patch-extras_nest__vars.sh.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/files/patch-extras_nest__vars.sh.in Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,8 @@ +--- extras/nest_vars.sh.in.orig 2019-05-11 19:47:58 UTC ++++ extras/nest_vars.sh.in +@@ -1,4 +1,4 @@ +-#!/bin/bash ++#!/bin/sh + + # NEST is installed here. When you relocate NEST, change this variable. + export NEST_INSTALL_DIR=@CMAKE_INSTALL_PREFIX@ Added: head/science/nest/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/pkg-descr Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,13 @@ +NEST is a simulator for spiking neural network models that focuses on the +dynamics, size and structure of neural systems rather than on the exact +morphology of individual neurons. The development of NEST is coordinated +by the NEST Initiative. + +NEST is ideal for networks of spiking neurons of any size, for example: +* Models of information processing e.g. in the visual or auditory cortex of + mammals, +* Models of network activity dynamics, e.g. laminar cortical networks or + balanced random networks, +* Models of learning and plasticity. + +WWW: https://www.nest-simulator.org/ Added: head/science/nest/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/nest/pkg-plist Sat May 11 20:29:56 2019 (r501303) @@ -0,0 +1,520 @@ +bin/nest +bin/nest-config +bin/nest_indirect +bin/nest_serial +bin/nest_vars.sh +bin/sli +include/nest/ac_generator.h +include/nest/aeif_cond_alpha.h +include/nest/aeif_cond_alpha_RK5.h +include/nest/aeif_cond_alpha_multisynapse.h +include/nest/aeif_cond_beta_multisynapse.h +include/nest/aeif_cond_exp.h +include/nest/aeif_psc_alpha.h +include/nest/aeif_psc_delta.h +include/nest/aeif_psc_delta_clopath.h +include/nest/aeif_psc_exp.h +include/nest/aggregatedatum.h +include/nest/allocator.h +include/nest/amat2_psc_exp.h +include/nest/archiving_node.h +include/nest/arraydatum.h +include/nest/bernoulli_connection.h +include/nest/binary_neuron.h +include/nest/binomial_randomdev.h +include/nest/block_vector.h +include/nest/booldatum.h +include/nest/callbackdatum.h +include/nest/charcode.h +include/nest/clipped_randomdev.h +include/nest/clopath_archiving_node.h +include/nest/clopath_connection.h +include/nest/common_properties_hom_w.h +include/nest/common_synapse_properties.h +include/nest/completed_checker.h +include/nest/compose.hpp +include/nest/config.h +include/nest/conn_builder.h +include/nest/conn_builder_factory.h +include/nest/conn_builder_impl.h +include/nest/conn_parameter.h +include/nest/connection.h +include/nest/connection_creator.h +include/nest/connection_creator_impl.h +include/nest/connection_id.h +include/nest/connection_label.h +include/nest/connection_manager.h +include/nest/connection_manager_impl.h +include/nest/connector_base.h +include/nest/connector_base_impl.h +include/nest/connector_model.h +include/nest/connector_model_impl.h +include/nest/cont_delay_connection.h +include/nest/cont_delay_connection_impl.h +include/nest/correlation_detector.h +include/nest/correlomatrix_detector.h +include/nest/correlospinmatrix_detector.h +include/nest/datum.h +include/nest/dc_generator.h +include/nest/delay_checker.h +include/nest/device.h +include/nest/device_node.h +include/nest/dict.h +include/nest/dictdatum.h +include/nest/dictstack.h +include/nest/dictutils.h +include/nest/diffusion_connection.h +include/nest/doubledatum.h +include/nest/dynamicloader.h +include/nest/erfc_neuron.h +include/nest/event.h +include/nest/event_delivery_manager.h +include/nest/event_delivery_manager_impl.h +include/nest/exceptions.h +include/nest/exp_randomdev.h +include/nest/fdstream.h +include/nest/filesystem.h +include/nest/free_layer.h +include/nest/functional.h +include/nest/functiondatum.h +include/nest/gamma_randomdev.h +include/nest/gamma_sup_generator.h +include/nest/gap_junction.h +include/nest/gauss_rate.h +include/nest/generic_factory.h +include/nest/genericdatum.h +include/nest/genericmodel.h +include/nest/genericmodel_impl.h +include/nest/gid_collection.h +include/nest/gif_cond_exp.h +include/nest/gif_cond_exp_multisynapse.h +include/nest/gif_pop_psc_exp.h +include/nest/gif_psc_exp.h +include/nest/gif_psc_exp_multisynapse.h +include/nest/ginzburg_neuron.h +include/nest/gnureadline.h +include/nest/grid_layer.h +include/nest/grid_mask.h +include/nest/growth_curve.h +include/nest/growth_curve_factory.h +include/nest/gsl_binomial_randomdev.h +include/nest/gslrandomgen.h +include/nest/hh_cond_beta_gap_traub.h +include/nest/hh_cond_exp_traub.h +include/nest/hh_psc_alpha.h +include/nest/hh_psc_alpha_clopath.h +include/nest/hh_psc_alpha_gap.h +include/nest/histentry.h +include/nest/ht_connection.h +include/nest/ht_neuron.h +include/nest/iaf_chs_2007.h +include/nest/iaf_chxk_2008.h +include/nest/iaf_cond_alpha.h +include/nest/iaf_cond_alpha_mc.h +include/nest/iaf_cond_beta.h +include/nest/iaf_cond_exp.h +include/nest/iaf_cond_exp_sfa_rr.h +include/nest/iaf_psc_alpha.h +include/nest/iaf_psc_alpha_canon.h +include/nest/iaf_psc_alpha_multisynapse.h +include/nest/iaf_psc_alpha_presc.h +include/nest/iaf_psc_delta.h +include/nest/iaf_psc_delta_canon.h +include/nest/iaf_psc_exp.h +include/nest/iaf_psc_exp_multisynapse.h +include/nest/iaf_psc_exp_ps.h +include/nest/iaf_psc_exp_ps_lossless.h +include/nest/iaf_tum_2000.h +include/nest/inhomogeneous_poisson_generator.h +include/nest/integerdatum.h +include/nest/interpret.h +include/nest/io_manager.h +include/nest/iostreamdatum.h +include/nest/iteratordatum.h +include/nest/izhikevich.h +include/nest/kernel_manager.h +include/nest/knuthlfg.h 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+include/nest/music_event_out_proxy.h +include/nest/music_manager.h +include/nest/music_message_in_proxy.h +include/nest/name.h +include/nest/namedatum.h +include/nest/nest.h +include/nest/nest_datums.h +include/nest/nest_names.h +include/nest/nest_time.h +include/nest/nest_timeconverter.h +include/nest/nest_types.h +include/nest/nestmodule.h +include/nest/neststartup.h +include/nest/node.h +include/nest/node_manager.h +include/nest/nodelist.h +include/nest/noise_generator.h +include/nest/normal_randomdev.h +include/nest/ntree.h +include/nest/ntree_impl.h +include/nest/numericdatum.h +include/nest/numericdatum_impl.h +include/nest/numerics.h +include/nest/oosupport.h +include/nest/parrot_neuron.h +include/nest/parrot_neuron_ps.h +include/nest/parser.h +include/nest/parserdatum.h +include/nest/poisson_generator.h +include/nest/poisson_generator_ps.h +include/nest/poisson_randomdev.h +include/nest/position.h +include/nest/pp_pop_psc_delta.h +include/nest/pp_psc_delta.h +include/nest/ppd_sup_generator.h +include/nest/precisemodule.h +include/nest/processes.h +include/nest/propagator_stability.h +include/nest/proxynode.h +include/nest/pseudo_recording_device.h +include/nest/psignal.h +include/nest/pulsepacket_generator.h +include/nest/quantal_stp_connection.h +include/nest/quantal_stp_connection_impl.h +include/nest/random.h +include/nest/random_datums.h +include/nest/random_numbers.h +include/nest/randomdev.h +include/nest/randomgen.h +include/nest/rate_connection_delayed.h +include/nest/rate_connection_instantaneous.h +include/nest/rate_neuron_ipn.h +include/nest/rate_neuron_ipn_impl.h +include/nest/rate_neuron_opn.h +include/nest/rate_neuron_opn_impl.h +include/nest/rate_transformer_node.h +include/nest/rate_transformer_node_impl.h +include/nest/recordables_map.h +include/nest/recording_device.h +include/nest/ring_buffer.h +include/nest/rng_manager.h +include/nest/scanner.h +include/nest/selector.h +include/nest/send_buffer_position.h 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