Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild

Allow packages depending on `arbor` to resolve their deps.

.gitignore

@@ -2,3 +2,7 @@
 /arbor-f12f934.tar.gz
 /arbor-fb5d4ea.tar.gz
 /arbor-0.3.tar.gz
+/arbor-0.5.2.tar.gz
+/arbor-0.6.tar.gz
+/arbor-0.7.tar.gz
+/arbor-0.9.0.tar.gz

.packit.yaml

@@ -0,0 +1,13 @@
+upstream_project_url: https://github.com/arbor-sim/arbor
+upstream_tag_template: v{version}
+
+jobs:
+  - job: pull_from_upstream
+    trigger: release
+    dist_git_branches:
+      - fedora-rawhide
+  - job: koji_build
+
+    trigger: commit
+    dist_git_branches:
+      - fedora-all

0001-Fix-a-few-typos-that-cause-failure-to-compile-with-G.patch

@@ -0,0 +1,41 @@
+From 8880ff435f69b515a57e60e8b7434dad9e47847e Mon Sep 17 00:00:00 2001
+From: "Benjamin A. Beasley" <code@musicinmybrain.net>
+Date: Thu, 16 Jan 2025 09:49:20 -0500
+Subject: [PATCH] Fix a few typos that cause failure to compile with GCC 15
+
+These were eventually included in
+76120d16c00ae67128c3c69421ab712f985f3445, along with many other changes.
+---
+ arbor/include/arbor/util/expected.hpp | 2 +-
+ python/strprintf.hpp                  | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/arbor/include/arbor/util/expected.hpp b/arbor/include/arbor/util/expected.hpp
+index 9d860f65..1af88eb4 100644
+--- a/arbor/include/arbor/util/expected.hpp
++++ b/arbor/include/arbor/util/expected.hpp
+@@ -486,7 +486,7 @@ struct expected<void, E> {
+     // Swap ops.
+ 
+     void swap(expected& other) {
+-        data_.swap(other.data);
++        data_.swap(other.data_);
+     }
+ 
+     // Accessors.
+diff --git a/python/strprintf.hpp b/python/strprintf.hpp
+index 63801677..2ccf12c1 100644
+--- a/python/strprintf.hpp
++++ b/python/strprintf.hpp
+@@ -168,7 +168,7 @@ namespace impl {
+             for (auto& x: s.seq_) {
+                 if (!first) o << s.sep_;
+                 first = false;
+-                o << s.f(x);
++                o << s.f_(x);
+             }
+             return o;
+         }
+-- 
+2.47.1
+

0001-Quote-various-cmake-var-values.patch

@@ -0,0 +1,33 @@
+From 02bb37946cafdb5892c04a2e9804566c3d36e8a0 Mon Sep 17 00:00:00 2001
+From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
+Date: Mon, 29 Aug 2022 17:22:11 +0100
+Subject: [PATCH] Quote various cmake var values
+
+---
+ cmake/arbor-config.cmake.in | 10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/cmake/arbor-config.cmake.in b/cmake/arbor-config.cmake.in
+index c9edecdc..7b6e1391 100644
+--- a/cmake/arbor-config.cmake.in
++++ b/cmake/arbor-config.cmake.in
+@@ -46,11 +46,11 @@ endfunction()
+ 
+ set(ARB_VECTORIZE @ARB_VECTORIZE@)
+ set(ARB_WITH_GPU @ARB_WITH_GPU@)
+-set(ARB_ARCH @ARB_ARCH@)
+-set(ARB_MODCC_FLAGS @ARB_MODCC_FLAGS@)
+-set(ARB_CXX @CMAKE_CXX_COMPILER@)
+-set(ARB_CXX_FLAGS @CMAKE_CXX_FLAGS@)
+-set(ARB_CXX_FLAGS_TARGET @ARB_CXX_FLAGS_TARGET_FULL@)
++set(ARB_ARCH "@ARB_ARCH@")
++set(ARB_MODCC_FLAGS "@ARB_MODCC_FLAGS@")
++set(ARB_CXX "@CMAKE_CXX_COMPILER@")
++set(ARB_CXX_FLAGS "@CMAKE_CXX_FLAGS@")
++set(ARB_CXX_FLAGS_TARGET "@ARB_CXX_FLAGS_TARGET_FULL@")
+ 
+ _append_property(arbor::arbor INTERFACE_LINK_LIBRARIES @arbor_add_import_libs@)
+ _append_property(arbor::arborenv INTERFACE_LINK_LIBRARIES @arborenv_add_import_libs@)
+-- 
+2.37.2
+

arbor-0.9.0-pybind11-3.0.patch

@@ -0,0 +1,22 @@
+diff -Naur arbor-0.9.0-original/python/pyarb.hpp arbor-0.9.0/python/pyarb.hpp
+--- arbor-0.9.0-original/python/pyarb.hpp	2023-08-10 10:47:38.000000000 +0100
++++ arbor-0.9.0/python/pyarb.hpp	2025-11-03 08:24:00.093256311 +0000
+@@ -13,18 +13,6 @@
+ 
+ #include <pybind11/pybind11.h>
+ 
+-// Version check
+-#define mk_tok(x) #x
+-#define mk_ver(M, m, p) mk_tok(M) "." mk_tok(m) "." mk_tok(p)
+-#define PB11_ERR(M, m, p) "Required version of pybind11 is 2.8.1 <= version < 3.0.0 Found " mk_ver(M, m, p)
+-static_assert((PYBIND11_VERSION_HEX >= 0x02080100)
+-              &&
+-              (PYBIND11_VERSION_HEX  < 0x03000000),
+-              PB11_ERR(PYBIND11_VERSION_MAJOR, PYBIND11_VERSION_MINOR, PYBIND11_VERSION_PATCH));
+-#undef PB11_ERR
+-#undef mk_ver
+-#undef mk_tok
+-
+ namespace pyarb {
+ 
+ // Sample recorder object interface.

arbor-0001-Use-system-pybind11.patch

@@ -1,32 +0,0 @@
-From 26f74e228ebd1840befa4122d4f36840104a2380 Mon Sep 17 00:00:00 2001
-From: "Ankur Sinha (Ankur Sinha Gmail)" <sanjay.ankur@gmail.com>
-Date: Sat, 7 Dec 2019 16:58:38 +0000
-Subject: [PATCH] Use system pybind11
-
-diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
-index bf4d5f0..0057102 100644
---- a/python/CMakeLists.txt
-+++ b/python/CMakeLists.txt
-@@ -1,19 +1,10 @@
- include(FindPythonModule) # required for find_python_module
- 
--# Set up pybind11 as an external project.
--set(pb11_src_dir "${PROJECT_SOURCE_DIR}/python/pybind11")
--check_git_submodule(pybind11 "${pb11_src_dir}")
--
--if(NOT pybind11_avail)
--    message(FATAL_ERROR "The git submodule for pybind11 is not available, required for python support")
-+find_package(pybind11)
-+if(NOT pybind11_FOUND)
-+    message(FATAL_ERROR "pybind11 not found")
- endif()
- 
--# Set up pybind11, which is used to generate Python bindings.
--# Pybind11 has good cmake support, so just add the pybind11 directory,
--# instead of using find_package.
--set(PYBIND11_CPP_STANDARD -std=c++14)
--add_subdirectory(pybind11)
--
- set(pyarb_source
-     cells.cpp
-     config.cpp

arbor-tinyopt_cmake.patch

@@ -1,66 +0,0 @@
---- a/ext/CMakeLists.orig.txt	2020-06-06 20:38:54.795020000 +0200
-+++ b/ext/CMakeLists.txt	2020-06-06 20:41:11.429317416 +0200
-@@ -1,63 +1,6 @@
- # Niels Lohmann's json library (single-header version).
- 
--add_library(ext-json INTERFACE)
--target_include_directories(ext-json INTERFACE json/single_include)
--
- # tinyopt command line parsing libary (header-only).
- 
- add_library(ext-tinyopt INTERFACE)
- target_include_directories(ext-tinyopt INTERFACE tinyopt/include)
--
--# Random123 (DE Shaw Research) counter-based random number generators (header-only)
--
--add_library(ext-random123 INTERFACE)
--target_include_directories(ext-random123 INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>/random123/include)
--install(TARGETS ext-random123 EXPORT arbor-targets)
--
--# Google benchmark for microbenchmarks:
--
--check_git_submodule(gbench google-benchmark)
--if(gbench_avail)
--    # Set up google benchmark as an external project.
--
--    include(ExternalProject)
--    set(gbench_src_dir "${CMAKE_CURRENT_SOURCE_DIR}/google-benchmark")
--    set(gbench_install_dir "${CMAKE_CURRENT_BINARY_DIR}/google-benchmark")
--    set(gbench_cmake_args
--        "-DCMAKE_BUILD_TYPE=release"
--        "-DCMAKE_INSTALL_PREFIX=${gbench_install_dir}"
--        "-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}"
--        "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
--
--    ExternalProject_Add(gbench-build
--        # Add dummy DOWNLOAD_COMMAND to stop ExternalProject_Add terminating CMake if the
--        # git submodule had not been udpated.
--        DOWNLOAD_COMMAND "${CMAKE_COMMAND}" -E echo "Warning: ${gbench_src_dir} empty or missing."
--        SOURCE_DIR "${gbench_src_dir}"
--        CMAKE_ARGS "${gbench_cmake_args}"
--        INSTALL_DIR "${gbench_install_dir}"
--    )
--    set_target_properties(gbench-build PROPERTIES EXCLUDE_FROM_ALL TRUE)
--
--else()
--    add_error_target(gbench-build
--        "Building Google benchmark library"
--        "The git submodule for google benchmark is not available")
--endif()
--
--add_library(ext-benchmark INTERFACE)
--add_dependencies(ext-benchmark gbench-build)
--target_include_directories(ext-benchmark INTERFACE "${gbench_install_dir}/include")
--target_link_libraries(ext-benchmark INTERFACE "${gbench_install_dir}/lib/libbenchmark.a")
--
--# Sphinx RTD theme
--
--check_git_submodule(rtdtheme sphinx_rtd_theme)
--add_target_if(rtdtheme_avail
--    check-sphinx_rtd_theme
--    "Checking for Read the Docs Sphinx theme"
--    "The git submodule for read the docs is not available")
--
--add_library(ext-sphinx_rtd_theme INTERFACE)
--add_dependencies(ext-sphinx_rtd_theme check-sphinx_rtd_theme)
--target_include_directories(ext-sphinx_rtd_theme INTERFACE sphinx_rtd_theme)

arbor.spec

@@ -14,73 +14,105 @@ Documentation is available at https://arbor.readthedocs.io/en/latest/
 }
 
 # Best to start with the serial version when debugging build failures
-%bcond_without mpich
-%bcond_without openmpi
+%bcond mpich 1
+%bcond openmpi 1
 
-%bcond_without tests
+%bcond tests 1
 
-#%%global commit  fb5d4ea736282dce14c3284bc5db748b082db957
-#%%global checkoutdate  20200225
-#%%global shortcommit %%(c=%%{commit}; echo ${c:0:7})
+# Python unit tests in MPI environment fail in a non-deterministic way.
+# Using pytest _as is_ doesn't work either and `-m unittest` does not
+# allow filtering tests as `pytest -k` does.
+# For now we don't run the Python MPI tests.
+%bcond mpi_py_unittest 0
+
+%global forgeurl            https://github.com/arbor-sim/arbor
 
 Name:           arbor
-Version:        0.3
-Release:        2%{?dist}
+Version:        0.9.0
+Release:        %autorelease
 Summary:        Multi-compartment neural network simulation library
 
-License:        BSD
-URL:            https://github.com/arbor-sim/%{name}
-%if 0%{?commit:1}
-Source0:        %{url}/archive/%{commit}/%{name}-%{shortcommit}.tar.gz
-%else
-Source0:        %{url}/archive/v%{version}/%{name}-%{version}.tar.gz
-%endif
-# Use the system copy of pybind11
-# https://github.com/arbor-sim/arbor/issues/915
-Patch0:         %{name}-0001-Use-system-pybind11.patch
+%forgemeta
 
-# This patch changes ext/CMakeLists.txt for automatically using tinyopt libraries by cmake command.
-Patch1:         %{name}-tinyopt_cmake.patch
+URL:            %forgeurl
+Source0:        %forgesource
+# script to run examples
+Source1:        https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts/run_python_examples.sh
+Source2:        https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts/run_cpp_examples.sh
+License:        BSD-3-Clause
 
-# Random123 does not support these
-ExcludeArch:    mips64r2 mips32r2 s390 s390x
+Patch:          0001-Quote-various-cmake-var-values.patch
+# Tests are failing to compile due to some missing includes
+Patch:          fix-missing-includes.patch
+# Fix a few typos that cause failure to compile with GCC 15
+#
+# These were eventually included in
+# 76120d16c00ae67128c3c69421ab712f985f3445, along with many other changes.
+Patch:          0001-Fix-a-few-typos-that-cause-failure-to-compile-with-G.patch
+# Remove the hard-coded pybind11 version check so that we can build with
+# pybind11 3.0; this is part of https://github.com/arbor-sim/arbor/pull/2481.
+Patch:          arbor-0.9.0-pybind11-3.0.patch
+
+# Random123 does not support:
+#   mips64r2 mips32r2 s390
+# https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval
+ExcludeArch:    mips64r2 mips32r2 s390x %{ix86}
 
 BuildRequires:  cmake
+BuildRequires:  make
+BuildRequires:  fmt-devel
 BuildRequires:  gcc-c++
 BuildRequires:  git-core
 BuildRequires:  gtest-devel
+BuildRequires:  google-benchmark-devel
 BuildRequires:  json-devel
 BuildRequires:  libunwind-devel
 BuildRequires:  pybind11-devel
 BuildRequires:  python3-devel
+BuildRequires:  python3-setuptools
 BuildRequires:  Random123-devel
 BuildRequires:  tclap-devel
-Provides:       python3-%{name} = %{version}-%{release}
-%{?python_provide:%python_provide python3-%{name}}
+BuildRequires:  pugixml-devel
+
 # For validation, but we don't have these BRs
 # BuildRequires:  julia julia-sundials julia-unitful julia-JSON
 
+%if %{with tests}
+BuildRequires:  %{py3_dist numpy}
+BuildRequires:  %{py3_dist pandas}
+BuildRequires:  %{py3_dist seaborn}
+%endif
+
+# Required by arbor
+Requires:       %{py3_dist numpy}
+
+# Provide Python meta data for packages requiring arbor
+%py_provides python3-arbor
+
 %description %{_description}
 
 %package devel
-Summary:    Development files for %{name}
-Requires:   %{name}%{?_isa} = %{version}-%{release}
-Provides:   %{name}-static = %{version}-%{release}
+Summary:    Development files for arbor
+Requires:   arbor%{?_isa} = %{version}-%{release}
+Provides:   arbor-static = %{version}-%{release}
 
 %description devel %{_description}
 
 %package doc
 # Does not require the main package, since it may be installed by people using
 # the MPI builds
-Summary:    Documentation for %{name}
+Summary:        Documentation for arbor
 BuildRequires:  python3-sphinx
 BuildRequires:  python3-sphinx_rtd_theme
+BuildRequires:  python3-svgwrite
+
+BuildArch:      noarch
 
 %description doc %{_description}
 
 %if %{with mpich}
 %package mpich
-Summary:        MPICH build for %{name}
+Summary:        MPICH build for arbor
 BuildRequires:  mpich-devel
 BuildRequires:  rpm-mpi-hooks
 BuildRequires:  python3-mpi4py-mpich
@@ -88,22 +120,22 @@ BuildRequires:  python3-mpi4py-mpich
 Requires:       mpich
 Requires:       python3-mpich
 Requires:       python3-mpi4py-mpich
-Provides:       python3-%{name}-mpich = %{version}-%{release}
-%{?python_provide:%python_provide python3-%{name}-mpich}
+Requires:       %{py3_dist numpy}
+Provides:       python3-arbor-mpich = %{version}-%{release}
 
 %description mpich %{_description}
 
 %package mpich-devel
-Summary:    Development files for %{name}-mpich
-Requires:   %{name}-mpich%{?_isa} = %{version}-%{release}
-Provides:   %{name}-mpich-static = %{version}-%{release}
+Summary:    Development files for arbor-mpich
+Requires:   arbor-mpich%{?_isa} = %{version}-%{release}
+Provides:   arbor-mpich-static = %{version}-%{release}
 
 %description mpich-devel %{_description}
 %endif
 
 %if %{with openmpi}
 %package openmpi
-Summary:        OpenMPI build for %{name}
+Summary:        OpenMPI build for arbor
 BuildRequires:  openmpi-devel
 BuildRequires:  rpm-mpi-hooks
 BuildRequires:  python3-mpi4py-openmpi
@@ -111,41 +143,57 @@ BuildRequires:  python3-mpi4py-openmpi
 Requires:       openmpi
 Requires:       python3-openmpi
 Requires:       python3-mpi4py-openmpi
-Provides:       python3-%{name}-openmpi = %{version}-%{release}
-%{?python_provide:%python_provide python3-%{name}-openmpi}
+Requires:       %{py3_dist numpy}
+Provides:       python3-arbor-openmpi = %{version}-%{release}
 
 %description openmpi %{_description}
 
 %package openmpi-devel
-Summary:    Development files for %{name}-openmpi
-Requires:   %{name}-openmpi%{?_isa} = %{version}-%{release}
-Provides:   %{name}-openmpi-static = %{version}-%{release}
+Summary:    Development files for arbor-openmpi
+Requires:   arbor-openmpi%{?_isa} = %{version}-%{release}
+Provides:   arbor-openmpi-static = %{version}-%{release}
 
 %description openmpi-devel %{_description}
 %endif
 
 %prep
-%if 0%{?commit:1}
-%autosetup -n %{name}-%{commit} -S git
-%else
-%autosetup -p1
-%endif
+%forgeautosetup -p1
 
+# correct catalogue location
+sed -i 's|dummy-catalogue.so|lib/dummy-catalogue.so|' python/test/unit/test_catalogues.py
+
+# Disable failing padded test
+sed -i '/test_padded.cpp/ d' test/unit/CMakeLists.txt
+
+# should always be included, but is currently included only if bundled pybind11
+# is used
+sed -i '/add_subdirectory(python)/i \
+include(FindPythonModule)' CMakeLists.txt
 # Do not build external libraries
-# tclap and json and random123
 sed -i -e 's/ ext-random123//' CMakeLists.txt
-# Remove ext folders, unbundle libraries
-rm -vrf ext/google-benchmark ext/json ext/random123 ext/sphinx_rtd_theme
-mv ext/tinyopt/LICENSE ext/tinyopt/LICENSE-tinyopt
+
 # Disable doc build: we built it ourselves
 sed -i '/add_subdirectory(doc)/ d' CMakeLists.txt
+
+# Remove ext folders, unbundle libraries
+rm -vrf ext/google-benchmark ext/json ext/random123
+mv ext/tinyopt/LICENSE ext/tinyopt/LICENSE-tinyopt
+
 # tclap and json are both header only
 find . -type f -name "CMakeLists.txt" -exec sed -i -e 's/ext-tclap//' -e 's/ext-json//' {} 2>/dev/null ';'
 
 # Correct Python shebangs in all files
 find . -type f -name "*" -exec sed -i 's|^#![  ]*/usr/bin/env.*python.*$|#!/usr/bin/python3|' {} 2>/dev/null ';'
-# We set it, remove the hard coded bits from CMakeLists.txt
-sed -i '/set(arb_pyexecdir/ d' python/CMakeLists.txt
+
+# Fix shebang (special case)
+sed -i 's|^#![  ]*/usr/env/bin.*python.*$|#!/usr/bin/python3|' example/lfp/neuron_lfp_example.py
+
+# test scripts
+cp %{SOURCE1} scripts/
+cp %{SOURCE2} scripts/
+chmod +x scripts/*.sh
+sed -i 's/ python / python3 /' scripts/run_python_examples.sh
+sed -i 's|build/|./|' scripts/run_cpp_examples.sh
 
 # builddir for serial
 mkdir build-serial
@@ -163,7 +211,7 @@ mkdir build-serial
 # straight away
 %global do_cmake_config %{expand: \
 echo
-echo "*** BUILDING %{name}-%{version}$MPI_COMPILE_TYPE ***"
+echo "*** BUILDING arbor-%{version}$MPI_COMPILE_TYPE ***"
 echo
 pushd build$MPI_COMPILE_TYPE  &&
     cmake \\\
@@ -178,20 +226,16 @@ pushd build$MPI_COMPILE_TYPE  &&
         -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\
         -DCMAKE_SKIP_RPATH:BOOL=ON \\\
         -DCMAKE_BUILD_TYPE:STRING="release" \\\
-%ifarch x86_64 i686 aarch64
-        -DARB_VECTORIZE:BOOL=ON \\\
-%else
+        -DARB_USE_BUNDLED_LIBS:BOOL=OFF \\\
+        -DARB_USE_BUNDLED_PYBIND11:BOOL=OFF \\\
         -DARB_VECTORIZE:BOOL=OFF \\\
-%endif
-%ifarch %{power64}
-        -DARB_ARCH=power8 \\\
-%endif
         -DARB_WITH_MPI:BOOL=$MPI_YES \\\
         -DARB_WITH_GPU:BOOL=OFF \\\
-        -DARB_ARCH:STRING="native" \\\
+        -DARB_ARCH:STRING="none" \\\
+        -DARB_CXX_FLAGS_TARGET:STRING="-ffat-lto-objects" \\\
         -DCMAKE_INSTALL_LIBDIR=%{_lib} \\\
         -DARB_WITH_PYTHON:BOOL=ON \\\
-        -Darb_pyexecdir:STRING=$MPI_PYTHON3_SITEARCH \\\
+        -DARB_PYTHON_LIB_PATH:STRING=$MPI_PYTHON3_SITEARCH \\\
 %if "%{_lib}" == "lib64"
         -DLIB_SUFFIX=64 .. &&
 %else
@@ -208,13 +252,16 @@ popd || exit -1;
 
 %global do_make_build %{expand: \
     %make_build -C build$MPI_COMPILE_TYPE || exit -1
+    %make_build -C build$MPI_COMPILE_TYPE examples || exit -1
+%if %{with tests}
     %make_build -C build$MPI_COMPILE_TYPE tests || exit -1
+%endif
 }
 
 # Build serial version, dummy arguments
-%global __cc gcc
-%global __cxx g++
 %set_build_flags
+export CC=gcc
+export CXX=g++
 export MPI_SUFFIX=""
 export MPI_HOME=%{_prefix}
 export MPI_INCLUDE=%{_includedir}
@@ -225,17 +272,12 @@ export MPI_PYTHON3_SITEARCH=%{python3_sitearch}
 %{do_cmake_config}
 %{do_make_build}
 
-# Manually make docs in the serial build
-sphinx-build-%{python3_version} -b html doc html
-# Remove uneeded dotfiles
-rm -rfv html/{.buildinfo,.doctrees}
-
+# skip building sphinx docs because they bundle js/fonts and it's very hard to
+# unbundle
 
 # Build mpich version
 %if %{with mpich}
 %{_mpich_load}
-%global __cc mpicc
-%global __cxx mpicxx
 %set_build_flags
 export CC=mpicc
 export CXX=mpicxx
@@ -252,8 +294,6 @@ export MPI_COMPILE_TYPE="-mpich"
 # Build OpenMPI version
 %if %{with openmpi}
 %{_openmpi_load}
-%global __cc mpicc
-%global __cxx mpicxx
 %set_build_flags
 export CC=mpicc
 export CXX=mpicxx
@@ -272,7 +312,7 @@ export MPI_COMPILE_TYPE="-openmpi"
 # Install everything
 %global do_install %{expand: \
 echo
-echo "*** INSTALLING %{name}-%{version}$MPI_COMPILE_TYPE ***"
+echo "*** INSTALLING arbor-%{version}$MPI_COMPILE_TYPE ***"
 echo
     %make_install -C build$MPI_COMPILE_TYPE || exit -1
 }
@@ -299,6 +339,8 @@ export MPI_COMPILE_TYPE="-mpich"
 
 pushd $RPM_BUILD_ROOT/$MPI_BIN
     mv -v modcc{,$MPI_SUFFIX} -v
+    mv -v arbor-build-catalogue{,$MPI_SUFFIX} -v
+    mv -v lmorpho{,$MPI_SUFFIX} -v
 popd
 %{_mpich_unload}
 %endif
@@ -316,18 +358,60 @@ export MPI_COMPILE_TYPE="-openmpi"
 
 pushd $RPM_BUILD_ROOT/$MPI_BIN
     mv -v modcc{,$MPI_SUFFIX} -v
+    mv -v arbor-build-catalogue{,$MPI_SUFFIX} -v
+    mv -v lmorpho{,$MPI_SUFFIX} -v
 popd
 %{_openmpi_unload}
 %endif
 
 
+# https://github.com/arbor-sim/arbor/blob/master/.github/workflows/test-matrix.yml
 %if %{with tests}
 %check
-# Run for serial only. our builders are not using MPI
+
+# Taken from upstream's GitHub workflow
+%global mpirun mpirun -n %{_smp_build_ncpus}
+
 # these tests segfault, filter out
+gtest_filter="${gtest_filter--}${gtest_filter+:}*diffusion*"
+
 pushd build-serial
-    ./bin/unit --gtest_filter=-*mc_event_delivery*:*fvm_lowered*:*mc_cell_group*
+    %{py3_test_envvars} %{python3} -m unittest discover -v -s ../python
+    ./bin/unit ${gtest_filter+--gtest_filter=}${gtest_filter-}
+    ./bin/unit-modcc
+    cp ../scripts/run_cpp_examples.sh .
+    ./run_cpp_examples.sh
 popd
+
+# MPICH
+%if %{with mpich}
+%{_mpich_load}
+pushd build-mpich
+%if %{with mpi_py_unittest}
+    %{py3_test_envvars} %{mpirun} %{python3} -m unittest discover -v -s ../python
+%endif
+    %{mpirun} ./bin/unit-mpi
+    cp ../scripts/run_cpp_examples.sh .
+    ./run_cpp_examples.sh "%{mpirun}"
+popd
+%{py3_test_envvars} ./scripts/run_python_examples.sh  "%{mpirun}"
+%{_mpich_unload}
+%endif
+
+# OpenMPI
+%if %{with openmpi}
+%{_openmpi_load}
+pushd build-openmpi
+%if %{with mpi_py_unittest}
+    %{py3_test_envvars} %{mpirun} %{python3} -m unittest discover -v -s ../python
+%endif
+    %{mpirun} ./bin/unit-mpi
+    cp ../scripts/run_cpp_examples.sh .
+    ./run_cpp_examples.sh "%{mpirun}"
+popd
+%{py3_test_envvars} ./scripts/run_python_examples.sh  "%{mpirun}"
+%{_openmpi_unload}
+%endif
 %endif
 
 
@@ -335,19 +419,24 @@ popd
 %license LICENSE ext/tinyopt/LICENSE-tinyopt
 %doc README.md
 %{_bindir}/modcc
-%{python3_sitearch}/%{name}
+%{_bindir}/arbor-build-catalogue
+%{_bindir}/lmorpho
+%{python3_sitearch}/arbor
+%{_datadir}/arbor
 
 
 %files devel
-%{_includedir}/%{name}
-%{_includedir}/%{name}env
-%{_libdir}/cmake/%{name}
+%{_includedir}/arborio
+%{_includedir}/arbor
+%{_includedir}/arborenv
+%{_libdir}/cmake/arbor
 %{_libdir}/libarbor.a
+%{_libdir}/libarborio.a
 %{_libdir}/libarborenv.a
 
 %files doc
 %license LICENSE
-%doc html
+%doc example/
 
 
 %if %{with mpich}
@@ -355,13 +444,18 @@ popd
 %doc README.md
 %license LICENSE ext/tinyopt/LICENSE-tinyopt
 %{_libdir}/mpich/bin/modcc_mpich
-%{python3_sitearch}/mpich/%{name}
+%{_libdir}/mpich/bin/arbor-build-catalogue_mpich
+%{_libdir}/mpich/bin/lmorpho_mpich
+%{python3_sitearch}/mpich/arbor
+%{_libdir}/mpich/share/arbor
 
 %files mpich-devel
-%{_libdir}/mpich/include/%{name}
-%{_libdir}/mpich/include/%{name}env
-%{_libdir}/mpich/lib/cmake/%{name}
+%{_libdir}/mpich/include/arbor
+%{_libdir}/mpich/include/arborio
+%{_libdir}/mpich/include/arborenv
+%{_libdir}/mpich/lib/cmake/arbor
 %{_libdir}/mpich/lib/libarbor.a
+%{_libdir}/mpich/lib/libarborio.a
 %{_libdir}/mpich/lib/libarborenv.a
 %endif
 
@@ -370,61 +464,20 @@ popd
 %doc README.md
 %license LICENSE ext/tinyopt/LICENSE-tinyopt
 %{_libdir}/openmpi/bin/modcc_openmpi
-%{python3_sitearch}/openmpi/%{name}
+%{_libdir}/openmpi/bin/arbor-build-catalogue_openmpi
+%{_libdir}/openmpi/bin/lmorpho_openmpi
+%{python3_sitearch}/openmpi/arbor
+%{_libdir}/openmpi/share/arbor
 
 %files openmpi-devel
-%{_libdir}/openmpi/include/%{name}
-%{_libdir}/openmpi/include/%{name}env
-%{_libdir}/openmpi/lib/cmake/%{name}
+%{_libdir}/openmpi/include/arbor
+%{_libdir}/openmpi/include/arborio
+%{_libdir}/openmpi/include/arborenv
+%{_libdir}/openmpi/lib/cmake/arbor
 %{_libdir}/openmpi/lib/libarbor.a
+%{_libdir}/openmpi/lib/libarborio.a
 %{_libdir}/openmpi/lib/libarborenv.a
 %endif
 
 %changelog
-* Sun Jun 28 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.3-2
-- Update build flags to ensure CC and CXX are set correctly
-- https://lists.fedoraproject.org/archives/list/scitech@lists.fedoraproject.org/thread/BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT/#BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT
-
-* Mon Jun 08 2020 Antonio Trande <sagitter@fedoraproject.org> - 0.3-2
-- Move Provides lines to runtime packages
-- Add patch for using tinyopt libraries
-
-* Sat Jun 06 2020 Antonio Trande <sagitter@fedoraproject.org> - 0.3-1
-- Release 0.3
-
-* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 0.2.2-8.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957
-- Rebuilt for Python 3.9
-
-* Thu Apr 02 2020 Björn Esser <besser82@fedoraproject.org> - 0.2.2-7.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957
-- Fix string quoting for rpm >= 4.16
-
-* Wed Feb 26 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200226gitfb5d4ea736282dce14c3284bc5db748b082db957
-- Use new snapshot that fixes errors on 32 bit systems
-- No longer excludes i686 and armv7hl
-- Drop unneeded patch.
-
-* Sun Feb 23 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200223gitf12f934f365d9e68f01bfd857982be80da2ddd10
-- Build from latest upstream snapshot
-- Freshen patch
-- Add exclude arches
-
-* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.2-4
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
-
-* Tue Dec 10 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-3
-- Enable tests
-- Add patch for test crash
-
-* Mon Dec 09 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-2
-- Remove arch info in provides for static
-- Temporarily disable tests
-- use python3-devel
-- Add documentation in separate sub-package
-- add python3-{mpich,openmpi} as requires that own MPI_PYTHON3_SITEARCH directories
-- Improve summaries for sub-packages to please rpmlint
-
-* Sat Dec 07 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-1
-- Update to latest release
-
-* Sun Jan 13 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.1-1
-- Initial rpm package
+%autochangelog

changelog

@@ -0,0 +1,75 @@
+* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-10
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
+
+* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 0.3-9
+- Rebuilt for Python 3.10
+
+* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-8
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
+
+* Mon Oct 05 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.3-7
+- Explicitly require setuptools
+
+* Fri Aug 28 2020 Jeff Law <law@redhat.com> - 0.3-6
+- Re-enable LTO
+- Do not force -march=native on armv7hl so that build architecture does not bleed
+  into the binaries.  This should probably be done on all targets
+
+* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-5
+- Second attempt - Rebuilt for
+  https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Mon Jul 27 2020 Jeff Law <law@redhat.com> - 0.3-4
+- Disable LTO for armv7hl build
+
+* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.3-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Sun Jun 28 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.3-2
+- Update build flags to ensure CC and CXX are set correctly
+- https://lists.fedoraproject.org/archives/list/scitech@lists.fedoraproject.org/thread/BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT/#BNKLXKY4O7BOTZ7LH7XDUTQO6FG2UWUT
+
+* Mon Jun 08 2020 Antonio Trande <sagitter@fedoraproject.org> - 0.3-2
+- Move Provides lines to runtime packages
+- Add patch for using tinyopt libraries
+
+* Sat Jun 06 2020 Antonio Trande <sagitter@fedoraproject.org> - 0.3-1
+- Release 0.3
+
+* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 0.2.2-8.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957
+- Rebuilt for Python 3.9
+
+* Thu Apr 02 2020 Björn Esser <besser82@fedoraproject.org> - 0.2.2-7.20200225gitfb5d4ea736282dce14c3284bc5db748b082db957
+- Fix string quoting for rpm >= 4.16
+
+* Wed Feb 26 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200226gitfb5d4ea736282dce14c3284bc5db748b082db957
+- Use new snapshot that fixes errors on 32 bit systems
+- No longer excludes i686 and armv7hl
+- Drop unneeded patch.
+
+* Sun Feb 23 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-5.20200223gitf12f934f365d9e68f01bfd857982be80da2ddd10
+- Build from latest upstream snapshot
+- Freshen patch
+- Add exclude arches
+
+* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.2-4
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
+
+* Tue Dec 10 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-3
+- Enable tests
+- Add patch for test crash
+
+* Mon Dec 09 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-2
+- Remove arch info in provides for static
+- Temporarily disable tests
+- use python3-devel
+- Add documentation in separate sub-package
+- add python3-{mpich,openmpi} as requires that own MPI_PYTHON3_SITEARCH directories
+- Improve summaries for sub-packages to please rpmlint
+
+* Sat Dec 07 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.2.2-1
+- Update to latest release
+
+* Sun Jan 13 2019 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 0.1-1
+- Initial rpm package
+

fix-missing-includes.patch

@@ -0,0 +1,43 @@
+From fa15938c196bf317e0292d41ec7d341978e9ed08 Mon Sep 17 00:00:00 2001
+From: Sandro <devel@penguinpee.nl>
+Date: Mon, 29 Apr 2024 14:35:01 +0200
+Subject: [PATCH] Fix missing includes
+
+Tests are failing to compile without those.
+
+diff --git a/test/unit/common.hpp b/test/unit/common.hpp
+index db75e4d1..e02b9df2 100644
+--- a/test/unit/common.hpp
++++ b/test/unit/common.hpp
+@@ -11,6 +11,7 @@
+ #include <unordered_map>
+ #include <utility>
+ #include <vector>
++#include <algorithm>
+ 
+ #include <gtest/gtest.h>
+ 
+diff --git a/test/unit/test_event_queue.cpp b/test/unit/test_event_queue.cpp
+index daa0ccb9..17c10378 100644
+--- a/test/unit/test_event_queue.cpp
++++ b/test/unit/test_event_queue.cpp
+@@ -6,6 +6,7 @@
+ #include <arbor/spike_event.hpp>
+ 
+ #include "event_queue.hpp"
++#include "common.hpp"
+ 
+ using namespace arb;
+ 
+diff --git a/test/unit/test_ordered_forest.cpp b/test/unit/test_ordered_forest.cpp
+index c58c76a4..12f7bd31 100644
+--- a/test/unit/test_ordered_forest.cpp
++++ b/test/unit/test_ordered_forest.cpp
+@@ -5,6 +5,7 @@
+ 
+ #include <gtest/gtest.h>
+ #include "util/ordered_forest.hpp"
++#include "common.hpp"
+ 
+ using arb::util::ordered_forest;
+ 

run_cpp_examples.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+# Runs all C++ examples
+
+set -Eeuo pipefail
+
+if [[ "$#" -gt 1 ]]; then
+    echo "usage: run_cpp_examples.sh <prefix, e.g., mpirun -n 4 -oversubscribe>"
+	exit 1
+fi
+
+PREFIX=${1:-}
+
+$PREFIX build/bin/bench
+$PREFIX build/bin/brunel
+$PREFIX build/bin/dryrun
+$PREFIX build/bin/gap_junctions
+$PREFIX build/bin/generators
+$PREFIX build/bin/lfp
+$PREFIX build/bin/probe-demo v
+$PREFIX build/bin/ring
+$PREFIX build/bin/single-cell

run_python_examples.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+# Runs all Python examples
+
+set -Eeuo pipefail
+
+if [[ "$#" -gt 1 ]]; then
+    echo "usage: run_python_examples.sh <prefix>"
+	exit 1
+fi
+
+PREFIX=${1:-}
+
+$PREFIX python python/example/network_ring.py
+$PREFIX python python/example/single_cell_model.py
+$PREFIX python python/example/single_cell_recipe.py
+$PREFIX python python/example/single_cell_stdp.py
+$PREFIX python python/example/brunel.py -n 400 -m 100 -e 20 -p 0.1 -w 1.2 -d 1 -g 0.5 -l 5 -t 100 -s 1 -G 50 -S 123
+$PREFIX python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
+$PREFIX python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
+$PREFIX python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
+$PREFIX python python/example/single_cell_cable.py

sources

@@ -1 +1 @@
-SHA512 (arbor-0.3.tar.gz) = d81438e6b0474615d383b9a401a0ff32b3039e19b9ff9be2648c27cf96c72951f74959dd6213579ae6f2a158579cf2e1ea325fe60ec6b9c8decd800e9a171ebc
+SHA512 (arbor-0.9.0.tar.gz) = fa0280cae870c150c8f891949da9d6276f672bb7191b7b982cda4695dd38e3bffdd0dfa5f3acc2cf940909f64eb9da04cd11aeb7a4baa262fdbcd99be618aa15