# Newest tag is release-1.1.10; master is one commit past it and is what the
# ACES tree builds from. configure.ac still says 1.1.1.
%global commit  239a1a21676f598bb716f5b5237da191953218d0
%global shortcommit %(c=%{commit}; echo ${c:0:7})
%global date    20120308

Name:           classify
Version:        1.1.10
Release:        1.%{date}git%{shortcommit}%{?dist}
Summary:        Tissue classification for MINC volumes

# COPYING: the classic MNI/BIC permissive notice, Vasken Kollokian 1997.
# docs/civet-licensing.md (tier 1).
License:        HPND
URL:            https://github.com/aces/classify
Source0:        %{url}/archive/%{commit}/%{name}-%{shortcommit}.tar.gz
# m4/ is a git submodule (BIC-MNI/mni-acmacros) and absent from the archive.
Source1:        https://github.com/BIC-MNI/mni-acmacros/archive/master.tar.gz#/mni-acmacros.tar.gz
# Maps the pre-VIO_ volume_io spellings this code uses onto current libminc.
Source2:        mni-volume-io-compat.h
# libminc 2.x dropped volume_io's allocation tracker; classify calls it from a
# debug-only branch. See docs/upstream/mni-libminc2-api-drift.md
Patch0:         classify-libminc2-no-alloc-tracker.patch

BuildRequires:  autoconf
BuildRequires:  automake
BuildRequires:  gcc
BuildRequires:  gcc-c++
BuildRequires:  libtool
BuildRequires:  make
BuildRequires:  perl-interpreter
BuildRequires:  EBTKS-devel
BuildRequires:  libminc-devel
BuildRequires:  netcdf-devel
BuildRequires:  zlib-devel
# %%check syntax-checks the driver scripts.
BuildRequires:  perl-MNI
BuildRequires:  perl(Getopt::Tabular)

# insect and classify_clean are MNI::Startup scripts driving the MINC tools.
Requires:       perl-MNI
Requires:       perl(Getopt::Tabular)
Requires:       minc-tools

%description
classify assigns each voxel of a MINC volume to a tissue class, by one of
several classifiers: nearest neighbour (ann, knn), Bayesian, fuzzy and hard
c-means, and minimum distance. It is the tissue classification step of the
MNI/BIC pipelines and of CIVET.

The package also provides insect (Intensity-Normalized Stereotaxic Environment
for Classification of Tissues), the driver that runs a full classification, and
classify_clean, plus the sample tag sets the classifiers train on.

%prep
%autosetup -p1 -n %{name}-%{commit}

# Supply the mni-acmacros submodule that the tarball cannot carry.
mkdir -p m4
tar -xf %{SOURCE1} --strip-components=1 -C m4
test -f m4/smr_WITH_BUILD_PATH.m4

%build
autoreconf -ifv -I m4

# Fedora's libminc names its volume_io library libminc_io, not libvolume_io2.
sed -i 's/volume_io2/minc_io/g' configure
grep -q 'minc_io' configure

cp %{SOURCE2} compat_minc.h

# The axis macros are wanted in both languages here: cleantag.cc and the
# classifiers index coordinates as X, Y, Z and never use those names as
# variables (checked), unlike N3 whose C++ names two matrices X and Y.
export CXXFLAGS="%{optflags} -std=gnu++17 -fpermissive -I%{_includedir}/libminc \
    -include $(pwd)/compat_minc.h -DMNI_COMPAT_AXIS_MACROS"
# The MNI configure probes are pre-C99 and GCC 14+ makes their constructs hard
# errors, so they fail to compile and configure reports the libraries missing.
# Demote them, as bicpl, N3 and inormalize do.
export CFLAGS="%{optflags} -std=gnu17 -I%{_includedir}/libminc \
    -Wno-error=implicit-function-declaration -Wno-error=implicit-int \
    -Wno-error=incompatible-pointer-types -Wno-error=int-conversion \
    -include $(pwd)/compat_minc.h -DMNI_COMPAT_AXIS_MACROS"

%configure \
    --with-minc2 \
    --with-build-path=%{_prefix} \
    LIBS="-lminc_io -lminc2 -lnetcdf -lhdf5 -lz -lm"
%make_build

%install
%make_install
find %{buildroot} -name '*.la' -delete

%check
# No test suite upstream. Run the binaries and syntax-check the drivers: they
# are generated by sed from .in files, so a broken substitution would ship
# silently. inormalize's lgmask reached %%check with a Perl construct removed
# in 5.22 that way.
./classify -help 2>&1 | grep -qi 'usage\|classify' || ./classify 2>&1 | grep -qi 'usage\|classify'
for f in scripts/insect scripts/classify_clean; do
    test -f "$f" && %{__perl} -c "$f"
done

%files
%license COPYING
%doc AUTHORS ChangeLog NEWS README
%{_bindir}/classify
%{_bindir}/voldiff
%{_bindir}/insect
%{_bindir}/classify_clean
%{_bindir}/cleantag
%{_datadir}/classify/

%changelog
* Thu Sep 24 2026 Morgan Hough <morgan.hough@gmail.com> - 1.1.10-1.20120308git239a1a2
- Initial package, from the tip of upstream master. CIVET/MNI tier 1
  (docs/civet-licensing.md); the fifth of the eight permissive components.