diff --git a/science/arbor/Makefile b/science/arbor/Makefile index d4bb0259284a..cb774c521698 100644 --- a/science/arbor/Makefile +++ b/science/arbor/Makefile @@ -1,44 +1,46 @@ PORTNAME= arbor DISTVERSIONPREFIX= v -DISTVERSION= 0.8.1 +DISTVERSION= 0.9.0 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Multi-compartment neural network simulation library WWW= https://arbor-sim.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails: unknown type name 'float64x2_t' BUILD_DEPENDS= bash:shells/bash \ libfmt>0:devel/libfmt \ nlohmann-json>0:devel/nlohmann-json \ random123>0:devel/random123 \ ${PYTHON_PKGNAMEPREFIX}svgwrite>0:graphics/py-svgwrite@${PY_FLAVOR} -LIB_DEPENDS= libpugixml.so:textproc/pugixml +BUILD_DEPENDS+= ${LOCALBASE}/lib/cmake/GTest/GTestConfig.cmake:devel/googletest # https://github.com/arbor-sim/arbor/issues/2205 +LIB_DEPENDS= libhwloc.so:devel/hwloc2 \ + libpugixml.so:textproc/pugixml RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}svgwrite>0:graphics/py-svgwrite@${PY_FLAVOR} TEST_DEPENDS= googletest>=0:devel/googletest USES= cmake compiler:c++17-lang localbase python shebangfix USE_GITHUB= yes GH_ACCOUNT= arbor-sim SHEBANG_FILES= scripts/arbor-build-catalogue CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} OPTIONS_DEFINE= NATIVE NATIVE_CMAKE_ON= -DARB_ARCH=native NATIVE_CMAKE_OFF= -DARB_ARCH=none TEST_TARGET= tests # tests fail to build, see https://github.com/arbor-sim/arbor/issues/2075 post-install: @${RMDIR} ${STAGEDIR}${DOCSDIR} .include diff --git a/science/arbor/distinfo b/science/arbor/distinfo index 2fd4d9cc91b9..467206167c80 100644 --- a/science/arbor/distinfo +++ b/science/arbor/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1671842310 -SHA256 (arbor-sim-arbor-v0.8.1_GH0.tar.gz) = 9d32edf5def9bbe30b5648d064291b86cf3f637b2dc0b82f7a276f5f41e6bcef -SIZE (arbor-sim-arbor-v0.8.1_GH0.tar.gz) = 7812575 +TIMESTAMP = 1691736150 +SHA256 (arbor-sim-arbor-v0.9.0_GH0.tar.gz) = 920c7926453379d367c6c8bb01ff867c03e44e8a7a6a5655d5eaa3d692618ca1 +SIZE (arbor-sim-arbor-v0.9.0_GH0.tar.gz) = 10164524 diff --git a/science/arbor/pkg-plist b/science/arbor/pkg-plist index 88f635490f8f..4afab017bce6 100644 --- a/science/arbor/pkg-plist +++ b/science/arbor/pkg-plist @@ -1,113 +1,119 @@ bin/arbor-build-catalogue bin/lmorpho bin/modcc include/arbor/arb_types.h include/arbor/arb_types.hpp include/arbor/arb_types.inc include/arbor/arbexcept.hpp include/arbor/assert.hpp include/arbor/assert_macro.hpp include/arbor/benchmark_cell.hpp include/arbor/cable_cell.hpp include/arbor/cable_cell_param.hpp include/arbor/common_types.hpp include/arbor/communication/mpi_error.hpp +include/arbor/communication/remote.hpp include/arbor/constants.hpp include/arbor/context.hpp include/arbor/cv_policy.hpp include/arbor/domain_decomposition.hpp include/arbor/domdecexcept.hpp include/arbor/event_generator.hpp include/arbor/export.hpp include/arbor/fvm_types.hpp include/arbor/generic_event.hpp include/arbor/gpu/cuda_api.hpp include/arbor/gpu/gpu_api.hpp include/arbor/gpu/gpu_common.hpp include/arbor/gpu/hip_api.hpp include/arbor/gpu/math_cu.hpp include/arbor/gpu/reduce_by_key.hpp include/arbor/iexpr.hpp include/arbor/lif_cell.hpp include/arbor/load_balance.hpp include/arbor/math.hpp include/arbor/mechanism.hpp include/arbor/mechanism_abi.h include/arbor/mechcat.hpp include/arbor/mechinfo.hpp include/arbor/morph/cv_data.hpp include/arbor/morph/embed_pwlin.hpp include/arbor/morph/isometry.hpp include/arbor/morph/label_dict.hpp include/arbor/morph/locset.hpp include/arbor/morph/mcable_map.hpp include/arbor/morph/morphexcept.hpp include/arbor/morph/morphology.hpp include/arbor/morph/mprovider.hpp include/arbor/morph/place_pwlin.hpp include/arbor/morph/primitives.hpp include/arbor/morph/region.hpp include/arbor/morph/segment_tree.hpp include/arbor/morph/stitch.hpp include/arbor/profile/clock.hpp include/arbor/profile/meter.hpp include/arbor/profile/meter_manager.hpp include/arbor/profile/profiler.hpp include/arbor/profile/timer.hpp include/arbor/recipe.hpp include/arbor/s_expr.hpp include/arbor/sampling.hpp include/arbor/schedule.hpp +include/arbor/serdes.hpp include/arbor/simd/approx.hpp include/arbor/simd/avx.hpp include/arbor/simd/avx512.hpp include/arbor/simd/generic.hpp include/arbor/simd/implbase.hpp include/arbor/simd/native.hpp include/arbor/simd/neon.hpp include/arbor/simd/simd.hpp include/arbor/simd/simd_io.hpp include/arbor/simd/sve.hpp +include/arbor/simd/sve_bits.hpp +include/arbor/simd/vls_sve.hpp +include/arbor/simd/vls_sve_bits.hpp include/arbor/simple_sampler.hpp include/arbor/simulation.hpp include/arbor/spike.hpp include/arbor/spike_event.hpp include/arbor/spike_source_cell.hpp include/arbor/symmetric_recipe.hpp include/arbor/util/any_cast.hpp include/arbor/util/any_ptr.hpp include/arbor/util/any_visitor.hpp include/arbor/util/compat.hpp include/arbor/util/expected.hpp include/arbor/util/extra_traits.hpp include/arbor/util/handle_set.hpp include/arbor/util/hash_def.hpp include/arbor/util/lexcmp_def.hpp include/arbor/util/pp_util.hpp include/arbor/util/scope_exit.hpp include/arbor/util/typed_map.hpp include/arbor/util/uninitialized.hpp include/arbor/util/unique_any.hpp include/arbor/util/visibility.hpp include/arbor/version.hpp include/arborenv/arbenvexcept.hpp include/arborenv/concurrency.hpp include/arborenv/default_env.hpp include/arborenv/export.hpp include/arborenv/gpu_env.hpp include/arborenv/with_mpi.hpp include/arborio/cableio.hpp include/arborio/cv_policy_parse.hpp include/arborio/export.hpp +include/arborio/json_serdes.hpp include/arborio/label_parse.hpp include/arborio/neurolucida.hpp include/arborio/neuroml.hpp include/arborio/swcio.hpp lib/cmake/arbor/arbor-config-version.cmake lib/cmake/arbor/arbor-config.cmake lib/cmake/arbor/arbor-targets-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/arbor/arbor-targets.cmake lib/libarbor.so lib/libarborenv.so lib/libarborio.so %%DATADIR%%/BuildModules.cmake diff --git a/science/py-arbor/Makefile b/science/py-arbor/Makefile index 8bd2028e8784..b6e559395a89 100644 --- a/science/py-arbor/Makefile +++ b/science/py-arbor/Makefile @@ -1,36 +1,37 @@ PORTNAME= arbor DISTVERSIONPREFIX= v -DISTVERSION= 0.8.1 +DISTVERSION= 0.9.0 CATEGORIES= science PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Multi-compartment neural network simulation library WWW= https://arbor-sim.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE -BUILD_DEPENDS= pybind11>0:devel/pybind11 +BUILD_DEPENDS= pybind11>0:devel/pybind11 \ + nlohmann-json>0:devel/nlohmann-json LIB_DEPENDS= libarbor.so:science/arbor USES= cmake compiler:c++17-lang localbase:ldflags python USE_PYTHON= flavors USE_GITHUB= yes GH_ACCOUNT= arbor-sim WRKSRC_SUBDIR= python CMAKE_ARGS= -DPython3_EXECUTABLE=${PYTHON_CMD} \ -DARB_PYTHON_LIB_PATH=${PYTHONPREFIX_SITELIBDIR} CXXFLAGS+= -fPIC post-patch: @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/arbor/_arbor${PYTHON_EXT_SUFFIX}.so .include diff --git a/science/py-arbor/distinfo b/science/py-arbor/distinfo index 4c6eb0df5332..249aad786e70 100644 --- a/science/py-arbor/distinfo +++ b/science/py-arbor/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1671874647 -SHA256 (arbor-sim-arbor-v0.8.1_GH0.tar.gz) = 9d32edf5def9bbe30b5648d064291b86cf3f637b2dc0b82f7a276f5f41e6bcef -SIZE (arbor-sim-arbor-v0.8.1_GH0.tar.gz) = 7812575 +TIMESTAMP = 1691740349 +SHA256 (arbor-sim-arbor-v0.9.0_GH0.tar.gz) = 920c7926453379d367c6c8bb01ff867c03e44e8a7a6a5655d5eaa3d692618ca1 +SIZE (arbor-sim-arbor-v0.9.0_GH0.tar.gz) = 10164524 diff --git a/science/py-arbor/files/patch-CMakeLists.txt b/science/py-arbor/files/patch-CMakeLists.txt index 9441da10091c..988f55467741 100644 --- a/science/py-arbor/files/patch-CMakeLists.txt +++ b/science/py-arbor/files/patch-CMakeLists.txt @@ -1,28 +1,34 @@ ---- CMakeLists.txt.orig 2022-11-15 15:19:19 UTC +--- CMakeLists.txt.orig 2023-08-10 09:47:38 UTC +++ CMakeLists.txt @@ -1,3 +1,7 @@ +cmake_minimum_required(VERSION 3.19) + +find_package(Python3 ${arb_py_version} COMPONENTS Interpreter Development REQUIRED) + include(GNUInstallDirs) set(PYBIND11_CPP_STANDARD -std=c++17) -@@ -79,14 +83,14 @@ if (ARB_WITH_MPI) +@@ -80,14 +84,14 @@ if (ARB_WITH_MPI) endif() # For unit tests on C++ side of Python wrappers -add_subdirectory(test) +#add_subdirectory(test) # Create the Python module in the build directory. # The module contains the dynamic library, __init__.py and VERSION information. set(python_mod_path "${CMAKE_CURRENT_BINARY_DIR}/arbor") set_target_properties(pyarb PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${python_mod_path}") -file(COPY "${PROJECT_SOURCE_DIR}/python/__init__.py" DESTINATION "${python_mod_path}") -file(COPY "${PROJECT_SOURCE_DIR}/VERSION" DESTINATION "${python_mod_path}") +file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/__init__.py" DESTINATION "${python_mod_path}") +file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/VERSION" DESTINATION "${python_mod_path}") # Set the installation path +@@ -117,4 +121,4 @@ endif() + + install(TARGETS pyarb DESTINATION ${_python_module_install_path}) + install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/__init__.py DESTINATION ${_python_module_install_path}) +-install(FILES ${PROJECT_SOURCE_DIR}/VERSION ${PROJECT_SOURCE_DIR}/README.md ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${_python_module_install_path}) ++install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../VERSION DESTINATION ${_python_module_install_path})