%global _lto_cflags %{nil}
%global install_dir %{_libdir}/%{name}

Name:           mrtrix3
Version:        3.0.8
Release:        1%{?dist}
Summary:        Advanced Diffusion MRI Processing and Visualisation

License:        MPL-2.0
URL:            https://www.mrtrix.org/
Source0:        https://github.com/MRtrix3/%{name}/archive/refs/tags/%{version}.tar.gz#/%{name}-%{version}.tar.gz

BuildRequires:  gcc-c++
BuildRequires:  git
BuildRequires:  python3
BuildRequires:  python3-devel
BuildRequires:  eigen3-devel
BuildRequires:  zlib-devel
BuildRequires:  fftw-devel
BuildRequires:  libtiff-devel
BuildRequires:  libpng-devel
# Qt5 Dependencies
BuildRequires:  qt5-qtbase-devel
BuildRequires:  qt5-qtsvg-devel
BuildRequires:  mesa-libGL-devel
BuildRequires:  mesa-libGLU-devel

Requires:       python3
Requires:       python3-numpy
Requires:       qt5-qtbase
Requires:       qt5-qtsvg
Requires:       mesa-libGL

%description
MRtrix3 provides a set of tools to perform various types of diffusion MRI
analyses, from various forms of tractography through to next-generation
group-level analyses.

%prep
%autosetup

%build
# 1. Fix build scripts to use python3
sed -i 's|#!/usr/bin/env python|#!/usr/bin/python3|' configure build


# 2. Set Compiler Flags
# Note: MRTrix3 configure only respects CFLAGS, not CXXFLAGS
export CFLAGS="%{optflags} -Wno-complain-wrong-lang -I /usr/include/eigen3 -fopenmp -std=c++14 -Wno-maybe-uninitialized -Wno-deprecated-declarations -Wno-error -include cassert"
export CXXFLAGS="%{optflags}"
export LDFLAGS="%{?__global_ldflags}"
export EIGEN_CFLAGS="-I /usr/include/eigen3 -std=c++14"
export LINKFLAGS="$LDFLAGS"

# 3. Qt5 Paths
export QMAKE=/usr/bin/qmake-qt5
export MOC=/usr/bin/moc-qt5
export RCC=/usr/bin/rcc-qt5

# 4. Configure
./configure \
    -noshared \
    -nogui \
    -openmp

# 5. Build
./build

%install
mkdir -p %{buildroot}%{install_dir}
mkdir -p %{buildroot}%{_bindir}

cp -a bin %{buildroot}%{install_dir}/
cp -a lib %{buildroot}%{install_dir}/
cp -a share %{buildroot}%{install_dir}/

# Symlinks
for b in %{buildroot}%{install_dir}/bin/*; do
    binary_name=$(basename "$b")
    if [ "$binary_name" != "python" ]; then
        ln -s %{install_dir}/bin/"$binary_name" %{buildroot}%{_bindir}/"$binary_name"
    fi
done

# Fix Shebangs utilizing standard Fedora macros
%py3_shebang_fix %{buildroot}%{install_dir}/bin/*

%check
# Basic smoke test to ensure binaries execute and libraries are found
export LD_LIBRARY_PATH=%{buildroot}%{install_dir}/lib
%{buildroot}%{install_dir}/bin/mrinfo --version
# If the source includes the test scripts and data:
# python3 testing/run_tests.py

%files
%license LICENCE.txt
%doc README.md
%{install_dir}/
%{_bindir}/*

%changelog
* Sun Jan 04 2026 Morgan Hough <morgan.hough@gmail.com> - 3.0.8-1
- Initial package for MRtrix3 version 3.0.8