Date: Thu, 21 Oct 2021 06:23:51 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: bbee7e139269 - main - science/nest: Update 2.20.1 -> 3.1 Message-ID: <202110210623.19L6NpUt021284@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=bbee7e13926922adb8a87ab9cb1416e792897b0a commit bbee7e13926922adb8a87ab9cb1416e792897b0a Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-10-21 06:22:22 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-10-21 06:23:16 +0000 science/nest: Update 2.20.1 -> 3.1 --- science/nest/Makefile | 21 +- science/nest/distinfo | 6 +- science/nest/files/patch-CMakeLists.txt | 41 +- .../nest/files/patch-cmake_ProcessOptions.cmake | 18 +- science/nest/pkg-plist | 723 ++++++++++++++++++--- 5 files changed, 680 insertions(+), 129 deletions(-) diff --git a/science/nest/Makefile b/science/nest/Makefile index 51658ab526a7..23b308f817dc 100644 --- a/science/nest/Makefile +++ b/science/nest/Makefile @@ -1,7 +1,6 @@ PORTNAME= nest DISTVERSIONPREFIX= v -DISTVERSION= 2.20.1 -PORTREVISION= 2 +DISTVERSION= 3.1 CATEGORIES= science biology # NEST is used in neuroscience MAINTAINER= yuri@FreeBSD.org @@ -12,29 +11,35 @@ LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= https://github.com/nest/nest-simulator/issues/1205 -LIB_DEPENDS= libgsl.so:math/gsl \ +LIB_DEPENDS= libboost_system.so:devel/boost-libs \ + libgsl.so:math/gsl \ libltdl.so:devel/libltdl +RUN_DEPENDS= bash:shells/bash + +USES= cmake:testing ncurses pkgconfig python readline shebangfix +USE_LDCONFIG= yes -USES= cmake:testing ncurses pkgconfig readline USE_GITHUB= yes GH_PROJECT= nest-simulator -USE_LDCONFIG= yes + +SHEBANG_FILES= extras/nest-server extras/nest-server-mpi testsuite/do_tests.sh OPTIONS_DEFINE= PYTHON DOCS -#OPTIONS_DEFAULT= PYTHON +OPTIONS_DEFAULT= PYTHON OPTIONS_SUB= yes PYTHON_CMAKE_BOOL= BUILD_PYTHON -PYTHON_USES= python PYTHON_USE= python=cython PYTHON_CMAKE_ON= -DCYTHON_EXECUTABLE:STRING=${PREFIX}/bin/cython-${PYTHON_VER} -PYTHON_BROKEN= https://github.com/nest/nest-simulator/issues/2193 PORTDOCS= * # 2 tests are known to fail, see https://github.com/nest/nest-simulator/issues/2190 # tests require the port to be installed with DOCS=ON, see https://github.com/nest/nest-simulator/issues/2191 +post-install: + @${REINPLACE_CMD} -i '' -e 's|^python3 |${PYTHON_CMD} |' ${STAGEDIR}${PREFIX}/share/nest/testsuite/do_tests.sh + .include <bsd.port.options.mk> .if ${ARCH} == powerpc diff --git a/science/nest/distinfo b/science/nest/distinfo index 862e0fa01692..58939e8d2162 100644 --- a/science/nest/distinfo +++ b/science/nest/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1607244359 -SHA256 (nest-nest-simulator-v2.20.1_GH0.tar.gz) = df3d32b5899d5d444f708037b290f889ac6ff8eae6b7be9e9faee2c0d660d8e5 -SIZE (nest-nest-simulator-v2.20.1_GH0.tar.gz) = 14735711 +TIMESTAMP = 1634790045 +SHA256 (nest-nest-simulator-v3.1_GH0.tar.gz) = 5c11dd6b451c4c6bf93037bf29d5231c6c75a0e1a8863344f6fb9bb225f279ca +SIZE (nest-nest-simulator-v3.1_GH0.tar.gz) = 12028051 diff --git a/science/nest/files/patch-CMakeLists.txt b/science/nest/files/patch-CMakeLists.txt index ac06547789ac..7f7fc651d7b8 100644 --- a/science/nest/files/patch-CMakeLists.txt +++ b/science/nest/files/patch-CMakeLists.txt @@ -1,36 +1,27 @@ ---- CMakeLists.txt.orig 2019-04-23 07:25:32 UTC +--- CMakeLists.txt.orig 2021-09-15 13:04:13 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 '${CMAKE_INSTALL_PREFIX}'. Please set -DCMAKE_INSTALL_PREFIX:PATH=<install prefix>." ) - endif () - -@@ -109,7 +109,7 @@ endif () +@@ -92,7 +92,7 @@ set( CMAKE_INSTALL_DATADIR "share/${PROJECT_NAME}" CAC ################################################################################ # 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") ) +-if ( ${with-python} STREQUAL "ON" ) ++if ( BUILD_PYTHON AND ${with-python} STREQUAL "ON" ) 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/ ) +@@ -194,7 +194,7 @@ message("-- NEST version: ${NEST_VERSION_STRING}") + enable_testing() + set( TEST_OPTS "" ) -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 ) + set( TEST_OPTS "${TEST_OPTS};--with-python=${PYTHON}" ) endif () + +@@ -223,8 +223,12 @@ add_custom_target( installcheck + ################## Define Subdirectories here ################## + ################################################################################ + -add_subdirectory( doc ) -add_subdirectory( examples ) +if (INSTALL_DOCS) @@ -42,10 +33,10 @@ add_subdirectory( extras ) add_subdirectory( lib ) add_subdirectory( libnestutil ) -@@ -238,7 +242,7 @@ add_subdirectory( nestkernel ) - add_subdirectory( precise ) +@@ -234,7 +238,7 @@ add_subdirectory( nest ) + add_subdirectory( nestkernel ) + add_subdirectory( thirdparty ) add_subdirectory( testsuite ) - add_subdirectory( topology ) -if ( HAVE_PYTHON ) +if ( BUILD_PYTHON AND HAVE_PYTHON ) add_subdirectory( pynest ) diff --git a/science/nest/files/patch-cmake_ProcessOptions.cmake b/science/nest/files/patch-cmake_ProcessOptions.cmake index c670929e7980..979ff8fc6835 100644 --- a/science/nest/files/patch-cmake_ProcessOptions.cmake +++ b/science/nest/files/patch-cmake_ProcessOptions.cmake @@ -1,11 +1,11 @@ ---- cmake/ProcessOptions.cmake.orig 2019-05-11 20:18:03 UTC +--- cmake/ProcessOptions.cmake.orig 2021-10-21 05:42:49 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 (" ${CYTHON_VERSION} ") is too old. Please install " - "newer version (0.19.2+)" ) - endif () +@@ -421,7 +421,7 @@ function( NEST_PROCESS_WITH_PYTHON ) + set( Python_INCLUDE_DIRS "${Python_INCLUDE_DIRS}" PARENT_SCOPE ) + set( Python_LIBRARIES "${Python_LIBRARIES}" PARENT_SCOPE ) +- if ( cythonize-pynest ) ++ if ( BUILD_PYTHON AND cythonize-pynest ) + # Need updated Cython because of a change in the C api in Python 3.7 + find_package( Cython 0.28.3 REQUIRED ) + if ( CYTHON_FOUND ) diff --git a/science/nest/pkg-plist b/science/nest/pkg-plist index 7765a85d9da4..884e8c3e70ae 100644 --- a/science/nest/pkg-plist +++ b/science/nest/pkg-plist @@ -1,12 +1,39 @@ bin/nest bin/nest-config +bin/nest-server +bin/nest-server-mpi bin/nest_indirect bin/nest_serial bin/nest_vars.sh +bin/run_all_cpptests bin/sli +include/nest/Random123/aes.h +include/nest/Random123/array.h +include/nest/Random123/ars.h +include/nest/Random123/conventional/gsl_cbrng.h +include/nest/Random123/features/clangfeatures.h +include/nest/Random123/features/compilerfeatures.h +include/nest/Random123/features/gccfeatures.h +include/nest/Random123/features/iccfeatures.h +include/nest/Random123/features/metalfeatures.h +include/nest/Random123/features/msvcfeatures.h +include/nest/Random123/features/nvccfeatures.h +include/nest/Random123/features/open64features.h +include/nest/Random123/features/openclfeatures.h +include/nest/Random123/features/pgccfeatures.h +include/nest/Random123/features/sse.h +include/nest/Random123/features/sunprofeatures.h +include/nest/Random123/features/xlcfeatures.h +include/nest/Random123/gsl_microrng.h +include/nest/Random123/philox.h +include/nest/Random123/tests/kat.h +include/nest/Random123/tests/kat_main.h +include/nest/Random123/tests/rngNxW.h +include/nest/Random123/tests/util.h +include/nest/Random123/threefry.h +include/nest/Random123/u01fixedpt.h 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 @@ -19,21 +46,21 @@ 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/bernoulli_synapse.h +include/nest/beta_normalization_factor.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/clopath_synapse.h include/nest/common_properties_hom_w.h include/nest/common_synapse_properties.h include/nest/compose.hpp include/nest/config.h include/nest/conn_builder.h +include/nest/conn_builder_conngen.h include/nest/conn_builder_factory.h include/nest/conn_builder_impl.h include/nest/conn_parameter.h @@ -48,17 +75,19 @@ 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/cont_delay_synapse.h +include/nest/cont_delay_synapse_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/deprecation_warning.h include/nest/device.h include/nest/device_node.h include/nest/dict.h +include/nest/dict_util.h include/nest/dictdatum.h include/nest/dictstack.h include/nest/dictutils.h @@ -71,13 +100,11 @@ 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 @@ -85,7 +112,6 @@ 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 @@ -99,16 +125,14 @@ 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/ht_synapse.h include/nest/iaf_chs_2007.h include/nest/iaf_chxk_2008.h include/nest/iaf_cond_alpha.h @@ -117,31 +141,27 @@ 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_alpha_ps.h include/nest/iaf_psc_delta.h include/nest/iaf_psc_delta_ps.h include/nest/iaf_psc_exp.h +include/nest/iaf_psc_exp_htum.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/io_manager_impl.h include/nest/iostreamdatum.h include/nest/iterator_pair.h -include/nest/iteratordatum.h include/nest/izhikevich.h +include/nest/jonke_synapse.h include/nest/kernel_manager.h -include/nest/knuthlfg.h include/nest/layer.h include/nest/layer_impl.h -include/nest/librandom_exceptions.h -include/nest/librandom_names.h include/nest/lin_rate.h include/nest/lockptr.h include/nest/lockptrdatum.h @@ -149,7 +169,6 @@ include/nest/lockptrdatum_impl.h include/nest/logging.h include/nest/logging_event.h include/nest/logging_manager.h -include/nest/lognormal_randomdev.h include/nest/manager_interface.h include/nest/mask.h include/nest/mask_impl.h @@ -164,9 +183,7 @@ include/nest/modelrange_manager.h include/nest/modelsmodule.h include/nest/mpi_manager.h include/nest/mpi_manager_impl.h -include/nest/mt19937.h include/nest/multimeter.h -include/nest/multirange.h include/nest/music_cont_in_proxy.h include/nest/music_cont_out_proxy.h include/nest/music_event_handler.h @@ -174,6 +191,9 @@ include/nest/music_event_in_proxy.h include/nest/music_event_out_proxy.h include/nest/music_manager.h include/nest/music_message_in_proxy.h +include/nest/music_rate_in_handler.h +include/nest/music_rate_in_proxy.h +include/nest/music_rate_out_proxy.h include/nest/name.h include/nest/namedatum.h include/nest/nest.h @@ -186,16 +206,16 @@ include/nest/nest_types.h include/nest/nestmodule.h include/nest/neststartup.h include/nest/node.h +include/nest/node_collection.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/parameter.h include/nest/parrot_neuron.h include/nest/parrot_neuron_ps.h include/nest/parser.h @@ -203,25 +223,21 @@ include/nest/parserdatum.h include/nest/per_thread_bool_indicator.h include/nest/poisson_generator.h include/nest/poisson_generator_ps.h -include/nest/poisson_randomdev.h include/nest/position.h +include/nest/pp_cond_exp_mc_urbanczik.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/quantal_stp_synapse.h +include/nest/quantal_stp_synapse_impl.h +include/nest/random_generators.h +include/nest/random_manager.h +include/nest/randutils.hpp include/nest/rate_connection_delayed.h include/nest/rate_connection_instantaneous.h include/nest/rate_neuron_ipn.h @@ -231,13 +247,17 @@ 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_backend.h +include/nest/recording_backend_ascii.h +include/nest/recording_backend_memory.h +include/nest/recording_backend_screen.h include/nest/recording_device.h +include/nest/regula_falsi.h include/nest/ring_buffer.h -include/nest/rng_manager.h +include/nest/ring_buffer_impl.h include/nest/scanner.h -include/nest/selector.h include/nest/send_buffer_position.h -include/nest/sibling_container.h +include/nest/sharedptrdatum.h include/nest/siegert_neuron.h include/nest/sigmoid_rate.h include/nest/sigmoid_rate_gg_1998.h @@ -245,7 +265,6 @@ include/nest/simulation_manager.h include/nest/sinusoidal_gamma_generator.h include/nest/sinusoidal_poisson_generator.h include/nest/sli_io.h -include/nest/sli_neuron.h include/nest/sliactions.h include/nest/sliarray.h include/nest/slibuiltins.h @@ -271,33 +290,36 @@ include/nest/source_table_position.h include/nest/sp_manager.h include/nest/sp_manager_impl.h include/nest/sparse_node_array.h +include/nest/spatial.h include/nest/specialfunctionsmodule.h include/nest/spike_data.h -include/nest/spike_detector.h include/nest/spike_dilutor.h include/nest/spike_generator.h +include/nest/spike_recorder.h include/nest/spikecounter.h include/nest/spin_detector.h include/nest/static_assert.h -include/nest/static_connection.h -include/nest/static_connection_hom_w.h -include/nest/stdp_connection.h -include/nest/stdp_connection_facetshw_hom.h -include/nest/stdp_connection_facetshw_hom_impl.h -include/nest/stdp_connection_hom.h -include/nest/stdp_dopa_connection.h -include/nest/stdp_nn_pre-centered_connection.h -include/nest/stdp_nn_restr_connection.h -include/nest/stdp_nn_symm_connection.h -include/nest/stdp_pl_connection_hom.h -include/nest/stdp_triplet_connection.h +include/nest/static_synapse.h +include/nest/static_synapse_hom_w.h +include/nest/stdp_dopamine_synapse.h +include/nest/stdp_nn_pre_centered_synapse.h +include/nest/stdp_nn_restr_synapse.h +include/nest/stdp_nn_symm_synapse.h +include/nest/stdp_pl_synapse_hom.h +include/nest/stdp_synapse.h +include/nest/stdp_synapse_facetshw_hom.h +include/nest/stdp_synapse_facetshw_hom_impl.h +include/nest/stdp_synapse_hom.h +include/nest/stdp_triplet_synapse.h include/nest/step_current_generator.h include/nest/step_rate_generator.h -include/nest/stimulating_device.h +include/nest/stimulation_backend.h +include/nest/stimulation_device.h include/nest/stopwatch.h +include/nest/streamers.h include/nest/string_utils.h include/nest/stringdatum.h -include/nest/subnet.h +include/nest/structural_plasticity_node.h include/nest/symboldatum.h include/nest/syn_id_delay.h include/nest/synaptic_element.h @@ -314,42 +336,66 @@ include/nest/token.h include/nest/tokenarray.h include/nest/tokenstack.h include/nest/tokenutils.h -include/nest/topology.h -include/nest/topology_names.h -include/nest/topology_parameter.h -include/nest/topologymodule.h include/nest/triedatum.h -include/nest/tsodyks2_connection.h -include/nest/tsodyks_connection.h -include/nest/tsodyks_connection_hom.h +include/nest/tsodyks2_synapse.h +include/nest/tsodyks_synapse.h +include/nest/tsodyks_synapse_hom.h include/nest/typearray.h include/nest/typechk.h -include/nest/uniform_randomdev.h -include/nest/uniformint_randomdev.h include/nest/universal_data_logger.h include/nest/universal_data_logger_impl.h +include/nest/urbanczik_archiving_node.h +include/nest/urbanczik_archiving_node_impl.h +include/nest/urbanczik_synapse.h include/nest/utils.h include/nest/vector_util.h -include/nest/vogels_sprekeler_connection.h -include/nest/voltmeter.h +include/nest/vogels_sprekeler_synapse.h include/nest/volume_transmitter.h -include/nest/vose.h include/nest/vp_manager.h include/nest/vp_manager_impl.h include/nest/weight_recorder.h -lib/libmodels.so -lib/libnest.so -lib/libnestkernel.so -lib/libnestutil.so -lib/libprecise.so -lib/librandom.so -lib/libsli.so -lib/libsli_readline.so -lib/libtopology.so +lib/nest/libmodels.so +lib/nest/libnest.so +lib/nest/libnestkernel.so +lib/nest/libnestutil.so +lib/nest/libsli.so +lib/nest/libsli_readline.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/hl_api.py 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