Fix missing includes

[skip changelog]

.gitignore

@@ -5,3 +5,4 @@
 /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

2080.patch

@@ -1,33 +0,0 @@
-From 884c568f96bc10079f28f4b2b7c8fc120c020053 Mon Sep 17 00:00:00 2001
-From: "Benjamin A. Beasley" <code@musicinmybrain.net>
-Date: Thu, 19 Jan 2023 10:10:21 -0500
-Subject: [PATCH] Add some missing #include directives
-
-Fixes failure to compile with GCC 13.
----
- arbor/include/arbor/morph/primitives.hpp | 1 +
- arbor/threading/threading.cpp            | 1 +
- 2 files changed, 2 insertions(+)
-
-diff --git a/arbor/include/arbor/morph/primitives.hpp b/arbor/include/arbor/morph/primitives.hpp
-index 4be04670b..9d75060df 100644
---- a/arbor/include/arbor/morph/primitives.hpp
-+++ b/arbor/include/arbor/morph/primitives.hpp
-@@ -2,6 +2,7 @@
- 
- #include <algorithm>
- #include <cstdlib>
-+#include <cstdint>
- #include <ostream>
- #include <vector>
- 
-diff --git a/arbor/threading/threading.cpp b/arbor/threading/threading.cpp
-index 552fda90a..4c786b867 100644
---- a/arbor/threading/threading.cpp
-+++ b/arbor/threading/threading.cpp
-@@ -1,4 +1,5 @@
- #include <atomic>
-+#include <stdexcept>
- 
- #include <arbor/assert.hpp>
- #include <arbor/util/scope_exit.hpp>

arbor.spec

@@ -14,15 +14,21 @@ 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
+
+# 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:        0.7
+Version:        0.9.0
 Release:        %autorelease
 Summary:        Multi-compartment neural network simulation library
 
@@ -36,13 +42,8 @@ Source2:        https://raw.githubusercontent.com/arbor-sim/arbor/master/scripts
 License:        BSD-3-Clause
 
 Patch:          0001-Quote-various-cmake-var-values.patch
-# Add some missing #include directives
-# Fixes failure to compile with GCC 13.
-# https://github.com/arbor-sim/arbor/pull/2080
-Patch:          %{forgeurl}/pull/2080.patch
-# Replace use of LooseVersion from distutils.version (removed in Python3.12)
-# https://github.com/arbor-sim/arbor/pull/2157
-Patch:          looseversion.patch
+# Tests are failing to compile due to some missing includes
+Patch:          fix-missing-includes.patch
 
 # Random123 does not support:
 #   mips64r2 mips32r2 s390
@@ -90,11 +91,13 @@ Provides:   arbor-static = %{version}-%{release}
 %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 arbor
 BuildRequires:  python3-sphinx
 BuildRequires:  python3-sphinx_rtd_theme
 BuildRequires:  python3-svgwrite
 
+BuildArch:      noarch
+
 %description doc %{_description}
 
 %if %{with mpich}
@@ -172,6 +175,9 @@ find . -type f -name "CMakeLists.txt" -exec sed -i -e 's/ext-tclap//' -e 's/ext-
 # 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.*$|#!/usr/bin/python3|' example/lfp/neuron_lfp_example.py
+
 # test scripts
 cp %{SOURCE1} scripts/
 cp %{SOURCE2} scripts/
@@ -216,6 +222,7 @@ pushd build$MPI_COMPILE_TYPE  &&
         -DARB_WITH_MPI:BOOL=$MPI_YES \\\
         -DARB_WITH_GPU:BOOL=OFF \\\
         -DARB_ARCH:STRING="none" \\\
+        -DARB_CXX_FLAGS_TARGET:STRING="-ffat-lto-objects" \\\
         -DCMAKE_INSTALL_LIBDIR=%{_lib} \\\
         -DARB_WITH_PYTHON:BOOL=ON \\\
         -DARB_PYTHON_LIB_PATH:STRING=$MPI_PYTHON3_SITEARCH \\\
@@ -348,51 +355,51 @@ popd
 %endif
 
 
-# https://github.com/arbor-sim/arbor/blob/master/.github/workflows/test-everything.yml
+# https://github.com/arbor-sim/arbor/blob/master/.github/workflows/test-matrix.yml
 %if %{with tests}
 %check
-# General tests
-export PYTHONPATH="%{buildroot}%{python3_sitearch}:%{buildroot}%{python3_sitelib}"
-# for arbor-build-catalogue
-export PATH="$PATH:%{buildroot}/%{_bindir}"
+
+# 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
-    %{python3} -m unittest discover -v -s ../python
-    ./bin/unit --gtest_filter=-*task_system.test_copy*:*notification_queue.test_copy*
+    %{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
-./scripts/run_python_examples.sh
 
 # MPICH
 %if %{with mpich}
 %{_mpich_load}
-export PYTHONPATH="%{buildroot}/$MPI_PYTHON3_SITEARCH"
-export PATH="$PATH:."
 pushd build-mpich
-    mpirun -n %{_smp_build_ncpus} %{python3} -m unittest discover -v -s ../python
-    mpirun -n %{_smp_build_ncpus} ./bin/unit-mpi
+%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 -n %{_smp_build_ncpus}"
+    ./run_cpp_examples.sh "%{mpirun}"
 popd
-./scripts/run_python_examples.sh  "mpirun -n %{_smp_build_ncpus}"
+%{py3_test_envvars} ./scripts/run_python_examples.sh  "%{mpirun}"
 %{_mpich_unload}
 %endif
 
 # OpenMPI
 %if %{with openmpi}
 %{_openmpi_load}
-export PYTHONPATH="%{buildroot}/$MPI_PYTHON3_SITEARCH"
-export PATH="$PATH:."
 pushd build-openmpi
-    mpirun -n %{_smp_build_ncpus} %{python3} -m unittest discover -v -s ../python
-    mpirun -n %{_smp_build_ncpus} ./bin/unit-mpi
+%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 -n %{_smp_build_ncpus}"
+    ./run_cpp_examples.sh "%{mpirun}"
 popd
-./scripts/run_python_examples.sh  "mpirun -n %{_smp_build_ncpus}"
+%{py3_test_envvars} ./scripts/run_python_examples.sh  "%{mpirun}"
 %{_openmpi_unload}
 %endif
 %endif

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;
+ 

looseversion.patch

@@ -1,25 +0,0 @@
-diff --git a/pyproject.toml b/pyproject.toml
-index 0d732541..12e003e2 100644
---- a/pyproject.toml
-+++ b/pyproject.toml
-@@ -46,6 +46,7 @@ requires = [
-     "scikit-build",
-     "cmake>=3.18",
-     "ninja",
-+    "looseversion",
- ]
- build-backend = "setuptools.build_meta"
- 
-diff --git a/scripts/tsplot b/scripts/tsplot
-index c64e7b18..10ddf3f4 100755
---- a/scripts/tsplot
-+++ b/scripts/tsplot
-@@ -11,7 +11,7 @@ import matplotlib as M
- import matplotlib.pyplot as P
- import numbers
- from functools import reduce
--from distutils.version import LooseVersion
-+from looseversion import LooseVersion
- from itertools import chain, islice, cycle
- 
- # Run-time check for matplot lib version for line style functionality.

sources

@@ -1 +1 @@
-SHA512 (arbor-0.7.tar.gz) = 66471172e159c87c930c89cfed20020cd7c770e0fd5f32b265197710c7bbd2920cfa018f384553130dd93645e149ccb71f64cc04208534c96b4e581f0c0acb50
+SHA512 (arbor-0.9.0.tar.gz) = fa0280cae870c150c8f891949da9d6276f672bb7191b7b982cda4695dd38e3bffdd0dfa5f3acc2cf940909f64eb9da04cd11aeb7a4baa262fdbcd99be618aa15