Date: Wed, 10 Jun 2026 18:13:41 +0000 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: 61edd3c17ad7 - main - science/nest: update=?utf-8?Q? 3.8 =E2=86=92?= 3.10 Message-ID: <6a29a955.41fa4.10282685@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=61edd3c17ad75743169efcbef9ad26bae2b62552 commit 61edd3c17ad75743169efcbef9ad26bae2b62552 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-06-10 04:45:37 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-06-10 18:13:36 +0000 science/nest: update 3.8 → 3.10 --- science/nest/Makefile | 13 +- science/nest/distinfo | 6 +- science/nest/files/patch-CMakeLists.txt | 27 +- science/nest/pkg-plist | 1079 +++++++++++++------------------ 4 files changed, 479 insertions(+), 646 deletions(-) diff --git a/science/nest/Makefile b/science/nest/Makefile index d754c7697769..1df2216fb298 100644 --- a/science/nest/Makefile +++ b/science/nest/Makefile @@ -1,7 +1,6 @@ PORTNAME= nest DISTVERSIONPREFIX= v -DISTVERSION= 3.8 -PORTREVISION= 6 +DISTVERSION= 3.10 CATEGORIES= science biology # NEST is used in neuroscience MAINTAINER= yuri@FreeBSD.org @@ -26,6 +25,7 @@ USE_GITHUB= yes GH_PROJECT= nest-simulator SHEBANG_FILES= bin/nest-server bin/nest-server-mpi testsuite/do_tests.sh +SHEBANG_GLOB= *.py BINARY_ALIAS= python3=${PYTHON_CMD} @@ -34,7 +34,7 @@ OPTIONS_DEFAULT= PYTHON OPTIONS_SUB= yes PYTHON_CMAKE_BOOL= BUILD_PYTHON -PYTHON_USE= python=cython0 +PYTHON_USE= python=cython PYTHON_CMAKE_ON= -DFREEBSD_PYTHON_VER:STRING=${PYTHON_VER} -DCYTHON_EXECUTABLE:STRING=${PREFIX}/bin/cython-${PYTHON_VER} PORTDOCS= * @@ -45,11 +45,10 @@ USES+= compiler:gcc-c++11-lib USES+= compiler:c++11-lang .endif -# 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 -# many tests fail, see https://github.com/nest/nest-simulator/issues/2848 - post-install: @${REINPLACE_CMD} -i '' -e 's|^python3 |${PYTHON_CMD} |' ${STAGEDIR}${PREFIX}/share/nest/testsuite/do_tests.sh +# tests as of 3.10: 100% tests passed, 0 tests failed out of 1 +# tests require the port to be installed with DOCS=ON, see https://github.com/nest/nest-simulator/issues/2191 + .include <bsd.port.mk> diff --git a/science/nest/distinfo b/science/nest/distinfo index eb38c9085b0c..ed32782d95d6 100644 --- a/science/nest/distinfo +++ b/science/nest/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1722665541 -SHA256 (nest-nest-simulator-v3.8_GH0.tar.gz) = eb255f8828be001abea0cddad2f14d78b70857fc82bece724551f27c698318c8 -SIZE (nest-nest-simulator-v3.8_GH0.tar.gz) = 30812352 +TIMESTAMP = 1781065797 +SHA256 (nest-nest-simulator-v3.10_GH0.tar.gz) = fd4def89c109e19d50e4630ab56bb9ddd4f15bf0ef735070189f0a83e2416a55 +SIZE (nest-nest-simulator-v3.10_GH0.tar.gz) = 36287666 diff --git a/science/nest/files/patch-CMakeLists.txt b/science/nest/files/patch-CMakeLists.txt index 919ae30612a7..c3b80f46b884 100644 --- a/science/nest/files/patch-CMakeLists.txt +++ b/science/nest/files/patch-CMakeLists.txt @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2023-02-16 13:40:33 UTC +--- CMakeLists.txt.orig 2026-06-09 13:32:28 UTC +++ CMakeLists.txt -@@ -197,7 +197,7 @@ printInfo("-- NEST version: ${NEST_VERSION_STRING}") +@@ -199,7 +199,7 @@ set( TEST_OPTS "" ) enable_testing() set( TEST_OPTS "" ) @@ -9,7 +9,7 @@ set( TEST_OPTS "${TEST_OPTS};--with-python=${PYTHON}" ) endif () -@@ -226,9 +226,13 @@ add_custom_target( installcheck +@@ -227,7 +227,9 @@ add_custom_target( installcheck ################## Define Subdirectories here ################## ################################################################################ @@ -17,13 +17,9 @@ add_subdirectory( doc ) +endif() add_subdirectory( bin ) -+if (INSTALL_EXAMPLES) - add_subdirectory( examples ) -+endif() add_subdirectory( build_support ) - add_subdirectory( lib ) add_subdirectory( libnestutil ) -@@ -238,7 +242,7 @@ add_subdirectory( nest ) +@@ -235,7 +237,7 @@ add_subdirectory( testsuite ) add_subdirectory( nestkernel ) add_subdirectory( thirdparty ) add_subdirectory( testsuite ) @@ -32,3 +28,18 @@ add_subdirectory( pynest ) endif () +@@ -348,12 +350,10 @@ endif() + set( CMAKE_INSTALL_DOCDIR "nest/doc") + endif() + +-install( FILES LICENSE README.md +- DESTINATION ${CMAKE_INSTALL_DOCDIR} +-) +- ++if (INSTALL_EXAMPLES) + install( DIRECTORY examples/ + DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples + ) ++endif() + + nest_print_config_summary() diff --git a/science/nest/pkg-plist b/science/nest/pkg-plist index 3dd892e8366f..f4f415a4aef6 100644 --- a/science/nest/pkg-plist +++ b/science/nest/pkg-plist @@ -1,12 +1,7 @@ -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 @@ -42,20 +37,14 @@ 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/astrocyte_lr_1994.h include/nest/bernoulli_synapse.h include/nest/beta_normalization_factor.h include/nest/binary_neuron.h include/nest/block_vector.h -include/nest/booldatum.h include/nest/buffer_resize_log.h -include/nest/callbackdatum.h -include/nest/charcode.h include/nest/clopath_archiving_node.h include/nest/clopath_synapse.h include/nest/cm_compartmentcurrents.h @@ -86,42 +75,44 @@ 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/cycle_time_log.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 +include/nest/dictionary.h include/nest/diffusion_connection.h -include/nest/doubledatum.h include/nest/enum_bitfield.h include/nest/eprop_archiving_node.h include/nest/eprop_archiving_node_impl.h +include/nest/eprop_archiving_node_readout.h +include/nest/eprop_archiving_node_recurrent.h +include/nest/eprop_archiving_node_recurrent_impl.h +include/nest/eprop_iaf.h +include/nest/eprop_iaf_adapt.h include/nest/eprop_iaf_adapt_bsshslm_2020.h include/nest/eprop_iaf_bsshslm_2020.h +include/nest/eprop_iaf_psc_delta.h +include/nest/eprop_iaf_psc_delta_adapt.h +include/nest/eprop_learning_signal_connection.h include/nest/eprop_learning_signal_connection_bsshslm_2020.h +include/nest/eprop_readout.h include/nest/eprop_readout_bsshslm_2020.h +include/nest/eprop_synapse.h include/nest/eprop_synapse_bsshslm_2020.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/fdstream.h -include/nest/filesystem.h +include/nest/flush_event_mechanism.h include/nest/free_layer.h -include/nest/functional.h -include/nest/functiondatum.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/gif_cond_exp.h @@ -133,7 +124,6 @@ include/nest/ginzburg_neuron.h include/nest/glif_cond.h include/nest/glif_psc.h include/nest/glif_psc_double_alpha.h -include/nest/gnureadline.h include/nest/grid_layer.h include/nest/grid_mask.h include/nest/growth_curve.h @@ -168,12 +158,10 @@ include/nest/iaf_psc_exp_ps.h include/nest/iaf_psc_exp_ps_lossless.h include/nest/iaf_tum_2000.h include/nest/ignore_and_fire.h +include/nest/ignore_and_spike_mechanism.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/izhikevich.h include/nest/jonke_synapse.h @@ -181,8 +169,6 @@ include/nest/kernel_manager.h include/nest/layer.h include/nest/layer_impl.h include/nest/lin_rate.h -include/nest/lockptr.h -include/nest/lockptrdatum.h include/nest/logging.h include/nest/logging_event.h include/nest/logging_manager.h @@ -212,32 +198,23 @@ 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 -include/nest/nest_datums.h include/nest/nest_extension_interface.h include/nest/nest_impl.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_collection.h include/nest/node_manager.h include/nest/noise_generator.h include/nest/ntree.h include/nest/ntree_impl.h -include/nest/numericdatum.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 -include/nest/parserdatum.h include/nest/per_thread_bool_indicator.h include/nest/poisson_generator.h include/nest/poisson_generator_ps.h @@ -245,7 +222,6 @@ include/nest/position.h include/nest/pp_cond_exp_mc_urbanczik.h include/nest/pp_psc_delta.h include/nest/ppd_sup_generator.h -include/nest/processes.h include/nest/proxynode.h include/nest/pseudo_recording_device.h include/nest/pulsepacket_generator.h @@ -271,11 +247,9 @@ include/nest/recording_device.h include/nest/regula_falsi.h include/nest/ring_buffer.h include/nest/ring_buffer_impl.h -include/nest/scanner.h include/nest/secondary_event.h include/nest/secondary_event_impl.h include/nest/send_buffer_position.h -include/nest/sharedptrdatum.h include/nest/sic_connection.h include/nest/siegert_neuron.h include/nest/sigmoid_rate.h @@ -283,25 +257,7 @@ include/nest/sigmoid_rate_gg_1998.h include/nest/simulation_manager.h include/nest/sinusoidal_gamma_generator.h include/nest/sinusoidal_poisson_generator.h -include/nest/sli_io.h -include/nest/sliactions.h -include/nest/sliarray.h -include/nest/slibuiltins.h include/nest/slice_ring_buffer.h -include/nest/slicontrol.h -include/nest/slidata.h -include/nest/slidict.h -include/nest/sliexceptions.h -include/nest/slifunction.h -include/nest/sligraphics.h -include/nest/slimath.h -include/nest/slimodule.h -include/nest/slinames.h -include/nest/sliregexp.h -include/nest/slistack.h -include/nest/slistartup.h -include/nest/slitype.h -include/nest/slitypecheck.h include/nest/sonata_connector.h include/nest/sort.h include/nest/source.h @@ -311,7 +267,6 @@ 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_dilutor.h include/nest/spike_generator.h @@ -337,10 +292,8 @@ include/nest/step_rate_generator.h include/nest/stimulation_backend.h include/nest/stimulation_device.h include/nest/stopwatch.h -include/nest/string_utils.h -include/nest/stringdatum.h +include/nest/stopwatch_impl.h include/nest/structural_plasticity_node.h -include/nest/symboldatum.h include/nest/syn_id_delay.h include/nest/synaptic_element.h include/nest/tanh_rate.h @@ -350,24 +303,15 @@ include/nest/target_identifier.h include/nest/target_table.h include/nest/target_table_devices.h include/nest/target_table_devices_impl.h -include/nest/tarrayobj.h include/nest/threshold_lin_rate.h -include/nest/token.h -include/nest/tokenarray.h -include/nest/tokenstack.h -include/nest/tokenutils.h -include/nest/triedatum.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/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_synapse.h include/nest/volume_transmitter.h @@ -375,21 +319,11 @@ include/nest/vp_manager.h include/nest/vp_manager_impl.h include/nest/weight_optimizer.h include/nest/weight_recorder.h -lib/nest/libnest.so -lib/nest/libnest.so.3 -lib/nest/libnest.so.3.8.0 -lib/nest/libsli.so -lib/nest/libsli.so.3 -lib/nest/libsli.so.3.8.0 -lib/nest/libsli_readline.so -lib/nest/libsli_readline.so.3 -lib/nest/libsli_readline.so.3.8.0 %%PYTHON_SITELIBDIR%%/nest/__init__.py %%PYTHON_SITELIBDIR%%/nest/lib/README.md %%PYTHON_SITELIBDIR%%/nest/lib/__init__.py %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_connection_helpers.py %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_connections.py -%%PYTHON_SITELIBDIR%%/nest/lib/hl_api_exceptions.py %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_helper.py %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_info.py %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_models.py @@ -400,13 +334,11 @@ lib/nest/libsli_readline.so.3.8.0 %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_spatial.py %%PYTHON_SITELIBDIR%%/nest/lib/hl_api_types.py %%PYTHON_SITELIBDIR%%/nest/ll_api.py -%%PYTHON_SITELIBDIR%%/nest/ll_api_kernel_attributes.py %%PYTHON_SITELIBDIR%%/nest/logic/__init__.py %%PYTHON_SITELIBDIR%%/nest/logic/hl_api_logic.py %%PYTHON_SITELIBDIR%%/nest/math/__init__.py %%PYTHON_SITELIBDIR%%/nest/math/hl_api_math.py -%%PYTHON_SITELIBDIR%%/nest/pynest-init.sli -%%PYTHON_SITELIBDIR%%/nest/pynestkernel.so +%%PYTHON_SITELIBDIR%%/nest/nestkernel_api.so %%PYTHON_SITELIBDIR%%/nest/random/__init__.py %%PYTHON_SITELIBDIR%%/nest/random/hl_api_random.py %%PYTHON_SITELIBDIR%%/nest/raster_plot.py @@ -419,22 +351,6 @@ lib/nest/libsli_readline.so.3.8.0 %%PYTHON_SITELIBDIR%%/nest/versionchecker.py %%PYTHON_SITELIBDIR%%/nest/visualization.py %%PYTHON_SITELIBDIR%%/nest/voltage_trace.py -%%DATADIR%%/sli/FormattedIO.sli -%%DATADIR%%/sli/arraylib.sli -%%DATADIR%%/sli/debug.sli -%%DATADIR%%/sli/filesystem.sli -%%DATADIR%%/sli/helpinit.sli -%%DATADIR%%/sli/library.sli -%%DATADIR%%/sli/mathematica.sli -%%DATADIR%%/sli/misc_helpers.sli -%%DATADIR%%/sli/nest-init.sli -%%DATADIR%%/sli/oosupport.sli -%%DATADIR%%/sli/processes.sli -%%DATADIR%%/sli/ps-lib.sli -%%DATADIR%%/sli/regexp.sli -%%DATADIR%%/sli/sli-init.sli -%%DATADIR%%/sli/typeinit.sli -%%DATADIR%%/sli/unittest.sli %%DATADIR%%/testsuite/cpptests/CMakeLists.txt %%DATADIR%%/testsuite/cpptests/README.md %%DATADIR%%/testsuite/cpptests/run_all.cpp @@ -445,544 +361,451 @@ lib/nest/libsli_readline.so.3.8.0 %%DATADIR%%/testsuite/cpptests/test_target_fields.h %%DATADIR%%/testsuite/do_tests.sh %%DATADIR%%/testsuite/junit_xml.sh -%%DATADIR%%/testsuite/mpi_selftests/fail/CMakeLists.txt -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_invariant_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_pass_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_process_invariant_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_process_invariant_events_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/crash_distributed_rank_invariant_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_invariant_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_pass_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_process_invariant_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_process_invariant_events_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/fail/fail_distributed_rank_invariant_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/CMakeLists.txt -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_invariant_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_pass_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_process_invariant_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_process_invariant_events_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_distributed_rank_invariant_collect_assert_or_die.sli -%%DATADIR%%/testsuite/mpi_selftests/pass/test_parse_message_line.sli -%%DATADIR%%/testsuite/mpitests/CMakeLists.txt -%%DATADIR%%/testsuite/mpitests/README -%%DATADIR%%/testsuite/mpitests/issue-1974.sli -%%DATADIR%%/testsuite/mpitests/issue-2119.sli -%%DATADIR%%/testsuite/mpitests/issue-281.sli -%%DATADIR%%/testsuite/mpitests/issue-600.sli -%%DATADIR%%/testsuite/mpitests/test_connect_array_all_to_all_mpi.sli -%%DATADIR%%/testsuite/mpitests/test_connect_array_fixed_indegree_mpi.sli -%%DATADIR%%/testsuite/mpitests/test_connect_array_fixed_outdegree_mpi.sli -%%DATADIR%%/testsuite/mpitests/test_delay_exchange.sli -%%DATADIR%%/testsuite/mpitests/test_fixed_indegree.sli -%%DATADIR%%/testsuite/mpitests/test_gamma_sup_generator.sli -%%DATADIR%%/testsuite/mpitests/test_gap_junctions_mpi.sli -%%DATADIR%%/testsuite/mpitests/test_get_nodes.sli -%%DATADIR%%/testsuite/mpitests/test_ginzburg_neuron.sli -%%DATADIR%%/testsuite/mpitests/test_global_rng.sli -%%DATADIR%%/testsuite/mpitests/test_iaf_ring.sli -%%DATADIR%%/testsuite/mpitests/test_localonly.sli -%%DATADIR%%/testsuite/mpitests/test_mip_generator.sli -%%DATADIR%%/testsuite/mpitests/test_multiple_synapses.sli -%%DATADIR%%/testsuite/mpitests/test_multiple_synapses_spatial_networks.sli -%%DATADIR%%/testsuite/mpitests/test_multiplicity.sli -%%DATADIR%%/testsuite/mpitests/test_neuron_vp.sli -%%DATADIR%%/testsuite/mpitests/test_neuron_vp_global.sli -%%DATADIR%%/testsuite/mpitests/test_noise_generator.sli -%%DATADIR%%/testsuite/mpitests/test_one_to_one.sli -%%DATADIR%%/testsuite/mpitests/test_pairwise_bernoulli.sli -%%DATADIR%%/testsuite/mpitests/test_parallel_conn_and_rand.sli -%%DATADIR%%/testsuite/mpitests/test_poisson_generator.sli -%%DATADIR%%/testsuite/mpitests/test_poisson_generator_ps.sli -%%DATADIR%%/testsuite/mpitests/test_pp_psc_delta.sli -%%DATADIR%%/testsuite/mpitests/test_ppd_sup_generator.sli -%%DATADIR%%/testsuite/mpitests/test_pulsepacket_generator.sli -%%DATADIR%%/testsuite/mpitests/test_rate_neurons_mpi.sli -%%DATADIR%%/testsuite/mpitests/test_sinusoidal_gamma_generator_1.sli -%%DATADIR%%/testsuite/mpitests/test_sinusoidal_gamma_generator_2.sli 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