# brainvisa-soma -- the core of the BrainVISA neuroimaging suite: the AIMS
# image, mesh and graph libraries with their ~220 command-line tools, soma-io
# (file I/O: NIfTI, GIFTI, DICOM, MINC, OpenSlide, ...), the pyaims Python
# bindings, the soma-base Python core, and the brainvisa-share templates and
# models. Upstream ships this group as one conda package, "soma"; Anatomist,
# Axon and Morphologist build on it.
#
# Layout facts the spec depends on (checked against the pinned commits):
# - Five repositories, one build. aims-free finds soma-io and soma-base with
#   find_package() against the build tree, so they cannot be built and
#   installed one by one; upstream's bv_maker builds them in one CMake tree
#   from brainvisa-cmake's brainvisa-compilation.cmake with a bv_maker.cmake
#   cache listing the components. %%build writes those two files itself.
# - The pins are the soma-env 6.0 branch's (conf/sources.d/soma-env.json on
#   brainvisa/soma-env@6.0), the commits BrainVISA 6.0.x is built from; all are
#   dated 2026-08-06. No 6.0 tags exist.
# - BrainVISA's own build pins NumPy < 2 and uses clang; this is GCC 16 and
#   NumPy 2.4, hence Patch0 (two GCC 15/16 errors, the NumPy 2 symbol export,
#   empty-vector reads, and PyWeakref_GetRef for Python 3.15).
# - Install goes through the install-runtime / install-dev targets with
#   BRAINVISA_INSTALL_PREFIX; libraries go to a hardcoded "lib" (about 40
#   install rules) and are moved to %%{_libdir} afterwards.
# - aims-free is a cleaned tarball without the nonfree ECAT library; see
#   brainvisa-soma-clean.sh and BUILD_ECAT=OFF below.
# - Morphologist's image-processing core (VIP, morphologist-nonfree) is
#   "Proprietary-NeuroSpin" and is not part of this or any free package.

%global bvver        6.0
%global snapdate     20260806
%global somabase_c   857c294babe65605d7d08d38584662f93a9020f7
%global somaio_c     7bf16700b33125dbe2473c6ac2d8794b2699b69b
%global aimsfree_c   9ea2121280033e60bdaabe487dc9efa762d853e2
%global aimsgpl_c    333d6d9fec7016aec434833089613edbf0b321aa
%global share_c      e86e904c54f74176245f533e0e35a8f059bb3d05
%global aimsfree_s   %(c=%{aimsfree_c}; echo ${c:0:7})
%global pyreldir     %(echo %{python3_sitearch} | sed 's|^%{_prefix}/||')

Name:           brainvisa-soma
Version:        6.0.20^%{snapdate}git%{aimsfree_s}
Release:        6%{?dist}
Summary:        BrainVISA core: AIMS image libraries, tools and Python bindings

# CeCILL-B: soma-base, soma-io, aims-free, brainvisa-share.
# CECILL-2.1: aims-gpl and aims-free's aimscifti.
# Bundled third-party code (see the Provides below): CiftiLib BSD-2-Clause,
# RPly MIT, nifticlib/znzlib LicenseRef-Fedora-Public-Domain. The bundled
# libkdtree++ is removed in %%prep; Fedora's libkdtree++ is used instead.
License:        CECILL-B AND CECILL-2.1 AND BSD-2-Clause AND MIT AND LicenseRef-Fedora-Public-Domain
URL:            https://brainvisa.info/

Source0:        https://github.com/populse/soma-base/archive/%{somabase_c}/soma-base-%{somabase_c}.tar.gz
Source1:        https://github.com/brainvisa/soma-io/archive/%{somaio_c}/soma-io-%{somaio_c}.tar.gz
# NOT an upstream tarball: brainvisa-soma-clean.sh removes the nonfree ECAT
# library (University of Louvain: non-commercial use only, no modified
# redistribution). Published in this project's COPR dist-git lookaside, which
# is public and content-addressed by md5, as for invesalius and opencv.
%global copr_lookaside https://copr-dist-git.fedorainfracloud.org/repo/pkgs/mhough/neurofedora/%{name}
%global aimsfree_md5   490f433ed6eac20bf0d15694e636ada5
Source2:        %{copr_lookaside}/aims-free-clean-%{aimsfree_s}.tar.xz/md5/%{aimsfree_md5}/aims-free-clean-%{aimsfree_s}.tar.xz
Source3:        https://github.com/brainvisa/aims-gpl/archive/%{aimsgpl_c}/aims-gpl-%{aimsgpl_c}.tar.gz
Source4:        https://github.com/brainvisa/brainvisa-share/archive/%{share_c}/brainvisa-share-%{share_c}.tar.gz
Source10:       brainvisa-soma-clean.sh

# aims-free (branch fedora-gcc16-fixes, submitted upstream by the packager,
# without its hunk for ecat/, which the cleaned tarball does not contain):
#  - greyLevelBlob other.node -> other._node (GCC 15 template-body check);
#  - export the NumPy C-API table from libpyaims (NumPy 2 hides it);
#  - mesh and FreeSurfer surface I/O took &v[0] of possibly empty vectors,
#    which aborts under _GLIBCXX_ASSERTIONS (writing a mesh without normals).
Patch0:         brainvisa-aims-fedora-fixes.patch
# soma-io (submitted upstream by the packager):
#  - DcmCodec::decodedBitsAllocated for the JPEG 2000 codecs (DCMTK 3.7);
#  - fostreambuf asserted on a nonexistent member (hidden by NDEBUG upstream);
#  - the NIfTI reader indexed one past the end of its buffer: every NIfTI read
#    aborted under _GLIBCXX_ASSERTIONS, Fedora's default;
#  - the MINC checker lacked <unistd.h>.
Patch1:         brainvisa-soma-io-fedora-fixes.patch
# aims-gpl: import aims.sip after the Qt modules in the aimsgui bindings;
# SIP 6.17 (rawhide) otherwise rejects PyQt6's %MinimumABIVersion.
Patch2:         brainvisa-aims-gpl-fedora-fixes.patch

# -2 finds the system libkdtree++ (FindLibKDTree looked in the wrong place).
BuildRequires:  brainvisa-cmake >= 6.0.0^20260918git850b6f3-3
BuildRequires:  cmake
BuildRequires:  make
BuildRequires:  gcc-c++
BuildRequires:  gcc-gfortran
BuildRequires:  python3-devel
BuildRequires:  python3-numpy
BuildRequires:  python3-pyyaml
BuildRequires:  python3-dateutil
# soma-base and brainvisa-share import six (about 70 modules, and a build
# script); f44/f45 pulled it in indirectly, rawhide does not.
BuildRequires:  python3-six
BuildRequires:  sip6
BuildRequires:  python3-pyqt6-devel
BuildRequires:  python3-pyqt6-sip
BuildRequires:  qt6-qtbase-devel
BuildRequires:  qt6-qt5compat-devel
BuildRequires:  qt6-qttools-devel
BuildRequires:  blitz-devel
BuildRequires:  libsigc++20-devel
BuildRequires:  boost-devel
BuildRequires:  libxml2-devel
# DCMTK 3.7 from this COPR; Patch1 also keeps 3.6 working.
BuildRequires:  dcmtk-devel
BuildRequires:  openjpeg-devel
BuildRequires:  libtiff-devel
BuildRequires:  jasper-devel
BuildRequires:  openslide-devel
BuildRequires:  hdf5-devel
BuildRequires:  libminc-devel
BuildRequires:  libkdtree++-devel
BuildRequires:  libtirpc-devel
BuildRequires:  expat-devel
BuildRequires:  libpng-devel
BuildRequires:  libjpeg-turbo-devel
BuildRequires:  zlib-devel
BuildRequires:  pkgconf-pkg-config

%description
The core of the BrainVISA neuroimaging suite: the AIMS libraries for images,
meshes, textures and graphs, their command-line tools, the soma-io file
format layer (NIfTI, GIFTI, DICOM, MINC, OpenSlide and more), the pyaims
Python bindings and the soma-base Python core. Anatomist, Axon and
Morphologist are built on it.

The ECAT PET file format is not supported: the library it needs is not free
software.

%package     -n brainvisa-aims
Summary:        AIMS neuroimaging libraries and command-line tools
Requires:       brainvisa-share = %{version}-%{release}
Provides:       bundled(ciftilib) = 1.5.1
Provides:       bundled(rply) = 1.1.1
Provides:       bundled(nifticlib)

%description -n brainvisa-aims
AIMS (Analysis of Images and Meshes Software) is the C++ library and toolset
at the core of BrainVISA: volumes, meshes, textures, graphs and transforms,
with readers and writers for the common neuroimaging formats, image
processing and resampling algorithms, and about 220 command-line tools
(AimsFileInfo, AimsApplyTransform, AimsThreshold, ...).

%package     -n brainvisa-aims-devel
Summary:        Development files for the AIMS libraries
Requires:       brainvisa-aims%{?_isa} = %{version}-%{release}
Requires:       brainvisa-cmake
# What the installed CMake configs find_package() as REQUIRED (soma-io,
# aims-free), and the headers the AIMS headers include.
Requires:       libsigc++20-devel
Requires:       libxml2-devel
Requires:       boost-devel
Requires:       blitz-devel
Requires:       libkdtree++-devel
Requires:       qt6-qtbase-devel

%description -n brainvisa-aims-devel
Headers, libraries and CMake configuration for building software, such as
Anatomist, against AIMS and soma-io.

%package     -n python3-brainvisa-aims
Summary:        Python bindings for AIMS (soma.aims)
Requires:       brainvisa-aims%{?_isa} = %{version}-%{release}
Requires:       python3-soma-base%{?_isa} = %{version}-%{release}
Requires:       python3-numpy
Requires:       python3-pyqt6

%description -n python3-brainvisa-aims
pyaims, the Python bindings for AIMS: read, write and process volumes,
meshes, textures and graphs from Python as NumPy arrays (soma.aims,
soma.aimsalgo).

%package     -n python3-soma-base
Summary:        Python core of the BrainVISA/populse suites (soma package)
Requires:       python3-six
Requires:       python3-pyyaml

%description -n python3-soma-base
soma-base, the common Python layer of BrainVISA and populse: controllers,
configuration, file-organisation models, subprocess and archive helpers.

%package     -n brainvisa-share
Summary:        Templates, atlases and models shared by BrainVISA tools
BuildArch:      noarch

%description -n brainvisa-share
Anatomical templates, standard meshes, nomenclatures, colour tables and
models used by AIMS, Anatomist and Morphologist.

%prep
%setup -q -c -T
tar -xzf %{SOURCE0} && mv soma-base-%{somabase_c} soma-base
tar -xzf %{SOURCE1} && mv soma-io-%{somaio_c} soma-io
tar -xJf %{SOURCE2} && mv aims-free-%{aimsfree_c} aims-free
tar -xzf %{SOURCE3} && mv aims-gpl-%{aimsgpl_c} aims-gpl
tar -xzf %{SOURCE4} && mv brainvisa-share-%{share_c} brainvisa-share
test ! -e aims-free/ecat
%patch -P0 -p1 -d aims-free
%patch -P1 -p1 -d soma-io
%patch -P2 -p1 -d aims-gpl
# Use Fedora's libkdtree++ (header-only), not the older bundled copy; with
# the bundled one brainvisa-aims-devel installed /usr/include/kdtree++ and
# conflicted with libkdtree++-devel.
rm -r aims-free/aimsdata/src/aimsdata/kdtree++

%build
%set_build_flags
mkdir -p bvbuild
cd bvbuild
# What bv_maker writes for a combined build (brainvisa_cmake/build.py).
S=$PWD/..
cat > bv_maker.cmake <<EOF
cmake_policy( SET CMP0074 NEW )
set( BRAINVISA_PROJECTS brainvisa-share soma aims CACHE STRING "" FORCE )
set( _BRAINVISA_PROJECTS brainvisa-share soma aims CACHE STRING "" FORCE )
set( BRAINVISA_COMPONENTS brainvisa-share soma-base soma-io aims-free aims-gpl CACHE STRING "" FORCE )
set( _BRAINVISA_COMPONENTS brainvisa-share soma-base soma-io aims-free aims-gpl CACHE STRING "" FORCE )
set( BRAINVISA_SOURCES_brainvisa-share "$S/brainvisa-share" CACHE STRING "" FORCE )
set( BRAINVISA_SOURCES_soma-base "$S/soma-base" CACHE STRING "" FORCE )
set( BRAINVISA_SOURCES_soma-io "$S/soma-io" CACHE STRING "" FORCE )
set( BRAINVISA_SOURCES_aims-free "$S/aims-free" CACHE STRING "" FORCE )
set( BRAINVISA_SOURCES_aims-gpl "$S/aims-gpl" CACHE STRING "" FORCE )
set( PYTHON_INSTALL_DIRECTORY %{pyreldir} )
EOF
cat > CMakeLists.txt <<EOF
cmake_minimum_required( VERSION 3.20 )
set( CMAKE_PREFIX_PATH "\${CMAKE_BINARY_DIR}" \${CMAKE_PREFIX_PATH} )
project( "Brainvisa" )
include( "%{_datadir}/brainvisa-cmake-%{bvver}/cmake/brainvisa-compilation.cmake" )
EOF
cmake . -G "Unix Makefiles" \
    -DCMAKE_BUILD_TYPE=RelWithDebInfo \
    -DCMAKE_INSTALL_PREFIX=%{_prefix} \
    -DDESIRED_QT_VERSION=6 \
    -DBUILD_ECAT=OFF \
    -DSIP4MAKE_EXECUTABLE=%{_bindir}/bv_sip4make \
    -DMINC_INCLUDE_DIR=%{_includedir}/libminc \
    -DMINC2_INCLUDE_DIR=%{_includedir}/libminc \
    -DMINC_minc_LIBRARY=%{_libdir}/libminc2.so \
    -DCMAKE_C_FLAGS_RELWITHDEBINFO="%{optflags}" \
    -DCMAKE_CXX_FLAGS_RELWITHDEBINFO="%{optflags}" \
    -DCMAKE_SKIP_RPATH=ON
%make_build

%install
cd bvbuild
make install-runtime install-dev BRAINVISA_INSTALL_PREFIX=%{buildroot}%{_prefix}
# pixi environment housekeeping from soma-base; nothing to do on a system.
rm -f %{buildroot}%{_bindir}/bv_pixi_cache_clean %{buildroot}%{_bindir}/bv_update_bin_links
# A Qt Designer form no program loads.
rm -f %{buildroot}%{_bindir}/dicom_converter.ui
# Modules and data with a shebang but no execute bit are not run directly:
# drop the shebang rather than rewrite it.
find %{buildroot}%{python3_sitearch} %{buildroot}%{_datadir} -type f ! -perm /111 \
    -exec sed -i '1{/^#!/d}' {} +
# Upstream's scripts say "#!/usr/bin/env python". Given a directory the
# fixer only looks at *.py files, so the commands are passed one by one.
%py3_shebang_fix %{buildroot}%{_bindir}/*
# Data, not programs (the Blender add-ons' "#!BPY" is Blender's marker line,
# already stripped above for the non-executable ones).
find %{buildroot}%{_datadir} -type f -perm /111 -exec sed -i '1{/^#!/d}' {} + -exec chmod 0644 {} +
# Hardcoded "lib" in upstream's install rules: move to the multilib path and
# fix the files that name it.
%if "%{_lib}" != "lib"
mkdir -p %{buildroot}%{_libdir}
mv %{buildroot}%{_prefix}/lib/* %{buildroot}%{_libdir}/
rmdir %{buildroot}%{_prefix}/lib
grep -rlZ -e '/lib/' -e '}/lib"' -e '/lib"' %{buildroot}%{_libdir}/pkgconfig %{buildroot}%{_datadir}/*/cmake 2>/dev/null \
    | xargs -0r sed -i -e 's|%{_prefix}/lib/|%{_libdir}/|g' -e 's|${prefix}/lib\b|${prefix}/%{_lib}|g'
%endif
# File lists instead of %%exclude: an excluded ELF file still gets its
# build-id link in the excluding package, dangling there.
(cd %{buildroot}
 ls -1d .%{_libdir}/lib*.so.* | sed 's|^\.||' | grep -v '/libpyaims' > %{_builddir}/aims-libs.files
 echo '%%dir %{python3_sitearch}/soma' > %{_builddir}/soma-base.files
 ls -1d .%{python3_sitearch}/soma/* | sed 's|^\.||' | grep -vE '/soma/(aims|aimsalgo|__pycache__)$' >> %{_builddir}/soma-base.files
 # Byte-compilation runs after %%install, so name its directory now.
 echo '%{python3_sitearch}/soma/__pycache__/' >> %{_builddir}/soma-base.files)

%check
export LD_LIBRARY_PATH=%{buildroot}%{_libdir}
export PATH=%{buildroot}%{_bindir}:$PATH
export PYTHONPATH=%{buildroot}%{python3_sitearch}
export BRAINVISA_SHARE=%{buildroot}%{_datadir}
# No ECAT anywhere.
! ls %{buildroot}%{_bindir} | grep -q -E '^(Ecat|AimsFovSplit|AimsSumPETFrame)'
! ls %{buildroot}%{_libdir} | grep -q -i ecat
# Round trips under Fedora's flags (_GLIBCXX_ASSERTIONS caught two
# out-of-range reads upstream does not see): volumes through NIfTI and the
# AIMS GIS format, a mesh without normals or textures through GIFTI, PLY and
# the AIMS mesh format, and a tool reading the result.
%{python3} -W ignore - <<'EOF'
import numpy as np, tempfile, os, subprocess
from soma import aims
d = tempfile.mkdtemp()
v = aims.Volume(np.arange(4 * 5 * 6, dtype=np.int16).reshape(4, 5, 6))
v.header()['voxel_size'] = [1.5, 2.0, 2.5]
for ext in ('.nii', '.nii.gz', '.ima'):
    f = os.path.join(d, 'v' + ext)
    aims.write(v, f)
    w = aims.read(f)
    assert np.array_equal(np.asarray(w)[..., 0], np.asarray(v)[..., 0]), ext
    assert np.allclose(list(w.header()['voxel_size'])[:3], [1.5, 2.0, 2.5]), ext
m = aims.SurfaceGenerator.sphere(aims.Point3df(0, 0, 0), 10., 50)
for ext in ('.gii', '.ply', '.mesh'):
    f = os.path.join(d, 'm' + ext)
    aims.write(m, f)
    assert len(aims.read(f).vertex()) == len(m.vertex()), ext
info = subprocess.run(['AimsFileInfo', '-i', os.path.join(d, 'v.nii.gz')],
                      capture_output=True, text=True, check=True).stdout
assert "'sizeX' : 4" in info, info[:400]
print('NIfTI, GIS, GIFTI, PLY and mesh round trips; AimsFileInfo reads the result')
EOF

%files -n brainvisa-aims -f %{_builddir}/aims-libs.files
%license aims-free/LICENSE soma-io/LICENSE aims-gpl/LICENSE
%doc aims-free/README.md
%{_bindir}/*
%{_datadir}/aims-%{bvver}/
%{_datadir}/aims-free-%{bvver}/
%{_datadir}/aims-gpl-%{bvver}/
%{_datadir}/soma-io-%{bvver}/
%{_datadir}/graph-%{bvver}/
%exclude %{_datadir}/*/cmake

%files -n brainvisa-aims-devel
%{_includedir}/*
%{_libdir}/lib*.so
%{_libdir}/pkgconfig/*
%{_datadir}/*/cmake

%files -n python3-brainvisa-aims
%{_libdir}/libpyaims*.so.*
%{python3_sitearch}/soma/aims/
%{python3_sitearch}/soma/aimsalgo/
%{python3_sitearch}/aims/
%{python3_sitearch}/brainvisa_share/

%files -n python3-soma-base -f %{_builddir}/soma-base.files
%license soma-base/README.md
%{_datadir}/soma-base-%{bvver}/

%files -n brainvisa-share
%license brainvisa-share/LICENCE
%{_datadir}/brainvisa-share-%{bvver}/

%changelog
* Thu Oct 15 2026 Morgan Hough <morgan.hough@gmail.com> - 6.0.20^20260806git9ea2121-6
- libaimsdata exports the graph reader/writer ObjectWrapper members: they
  were explicitly instantiated only on macOS, and GCC's LTO dropped the
  implicit instances, so libanatomist failed to link (fifth aims-free
  commit). Build against brainvisa-cmake -3.

* Thu Oct 15 2026 Morgan Hough <morgan.hough@gmail.com> - 6.0.20^20260806git9ea2121-5
- Build against Fedora's libkdtree++: the bundled copy is removed, and
  brainvisa-aims-devel no longer ships /usr/include/kdtree++ (it conflicted
  with libkdtree++-devel). Needs brainvisa-cmake -2.
- brainvisa-aims-devel requires the -devel packages its CMake configs need
  (sigc++, libxml2, Boost, blitz, libkdtree++, Qt 6); found configuring
  Anatomist against the installed tree.

* Thu Oct 15 2026 Morgan Hough <morgan.hough@gmail.com> - 6.0.20^20260806git9ea2121-4
- SIP 6.17 (rawhide): the aimsgui bindings imported aims.sip before the Qt
  modules, so PyQt6's %MinimumABIVersion came too late and sip-build
  failed. Patch2 (aims-gpl, on an upstream branch) imports Qt first.

* Thu Oct 15 2026 Morgan Hough <morgan.hough@gmail.com> - 6.0.20^20260806git9ea2121-3
- BuildRequires and Requires python3-six (rawhide no longer pulls it in);
  python3-soma-base also requires the PyYAML it imports (soma.fom).

* Thu Oct 15 2026 Morgan Hough <morgan.hough@gmail.com> - 6.0.20^20260806git9ea2121-2
- Python 3.15 (Fedora 45 and rawhide): pyaims used PyWeakref_GetObject,
  removed in 3.15; use PyWeakref_GetRef, owning the reference (also fixes a
  leaked weak reference on resize). Submitted upstream with the others.

* Thu Oct 15 2026 Morgan Hough <morgan.hough@gmail.com> - 6.0.20^20260806git9ea2121-1
- Initial package: AIMS, soma-io, aims-gpl, soma-base and brainvisa-share
  built together at the soma-env 6.0 pins, with Qt 6, SIP 6, NumPy 2 and
  DCMTK 3.7. ECAT support removed (nonfree library, cleaned tarball). MINC
  support through Fedora's libminc. Seven fixes submitted upstream, two of
  them out-of-range reads that abort every NIfTI read and mesh write under
  Fedora's hardening flags.