Name:           quit
Version:        3.4
Release:        3%{?dist}
Summary:        Quantitative Imaging Tools for MRI data processing

License:        MPL-2.0
URL:            https://github.com/spinicist/QUIT
Source0:        %{url}/archive/v%{version}/QUIT-%{version}.tar.gz
# Header-only argument parser library (not packaged in Fedora)
Source1:        https://github.com/Taywee/args/archive/refs/tags/6.4.8.tar.gz#/args-6.4.8.tar.gz
# CMake find module for bundled args library
Source2:        Findargs.cmake

BuildRequires:  cmake >= 3.12
BuildRequires:  gcc-c++
BuildRequires:  make
BuildRequires:  InsightToolkit5-devel >= 5.3.0
# eigen3-devel intentionally OMITTED: ITK 5.4 bundles Eigen 3.x at
# /usr/include/ITK-5.4/itkeigen/, while Fedora 44 ships system Eigen 5.0.1.
# Mixing both in one TU causes ODR-violation compile errors in
# Eigen::Quaternion. Force quit to use only ITK's bundled Eigen via -isystem.
BuildRequires:  ceres-solver-devel
BuildRequires:  suitesparse-devel
BuildRequires:  blas-devel
BuildRequires:  lapack-devel
# fmt v9 is bundled because QUIT relies on implicit ostream formatting removed in fmt v11
Source3:        https://github.com/fmtlib/fmt/archive/refs/tags/9.1.0.tar.gz#/fmt-9.1.0.tar.gz
BuildRequires:  json-devel

Requires:       InsightToolkit5%{?_isa}

Provides:       bundled(fmt) = 9.1.0
Provides:       bundled(args) = 6.4.8
Provides:       bundled(NumericalIntegration)

%description
QUIT (QUantitative Imaging Tools) is a collection of programs for processing
quantitative MRI data, including DESPOT, relaxometry, magnetization transfer,
perfusion, susceptibility mapping, and more. All tools are accessed via the
single 'qi' command with subcommands, similar to git or bart.

QUIT processes NIfTI format neuroimaging files and accepts sequence parameters
via JSON input.

%prep
%autosetup -n QUIT-%{version}

# Install bundled args header
tar xf %{SOURCE1}
install -p -m 0644 args-6.4.8/args.hxx External/include/

# Install cmake find module for args
install -p -m 0644 %{SOURCE2} cmake/Findargs.cmake

# Bundle fmt 9.1.0 (QUIT relies on implicit ostream formatting removed in fmt v11)
tar xf %{SOURCE3}
mv fmt-9.1.0 External/fmt

# Replace find_package(Eigen3) with a manual interface target pointing to
# ITK's bundled Eigen 3.x. The system Eigen3Config (5.0.1) is still installed
# transitively via ceres-solver-devel; mixing the two causes ODR violations.
sed -i '/^find_package(Eigen3 REQUIRED)$/c\
add_library(Eigen3::Eigen INTERFACE IMPORTED)\
target_include_directories(Eigen3::Eigen SYSTEM INTERFACE /usr/include/ITK-5.4/itkeigen)' \
    CMakeLists.txt

# Fix ambiguous format_to with Eigen expression templates in C++20
# Replace the custom formatter with a simple ostream-based one
sed -i '/template <typename FormatContext>/,/};/c\
    template <typename FormatContext> auto format(const QI::SSFPSequence \&s, FormatContext \&ctx) const {\
        std::ostringstream oss;\
        oss << "SSFP:\\n\\tTR: " << s.TR << "\\n\\tFA: " << (s.FA * 180. / M_PI).transpose() << "\\n\\tPhaseInc: " << (s.PhaseInc * 180. / M_PI).transpose();\
        return fmt::format_to(ctx.out(), "{}", oss.str());\
    }\
};' Source/Sequences/SSFPSequence.h
sed -i '1i #include <sstream>' Source/Sequences/SSFPSequence.h

%build
# Suppress GCC 15 -Wtemplate-body diagnostics in QUIT's own template code.
# Force ITK's bundled Eigen 3.x onto the include path before any other Eigen
# (system eigen3-devel is intentionally not BR'd; see comment above).
export CXXFLAGS="-isystem /usr/include/ITK-5.4/itkeigen %{optflags} -Wno-template-body"
# Build bundled fmt 9.1.0 first
cmake -S External/fmt -B External/fmt/build \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX=%{_builddir}/QUIT-%{version}/External/fmt/install \
    -DFMT_DOC=OFF -DFMT_TEST=OFF
%make_build -C External/fmt/build
%make_build -C External/fmt/build install
%cmake \
    -DCMAKE_MODULE_PATH:PATH="%{_builddir}/QUIT-%{version}/cmake" \
    -DExternal_Include_DIR:PATH="%{_builddir}/QUIT-%{version}/External/include" \
    -DBUILD_PARMESAN:BOOL=OFF \
    -Dfmt_DIR:PATH="%{_builddir}/QUIT-%{version}/External/fmt/install/lib64/cmake/fmt"
%cmake_build

%install
%cmake_install

%files
%license LICENSE.txt
%doc README.md CHANGELOG.md
%{_bindir}/qi

%changelog
* Tue May 05 2026 Morgan Hough <morgan.hough@gmail.com> - 3.4-3
- Replace find_package(Eigen3) with a manual Eigen3::Eigen IMPORTED INTERFACE
  pointing to ITK's bundled itkeigen. Previous attempt failed because system
  eigen3-devel is still pulled in transitively via ceres-solver-devel, and
  cmake's Eigen3::Eigen target adds /usr/include/eigen3 ahead of CXXFLAGS.

* Tue May 05 2026 Morgan Hough <morgan.hough@gmail.com> - 3.4-2
- Drop eigen3-devel BR; force ITK's bundled Eigen 3.x via -isystem and
  EIGEN3_INCLUDE_DIR / Eigen3_DIR overrides. System Eigen 5.x and ITK's
  bundled 3.x cause ODR violations on Eigen::Quaternion when mixed.

* Mon Mar 30 2026 Morgan Hough <morgan.hough@gmail.com> - 3.4-1
- Initial package for Fedora