Date: Thu, 27 Jan 2022 20:28:13 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: 96fe8f7ab1ef - main - science/nest: Update 3.1 -> 3.2 Message-ID: <202201272028.20RKSDlg024140@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=96fe8f7ab1ef31c13cf71d79b6f8d15466544c9a commit 96fe8f7ab1ef31c13cf71d79b6f8d15466544c9a Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2022-01-27 20:15:50 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2022-01-27 20:27:58 +0000 science/nest: Update 3.1 -> 3.2 Reported by: portscout --- science/nest/Makefile | 7 +- science/nest/distinfo | 6 +- science/nest/files/patch-CMakeLists.txt | 19 ++- .../nest/files/patch-cmake_ProcessOptions.cmake | 25 ++- science/nest/pkg-plist | 169 +-------------------- 5 files changed, 45 insertions(+), 181 deletions(-) diff --git a/science/nest/Makefile b/science/nest/Makefile index 01008b721fbd..5c3f17e9cebf 100644 --- a/science/nest/Makefile +++ b/science/nest/Makefile @@ -1,7 +1,6 @@ PORTNAME= nest DISTVERSIONPREFIX= v -DISTVERSION= 3.1 -PORTREVISION= 1 +DISTVERSION= 3.2 CATEGORIES= science biology # NEST is used in neuroscience MAINTAINER= yuri@FreeBSD.org @@ -23,7 +22,7 @@ USE_LDCONFIG= yes USE_GITHUB= yes GH_PROJECT= nest-simulator -SHEBANG_FILES= extras/nest-server extras/nest-server-mpi testsuite/do_tests.sh +SHEBANG_FILES= bin/nest-server bin/nest-server-mpi testsuite/do_tests.sh OPTIONS_DEFINE= PYTHON DOCS OPTIONS_DEFAULT= PYTHON @@ -31,7 +30,7 @@ OPTIONS_SUB= yes PYTHON_CMAKE_BOOL= BUILD_PYTHON PYTHON_USE= python=cython -PYTHON_CMAKE_ON= -DCYTHON_EXECUTABLE:STRING=${PREFIX}/bin/cython-${PYTHON_VER} +PYTHON_CMAKE_ON= -DFREEBSD_PYTHON_VER:STRING=${PYTHON_VER} -DCYTHON_EXECUTABLE:STRING=${PREFIX}/bin/cython-${PYTHON_VER} PORTDOCS= * diff --git a/science/nest/distinfo b/science/nest/distinfo index 58939e8d2162..e7aad6677eb6 100644 --- a/science/nest/distinfo +++ b/science/nest/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1634790045 -SHA256 (nest-nest-simulator-v3.1_GH0.tar.gz) = 5c11dd6b451c4c6bf93037bf29d5231c6c75a0e1a8863344f6fb9bb225f279ca -SIZE (nest-nest-simulator-v3.1_GH0.tar.gz) = 12028051 +TIMESTAMP = 1643310018 +SHA256 (nest-nest-simulator-v3.2_GH0.tar.gz) = 583d5725882ad5e8fd4fc7ffab425da97cbbb91fadbc327e940c184e8892b958 +SIZE (nest-nest-simulator-v3.2_GH0.tar.gz) = 10992802 diff --git a/science/nest/files/patch-CMakeLists.txt b/science/nest/files/patch-CMakeLists.txt index 7f7fc651d7b8..c77579033a51 100644 --- a/science/nest/files/patch-CMakeLists.txt +++ b/science/nest/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2021-09-15 13:04:13 UTC +--- CMakeLists.txt.orig 2022-01-21 18:01:36 UTC +++ CMakeLists.txt -@@ -92,7 +92,7 @@ set( CMAKE_INSTALL_DATADIR "share/${PROJECT_NAME}" CAC +@@ -100,7 +100,7 @@ set( CMAKE_INSTALL_DATADIR "share/${PROJECT_NAME}" CAC ################################################################################ # needed for pynest test suite @@ -9,7 +9,7 @@ find_program( NOSETESTS NAMES nosetests ) endif () -@@ -194,7 +194,7 @@ message("-- NEST version: ${NEST_VERSION_STRING}") +@@ -202,7 +202,7 @@ message("-- NEST version: ${NEST_VERSION_STRING}") enable_testing() set( TEST_OPTS "" ) @@ -18,22 +18,21 @@ set( TEST_OPTS "${TEST_OPTS};--with-python=${PYTHON}" ) endif () -@@ -223,8 +223,12 @@ add_custom_target( installcheck +@@ -231,9 +231,13 @@ add_custom_target( installcheck ################## Define Subdirectories here ################## ################################################################################ --add_subdirectory( doc ) --add_subdirectory( examples ) +if (INSTALL_DOCS) -+ add_subdirectory( doc ) + add_subdirectory( doc ) +endif() + add_subdirectory( bin ) +if (INSTALL_EXAMPLES) -+ add_subdirectory( examples ) + add_subdirectory( examples ) +endif() - add_subdirectory( extras ) + add_subdirectory( build_support ) add_subdirectory( lib ) add_subdirectory( libnestutil ) -@@ -234,7 +238,7 @@ add_subdirectory( nest ) +@@ -243,7 +247,7 @@ add_subdirectory( nest ) add_subdirectory( nestkernel ) add_subdirectory( thirdparty ) add_subdirectory( testsuite ) diff --git a/science/nest/files/patch-cmake_ProcessOptions.cmake b/science/nest/files/patch-cmake_ProcessOptions.cmake index 979ff8fc6835..1282cb5c2b40 100644 --- a/science/nest/files/patch-cmake_ProcessOptions.cmake +++ b/science/nest/files/patch-cmake_ProcessOptions.cmake @@ -1,6 +1,27 @@ ---- cmake/ProcessOptions.cmake.orig 2021-10-21 05:42:49 UTC +--- cmake/ProcessOptions.cmake.orig 2022-01-21 18:01:36 UTC +++ cmake/ProcessOptions.cmake -@@ -421,7 +421,7 @@ function( NEST_PROCESS_WITH_PYTHON ) +@@ -392,9 +392,9 @@ function( NEST_PROCESS_WITH_PYTHON ) + elseif ( ${with-python} STREQUAL "ON" ) + + # Localize the Python interpreter and ABI +- find_package( Python 3.8 QUIET COMPONENTS Interpreter Development.Module ) ++ find_package( Python ${FREEBSD_PYTHON_VER} EXACT QUIET COMPONENTS Interpreter Development.Module ) + if ( NOT Python_FOUND ) +- find_package( Python 3.8 REQUIRED Interpreter Development ) ++ find_package( Python ${FREEBSD_PYTHON_VER} EXACT REQUIRED Interpreter Development ) + string( CONCAT PYABI_WARN "Could not locate Python ABI" + ", using shared libraries and header file instead." + " Please clear your CMake cache and build folder and verify that CMake" +@@ -402,7 +402,7 @@ function( NEST_PROCESS_WITH_PYTHON ) + ) + message( WARNING "${PYABI_WARN}") + else() +- find_package( Python 3.8 REQUIRED Interpreter Development.Module ) ++ find_package( Python ${FREEBSD_PYTHON_VER} EXACT REQUIRED Interpreter Development.Module ) + endif() + + if ( Python_FOUND ) +@@ -432,7 +432,7 @@ function( NEST_PROCESS_WITH_PYTHON ) set( Python_INCLUDE_DIRS "${Python_INCLUDE_DIRS}" PARENT_SCOPE ) set( Python_LIBRARIES "${Python_LIBRARIES}" PARENT_SCOPE ) diff --git a/science/nest/pkg-plist b/science/nest/pkg-plist index 884e8c3e70ae..21eb7381cd56 100644 --- a/science/nest/pkg-plist +++ b/science/nest/pkg-plist @@ -165,7 +165,6 @@ include/nest/layer_impl.h include/nest/lin_rate.h include/nest/lockptr.h include/nest/lockptrdatum.h -include/nest/lockptrdatum_impl.h include/nest/logging.h include/nest/logging_event.h include/nest/logging_manager.h @@ -212,7 +211,6 @@ include/nest/noise_generator.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 @@ -316,7 +314,6 @@ include/nest/step_rate_generator.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/structural_plasticity_node.h @@ -361,8 +358,6 @@ 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 -%%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/import_libs.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/lib/README.md %%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/lib/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/lib/hl_api_connection_helpers.py @@ -395,161 +390,6 @@ lib/nest/libsli_readline.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/versionchecker.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/visualization.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/nest/voltage_trace.py -%%DATADIR%%/extras/EditorSupport/vim/syntax/sli.vim -%%DATADIR%%/help_generator/README.md -%%DATADIR%%/help_generator/assets/css/ie.css -%%DATADIR%%/help_generator/assets/css/jquery.mmenu.all.css -%%DATADIR%%/help_generator/assets/css/jss-style.min.css -%%DATADIR%%/help_generator/assets/css/moeppel1.png -%%DATADIR%%/help_generator/assets/css/moeppel2.png -%%DATADIR%%/help_generator/assets/css/nest-initiative-logo.png -%%DATADIR%%/help_generator/assets/css/prettify.css -%%DATADIR%%/help_generator/assets/css/style.css -%%DATADIR%%/help_generator/assets/images/arrow.png -%%DATADIR%%/help_generator/assets/js/code-prettify/COPYING -%%DATADIR%%/help_generator/assets/js/code-prettify/lang-apollo.js 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%%DATADIR%%/testsuite/cpptests/test_enum_bitfield.h %%DATADIR%%/testsuite/cpptests/test_parameter.h %%DATADIR%%/testsuite/cpptests/test_sort.h -%%DATADIR%%/testsuite/cpptests/test_streamers.h %%DATADIR%%/testsuite/cpptests/test_target_fields.h %%DATADIR%%/testsuite/do_tests.sh %%DATADIR%%/testsuite/junit_xml.sh @@ -647,6 +486,8 @@ lib/nest/libsli_readline.so %%DATADIR%%/testsuite/mpitests/test_sinusoidal_poisson_generator_4.sli %%DATADIR%%/testsuite/mpitests/test_sinusoidal_poisson_generator_5.sli %%DATADIR%%/testsuite/mpitests/test_sinusoidal_poisson_generator_6.sli +%%DATADIR%%/testsuite/mpitests/test_spatial_distributed_positions.sli +%%DATADIR%%/testsuite/mpitests/test_spatial_pairwise_bernoulli_on_source_param.sli %%DATADIR%%/testsuite/mpitests/test_symmetric_connections_mpi.sli %%DATADIR%%/testsuite/mpitests/ticket-400.sli %%DATADIR%%/testsuite/mpitests/ticket-516.sli @@ -688,7 +529,10 @@ lib/nest/libsli_readline.so %%DATADIR%%/testsuite/pytests/mpi/2/test_connect_pairwise_bernoulli.py %%DATADIR%%/testsuite/pytests/mpi/2/test_connect_symmetric_pairwise_bernoulli.py %%DATADIR%%/testsuite/pytests/mpi/2/test_issue_576.py +%%DATADIR%%/testsuite/pytests/mpi/2/test_spatial_positions.py +%%DATADIR%%/testsuite/pytests/mpi/2/test_synapsecollection_mpi.py %%DATADIR%%/testsuite/pytests/mpi/4/test_consistent_local_vps.py +%%DATADIR%%/testsuite/pytests/mpi/4/test_spatial_positions.py %%DATADIR%%/testsuite/pytests/mpi/README.md %%DATADIR%%/testsuite/pytests/test_NodeCollection.py %%DATADIR%%/testsuite/pytests/test_aeif_data_lsodar.dat @@ -755,7 +599,6 @@ lib/nest/libsli_readline.so %%DATADIR%%/testsuite/pytests/test_sp/test_sp_manager.py %%DATADIR%%/testsuite/pytests/test_sp/test_synaptic_elements.py %%DATADIR%%/testsuite/pytests/test_sp/test_update_synaptic_elements.py -%%DATADIR%%/testsuite/pytests/test_sp/utils.py %%DATADIR%%/testsuite/pytests/test_spatial/test_SynapseCollection_distance.py %%DATADIR%%/testsuite/pytests/test_spatial/test_basics.py %%DATADIR%%/testsuite/pytests/test_spatial/test_connect_layers.py @@ -769,11 +612,13 @@ lib/nest/libsli_readline.so %%DATADIR%%/testsuite/pytests/test_spatial/test_rotated_rect_mask.py %%DATADIR%%/testsuite/pytests/test_spatial/test_selection_function_and_elliptical_mask.py %%DATADIR%%/testsuite/pytests/test_spatial/test_spatial_distributions.py +%%DATADIR%%/testsuite/pytests/test_spatial_positions.py %%DATADIR%%/testsuite/pytests/test_split_simulation.py %%DATADIR%%/testsuite/pytests/test_stack.py %%DATADIR%%/testsuite/pytests/test_status.py %%DATADIR%%/testsuite/pytests/test_stdp_multiplicity.py %%DATADIR%%/testsuite/pytests/test_stdp_nn_synapses.py +%%DATADIR%%/testsuite/pytests/test_stdp_synapse.py %%DATADIR%%/testsuite/pytests/test_stdp_triplet_synapse.py %%DATADIR%%/testsuite/pytests/test_step_rate_generator.py %%DATADIR%%/testsuite/pytests/test_synapsecollection.py
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