13 changed files with 254 additions and 461 deletions
--- a/.gitignore
+++ b/.gitignore
@ -2,7 +2,3 @@
 /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
--- a/.packit.yaml
+++ b/.packit.yaml
@ -1,13 +0,0 @@
-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
--- a/0001-Fix-a-few-typos-that-cause-failure-to-compile-with-G.patch
+++ b/0001-Fix-a-few-typos-that-cause-failure-to-compile-with-G.patch
@ -1,41 +0,0 @@
-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
-
--- a/0001-Quote-various-cmake-var-values.patch
+++ b/0001-Quote-various-cmake-var-values.patch
@ -1,33 +0,0 @@
-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
-
--- a/arbor-0.9.0-pybind11-3.0.patch
+++ b/arbor-0.9.0-pybind11-3.0.patch
@ -1,22 +0,0 @@
-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.
--- a/arbor-0001-Use-system-pybind11.patch
+++ b/arbor-0001-Use-system-pybind11.patch
@ -0,0 +1,32 @@
+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
--- a/arbor-tinyopt_cmake.patch
+++ b/arbor-tinyopt_cmake.patch
@ -0,0 +1,66 @@
+--- 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)
--- a/arbor.spec
+++ b/arbor.spec
@ -14,57 +14,41 @@ Documentation is available at https://arbor.readthedocs.io/en/latest/
 }

 # Best to start with the serial version when debugging build failures
-%bcond mpich 1
-%bcond openmpi 1
+%bcond_without mpich
+%bcond_without openmpi

-%bcond tests 1
+%bcond_without tests

-# 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
+#%%global commit  fb5d4ea736282dce14c3284bc5db748b082db957
+#%%global checkoutdate  20200225
+#%%global shortcommit %%(c=%%{commit}; echo ${c:0:7})

 Name:           arbor
-Version:        0.9.0
-Release:        %autorelease
+Version:        0.3
+Release:        7%{?dist}
 Summary:        Multi-compartment neural network simulation library

-%forgemeta
+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

-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
+# This patch changes ext/CMakeLists.txt for automatically using tinyopt libraries by cmake command.
+Patch1:         %{name}-tinyopt_cmake.patch

-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}
+# Random123 does not support these
+ExcludeArch:    mips64r2 mips32r2 s390 s390x

 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
@ -72,47 +56,32 @@ BuildRequires:  python3-devel
 BuildRequires:  python3-setuptools
 BuildRequires:  Random123-devel
 BuildRequires:  tclap-devel
-BuildRequires:  pugixml-devel
-
+Provides:       python3-%{name} = %{version}-%{release}
+%{?python_provide:%python_provide python3-%{name}}
 # 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 arbor
-Requires:   arbor%{?_isa} = %{version}-%{release}
-Provides:   arbor-static = %{version}-%{release}
+Summary:    Development files for %{name}
+Requires:   %{name}%{?_isa} = %{version}-%{release}
+Provides:   %{name}-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 arbor
+Summary:    Documentation for %{name}
 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 arbor
+Summary:        MPICH build for %{name}
 BuildRequires:  mpich-devel
 BuildRequires:  rpm-mpi-hooks
 BuildRequires:  python3-mpi4py-mpich
@ -120,22 +89,22 @@ BuildRequires:  python3-mpi4py-mpich
 Requires:       mpich
 Requires:       python3-mpich
 Requires:       python3-mpi4py-mpich
-Requires:       %{py3_dist numpy}
-Provides:       python3-arbor-mpich = %{version}-%{release}
+Provides:       python3-%{name}-mpich = %{version}-%{release}
+%{?python_provide:%python_provide python3-%{name}-mpich}

 %description mpich %{_description}

 %package mpich-devel
-Summary:    Development files for arbor-mpich
-Requires:   arbor-mpich%{?_isa} = %{version}-%{release}
-Provides:   arbor-mpich-static = %{version}-%{release}
+Summary:    Development files for %{name}-mpich
+Requires:   %{name}-mpich%{?_isa} = %{version}-%{release}
+Provides:   %{name}-mpich-static = %{version}-%{release}

 %description mpich-devel %{_description}
 %endif

 %if %{with openmpi}
 %package openmpi
-Summary:        OpenMPI build for arbor
+Summary:        OpenMPI build for %{name}
 BuildRequires:  openmpi-devel
 BuildRequires:  rpm-mpi-hooks
 BuildRequires:  python3-mpi4py-openmpi
@ -143,57 +112,41 @@ BuildRequires:  python3-mpi4py-openmpi
 Requires:       openmpi
 Requires:       python3-openmpi
 Requires:       python3-mpi4py-openmpi
-Requires:       %{py3_dist numpy}
-Provides:       python3-arbor-openmpi = %{version}-%{release}
+Provides:       python3-%{name}-openmpi = %{version}-%{release}
+%{?python_provide:%python_provide python3-%{name}-openmpi}

 %description openmpi %{_description}

 %package openmpi-devel
-Summary:    Development files for arbor-openmpi
-Requires:   arbor-openmpi%{?_isa} = %{version}-%{release}
-Provides:   arbor-openmpi-static = %{version}-%{release}
+Summary:    Development files for %{name}-openmpi
+Requires:   %{name}-openmpi%{?_isa} = %{version}-%{release}
+Provides:   %{name}-openmpi-static = %{version}-%{release}

 %description openmpi-devel %{_description}
 %endif

 %prep
-%forgeautosetup -p1
+%if 0%{?commit:1}
+%autosetup -n %{name}-%{commit} -S git
+%else
+%autosetup -p1
+%endif

-# 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.*$|#!/usr/bin/python3|' {} 2>/dev/null ';'
-
-# Fix shebang (special case)
-sed -i 's|^#![  ]*/usr/env/bin.*python.*$|#!/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
+# We set it, remove the hard coded bits from CMakeLists.txt
+sed -i '/set(arb_pyexecdir/ d' python/CMakeLists.txt

 # builddir for serial
 mkdir build-serial
@ -211,7 +164,7 @@ mkdir build-serial
 # straight away
 %global do_cmake_config %{expand: \
 echo
-echo "*** BUILDING arbor-%{version}$MPI_COMPILE_TYPE ***"
+echo "*** BUILDING %{name}-%{version}$MPI_COMPILE_TYPE ***"
 echo
 pushd build$MPI_COMPILE_TYPE  &&
    cmake \\\
@ -226,16 +179,22 @@ pushd build$MPI_COMPILE_TYPE  &&
        -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\
        -DCMAKE_SKIP_RPATH:BOOL=ON \\\
        -DCMAKE_BUILD_TYPE:STRING="release" \\\
-        -DARB_USE_BUNDLED_LIBS:BOOL=OFF \\\
-        -DARB_USE_BUNDLED_PYBIND11:BOOL=OFF \\\
+%ifarch x86_64 i686 aarch64
+        -DARB_VECTORIZE:BOOL=ON \\\
+%else
        -DARB_VECTORIZE:BOOL=OFF \\\
+%endif
+%ifarch %{power64}
+        -DARB_ARCH=power8 \\\
+%endif
        -DARB_WITH_MPI:BOOL=$MPI_YES \\\
        -DARB_WITH_GPU:BOOL=OFF \\\
-        -DARB_ARCH:STRING="none" \\\
-        -DARB_CXX_FLAGS_TARGET:STRING="-ffat-lto-objects" \\\
+%ifnarch armv7hl
+        -DARB_ARCH:STRING="native" \\\
+%endif
        -DCMAKE_INSTALL_LIBDIR=%{_lib} \\\
        -DARB_WITH_PYTHON:BOOL=ON \\\
-        -DARB_PYTHON_LIB_PATH:STRING=$MPI_PYTHON3_SITEARCH \\\
+        -Darb_pyexecdir:STRING=$MPI_PYTHON3_SITEARCH \\\
 %if "%{_lib}" == "lib64"
        -DLIB_SUFFIX=64 .. &&
 %else
@ -252,16 +211,13 @@ 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}
@ -272,12 +228,17 @@ export MPI_PYTHON3_SITEARCH=%{python3_sitearch}
 %{do_cmake_config}
 %{do_make_build}

-# skip building sphinx docs because they bundle js/fonts and it's very hard to
-# unbundle
+# Manually make docs in the serial build
+sphinx-build-%{python3_version} -b html doc html
+# Remove uneeded dotfiles
+rm -rfv html/{.buildinfo,.doctrees}
+

 # Build mpich version
 %if %{with mpich}
 %{_mpich_load}
+%global __cc mpicc
+%global __cxx mpicxx
 %set_build_flags
 export CC=mpicc
 export CXX=mpicxx
@ -294,6 +255,8 @@ 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
@ -312,7 +275,7 @@ export MPI_COMPILE_TYPE="-openmpi"
 # Install everything
 %global do_install %{expand: \
 echo
-echo "*** INSTALLING arbor-%{version}$MPI_COMPILE_TYPE ***"
+echo "*** INSTALLING %{name}-%{version}$MPI_COMPILE_TYPE ***"
 echo
    %make_install -C build$MPI_COMPILE_TYPE || exit -1
 }
@ -339,8 +302,6 @@ 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
@ -358,60 +319,18 @@ 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
-
-# Taken from upstream's GitHub workflow
-%global mpirun mpirun -n %{_smp_build_ncpus}
-
+# Run for serial only. our builders are not using MPI
 # these tests segfault, filter out
-gtest_filter="${gtest_filter--}${gtest_filter+:}*diffusion*"
-
 pushd build-serial
-    %{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
+    ./bin/unit --gtest_filter=-*mc_event_delivery*:*fvm_lowered*:*mc_cell_group*
 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


@ -419,24 +338,19 @@ popd
 %license LICENSE ext/tinyopt/LICENSE-tinyopt
 %doc README.md
 %{_bindir}/modcc
-%{_bindir}/arbor-build-catalogue
-%{_bindir}/lmorpho
-%{python3_sitearch}/arbor
-%{_datadir}/arbor
+%{python3_sitearch}/%{name}


 %files devel
-%{_includedir}/arborio
-%{_includedir}/arbor
-%{_includedir}/arborenv
-%{_libdir}/cmake/arbor
+%{_includedir}/%{name}
+%{_includedir}/%{name}env
+%{_libdir}/cmake/%{name}
 %{_libdir}/libarbor.a
-%{_libdir}/libarborio.a
 %{_libdir}/libarborenv.a

 %files doc
 %license LICENSE
-%doc example/
+%doc html


 %if %{with mpich}
@ -444,18 +358,13 @@ popd
 %doc README.md
 %license LICENSE ext/tinyopt/LICENSE-tinyopt
 %{_libdir}/mpich/bin/modcc_mpich
-%{_libdir}/mpich/bin/arbor-build-catalogue_mpich
-%{_libdir}/mpich/bin/lmorpho_mpich
-%{python3_sitearch}/mpich/arbor
-%{_libdir}/mpich/share/arbor
+%{python3_sitearch}/mpich/%{name}

 %files mpich-devel
-%{_libdir}/mpich/include/arbor
-%{_libdir}/mpich/include/arborio
-%{_libdir}/mpich/include/arborenv
-%{_libdir}/mpich/lib/cmake/arbor
+%{_libdir}/mpich/include/%{name}
+%{_libdir}/mpich/include/%{name}env
+%{_libdir}/mpich/lib/cmake/%{name}
 %{_libdir}/mpich/lib/libarbor.a
-%{_libdir}/mpich/lib/libarborio.a
 %{_libdir}/mpich/lib/libarborenv.a
 %endif

@ -464,20 +373,79 @@ popd
 %doc README.md
 %license LICENSE ext/tinyopt/LICENSE-tinyopt
 %{_libdir}/openmpi/bin/modcc_openmpi
-%{_libdir}/openmpi/bin/arbor-build-catalogue_openmpi
-%{_libdir}/openmpi/bin/lmorpho_openmpi
-%{python3_sitearch}/openmpi/arbor
-%{_libdir}/openmpi/share/arbor
+%{python3_sitearch}/openmpi/%{name}

 %files openmpi-devel
-%{_libdir}/openmpi/include/arbor
-%{_libdir}/openmpi/include/arborio
-%{_libdir}/openmpi/include/arborenv
-%{_libdir}/openmpi/lib/cmake/arbor
+%{_libdir}/openmpi/include/%{name}
+%{_libdir}/openmpi/include/%{name}env
+%{_libdir}/openmpi/lib/cmake/%{name}
 %{_libdir}/openmpi/lib/libarbor.a
-%{_libdir}/openmpi/lib/libarborio.a
 %{_libdir}/openmpi/lib/libarborenv.a
 %endif

 %changelog
-%autochangelog
+* 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
--- a/75
+++ b/75
@ -1,75 +0,0 @@
-* 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
-
--- a/fix-missing-includes.patch
+++ b/fix-missing-includes.patch
@ -1,43 +0,0 @@
-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;
- 
--- a/run_cpp_examples.sh
+++ b/run_cpp_examples.sh
@ -1,21 +0,0 @@
-#!/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
-$PREFIX build/bin/single-cell
--- a/run_python_examples.sh
+++ b/run_python_examples.sh
@ -1,21 +0,0 @@
-#!/usr/bin/env bash
-# Runs all Python examples
-
-set -Eeuo pipefail
-
-if [[ "$#" -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
--- a/2
+++ b/2
@ -1 +1 @@
-SHA512 (arbor-0.9.0.tar.gz) = fa0280cae870c150c8f891949da9d6276f672bb7191b7b982cda4695dd38e3bffdd0dfa5f3acc2cf940909f64eb9da04cd11aeb7a4baa262fdbcd99be618aa15
+SHA512 (arbor-0.3.tar.gz) = d81438e6b0474615d383b9a401a0ff32b3039e19b9ff9be2648c27cf96c72951f74959dd6213579ae6f2a158579cf2e1ea325fe60ec6b9c8decd800e9a171ebc