Name:           bart
Version:        1.0.00
Release:        3%{?dist}
Summary:        The Berkeley Advanced Reconstruction Toolbox (BART)

License:        BSD-3-Clause
URL:            https://github.com/mrirecon/bart
Source0:        %{url}/archive/v%{version}.tar.gz#/%{name}-%{version}.tar.gz

BuildRequires:  make
BuildRequires:  gcc
BuildRequires:  fftw-devel
BuildRequires:  openblas-devel
BuildRequires:  lapack-devel
BuildRequires:  libpng-devel
# %%check: readelf asserts the stack is not executable.
BuildRequires:  binutils
# The Makefile says it requires make 4.0 or newer. Fedora has it.

%description
The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source
image-reconstruction framework for Computational Magnetic Resonance Imaging.
It consists of a library and a toolbox with many command-line algorithms
for MRI reconstruction, such as SENSE, POCS-enhanced SPIRiT, and 
compressed sensing.

%prep
%autosetup -n %{name}-%{version}
# Remove hardcoded rpath and -L/usr/lib which causes issues on Fedora
sed -i 's|BLAS_L := -Wl,-rpath $(BLAS_BASE)/lib -L$(BLAS_BASE)/lib|BLAS_L :=|' Makefile
sed -i 's|FFTW_L :=  -Wl,-rpath $(FFTW_BASE)/lib -L$(FFTW_BASE)/lib -lfftw3f|FFTW_L := -lfftw3f|' Makefile

%build
# BART's Makefile uses PREFIX for install, but not necessarily for build.
# We can use Makefile.local to configure.
cat > Makefile.local <<EOF
PREFIX=%{_prefix}
PARALLEL=1
OPENBLAS=1
FFTWTHREADS=1
CPPFLAGS += -I%{_includedir}/openblas
EOF
# NESTED FUNCTIONS WITHOUT AN EXECUTABLE STACK.
#
# BART's closures are GCC nested functions. GCC's default implementation puts
# a trampoline on the stack, which needs an executable stack. -1/-2 used
# NOEXEC_STACK=1 on x86_64, which makes NESTED_CALL (src/misc/nested.h) decode
# that stack trampoline byte by byte instead of calling it, and asserts the
# bytes are exactly mov/mov/jmp. Fedora's build flags include -fcf-protection,
# which makes GCC start the trampoline with endbr64, so the assert failed on the
# FIRST nested call: every real command (phantom, ones, zeros, fft, ...)
# aborted with
#   multind.c:76: md_nary_int: Assertion `(0xbb41 == __t->mov1) && ...' failed.
# -2's %%check ran only `bart version`, which makes no nested call, so this
# shipped. Found 2026-10-11 by the DeepInverse/BART comparison test.
#
# GCC 14+ can place trampolines on the heap instead (-ftrampoline-impl=heap,
# x86_64 and aarch64 Linux). That needs neither the byte-decoding hack nor an
# executable stack, on every arch -- so aarch64, which had to ship with an
# executable stack under -2, no longer does either.
echo "CFLAGS += -ftrampoline-impl=heap" >> Makefile.local
%make_build

%install
%make_install PREFIX=%{_prefix}

# The install target in the Makefile seems a bit incomplete for Fedora standards
# It doesn't install the man page.
mkdir -p %{buildroot}%{_mandir}/man1
install -p -m 644 doc/bart.1 %{buildroot}%{_mandir}/man1/

# The Makefile installs to %{_prefix}/share/doc/bart/ which is not where we want it in Fedora.
# Fedora uses %{_docdir}/%{name} which %doc takes care of.
# Let's remove the one installed by Makefile
rm -rf %{buildroot}%{_prefix}/share/doc/bart/

%check
# The stack must not be executable (that is the point of the heap trampolines).
readelf -lW %{buildroot}%{_bindir}/bart | grep -E '^\s+GNU_STACK'
readelf -lW %{buildroot}%{_bindir}/bart | grep -E '^\s+GNU_STACK' | grep -qv 'RWE'

# Exercise nested calls, which `bart version` (the -2 check) never did.
./bart ones 2 4 4 o
./bart phantom -x 32 p

# Upstream's unit tests and command-line tests.
%make_build utest
# One command-line test is dropped. test-ecalib-econ requires ESPIRiT's
# memory-saving mode (-e -1) to give BIT-IDENTICAL maps to the normal one
# (`nrmse -t 0.`); on f44 x86_64 they differ by an NRMSE of 4.4e-8, with
# OpenBLAS at 1 thread as well as many. Every other one of the 449 tests passed
# in that run (make -k test, local f44 mock, 2026-10-12), including
# test-ecalib-nystroem and the other ecalib tests with a 1e-5 tolerance.
sed -i '/^TESTS += tests\/test-ecalib-econ$/d' tests/ecalib.mk
! grep -q 'TESTS += tests/test-ecalib-econ' tests/ecalib.mk
%make_build test

%files
%license LICENSE
%doc README README.md doc/*.txt
%{_bindir}/bart
%{_mandir}/man1/bart.1*
%dir %{_prefix}/lib/bart
%dir %{_prefix}/lib/bart/commands

%changelog
* Sun Oct 11 2026 Morgan Hough <morgan.hough@gmail.com> - 1.0.00-3
- Fix every command aborting on x86_64. NOEXEC_STACK=1 decodes GCC's stack
  trampoline byte by byte and asserts mov/mov/jmp; Fedora's -fcf-protection
  prefixes it with endbr64, so the first nested call failed with
  "md_nary_int: Assertion `(0xbb41 == __t->mov1) && ...' failed" (phantom, ones,
  zeros and fft all rc 134). -2's %%check, `bart version`, never made a nested
  call, so it passed.
- Build with -ftrampoline-impl=heap on every arch instead: no decoding hack, no
  execstack -c, and aarch64 no longer ships with an executable stack.
- %%check now asserts GNU_STACK is not RWE and runs upstream's `make utest` and
  `make test` in place of `bart version`: all unit tests and 448 of 449
  command-line tests pass. test-ecalib-econ is dropped: it demands bit-identical
  ESPIRiT maps from two code paths and gets an NRMSE of 4.4e-8.
- Found by tests/deepinv-bart-mri.bats.

* Thu Sep 10 2026 Morgan Hough <morgan.hough@gmail.com> - 1.0.00-2
- Only enable NOEXEC_STACK and the matching execstack -c on x86_64.
  src/misc/nested.h guards that trampoline hack with
  "#ifndef __x86_64__ #error NOEXEC_STACK only supported on x86_64",
  so the aarch64 build failed outright. Elsewhere the header falls back
  to real GCC nested functions, whose trampolines need an executable
  stack -- so the flag is left in place there rather than stripped.
  NOTE: this means the aarch64 binary ships with an executable stack.

* Wed Feb 25 2026 Morgan Hough <morgan.hough@gmail.com> - 1.0.00-1
- Initial BART package