%if 0%{?fedora} > 12
%define with_python3 1
%else
%define with_python3 0
%endif

%define with_mpich 1

# Change '#' to '%' in the line below if you want to build to install
# somewhere other than the default /usr
#define _prefix /usr/local

Name:          IMP
Version:       2.10.0
Release:       1%{?dist}
License:       LGPLv2+ and GPLv3
Summary:       The Integrative Modeling Platform
Group:         Applications/Engineering
Packager:      Ben Webb <ben@salilab.org>
URL:           https://integrativemodeling.org/
Source0:       imp-%{version}.tar.gz
%if 0%{?with_python3}
BuildRequires: python3-devel, symlinks
%endif
BuildRequires: python-devel >= 2.6
# /usr/bin/python is provided by a separate package in recent Fedora
%if 0%{?fedora} >= 29
BuildRequires: python-unversioned-command
%endif
BuildRequires: hdf5-devel >= 1.8
BuildRequires: swig >= 1.3.40
BuildRequires: gsl-devel, fftw-devel
BuildRequires: zlib-devel, perl
BuildRequires: ann-devel, eigen3-devel
# Needed to build the cnmultifit module; obtain
# from https://integrativemodeling.org/libTAU.html
# (Or, if you don't need cnmultifit, you can comment out this line)
BuildRequires: libTAU-devel

# Need for npctransport module
BuildRequires: protobuf-devel
%if 0%{?fedora}
Requires: python2-protobuf
%else
Requires: protobuf-python
%endif

BuildRequires: cmake >= 2.8
BuildRequires: boost-devel >= 1.41

# RHEL doesn't have a CGAL package, so build without CGAL on RHEL. It also
# doesn't have a new enough OpenCV in the base distribution or in EPEL until
# RHEL7, so disable the em2d module.
# On Fedora, all of these packages are available; add them as dependencies
%if 0%{?fedora}
BuildRequires: CGAL-devel, opencv-devel
%endif
%if 0%{?rhel} >= 7
BuildRequires: opencv-devel
%endif

# If building in the Sali lab, pass '-D "RHEL_SALI_LAB 1"' to your rpmbuild
# invocation. This will pull in our custom OpenCV (on RHEL6) and CGAL packages
# and bundle the libraries with IMP.
# If building outside of the lab and you still want these packages, get them
# from https://integrativemodeling.org/build-extras/
%if 0%{?rhel} && 0%{?RHEL_SALI_LAB}
%if 0%{?rhel} < 7
BuildRequires: opencv-nogui-devel
%endif
BuildRequires: CGAL-nogui-devel
%if 0%{?rhel} < 7
%define bundled 'libcv\\.so\\|libcxcore\\.so\\|libhighgui.so\\|libTAU\\.so\\|libCGAL\\.so'
%else
%define bundled 'libTAU\\.so\\|libCGAL\\.so'
%endif
%else
%define bundled 'libTAU\\.so'
%endif

# Many modules use Python's numpy and scipy modules, so pull those in
# (at build time for tests; at install time for using the modules).
BuildRequires: numpy, scipy
Requires: numpy, scipy

# RHEL 6 ships with Python 2.6, which doesn't have the argparse module,
# so pull in the extra package that provides it
%if 0%{?rhel} == 6
BuildRequires: python-argparse
Requires: python-argparse
%endif

%define cmake_opts -DCMAKE_INSTALL_RPATH=%{_libdir}/IMP

%if 0%{?rhel} == 6
%define mpiprefix %{nil}
%else
%define mpiprefix mpi/
%endif

# Don't build debug source packages; they cause the build to fail with
# error: Empty %files file [...]/debugsourcefiles.list
%if 0%{?fedora} > 26
%undefine _debugsource_packages
%endif

%description
IMP's broad goal is to contribute to a comprehensive structural
characterization of biomolecules ranging in size and complexity from small
peptides to large macromolecular assemblies. Detailed structural
characterization of assemblies is generally impossible by any single existing
experimental or computational method. This barrier can be overcome by hybrid
approaches that integrate data from diverse biochemical and biophysical
experiments (eg, x-ray crystallography, NMR spectroscopy, electron microscopy,
immuno-electron microscopy, footprinting, chemical cross-linking, FRET
spectroscopy, small angle X-ray scattering, immunoprecipitation, genetic
interactions, etc...).

We formulate the hybrid approach to structure determination as an optimization
problem, the solution of which requires three main components:
    * the representation of the assembly,
    * the scoring function and
    * the optimization method.

The ensemble of solutions to the optimization problem embodies the most
accurate structural characterization given the available information.

We created IMP, the Integrative Modeling Platform, to make it easier to
implement such an integrative approach to structural and dynamics problems.
IMP is designed to allow mixing and matching of existing modeling components
as well as easy addition of new functionality.

%package devel
Group:         Applications/Engineering
Summary:       Development package for IMP developers.
Requires:      %{name} = %{version}-%{release}
Requires:      gsl-devel, fftw-devel, zlib-devel
Requires:      ann-devel, eigen3-devel
Requires:      boost-devel, python-devel, hdf5-devel, protobuf-devel
%if 0%{?fedora}
Requires:      CGAL-devel, opencv-devel
%endif
%if 0%{?rhel} >= 7
Requires:      opencv-devel
%endif

%description devel
This package contains the include files for building applications that link
against IMP.

%if 0%{?with_python3}
%package python3
Group:         Applications/Engineering
Summary:       Python wrappers for Python 3
Requires:      %{name} = %{version}-%{release}
Requires:      python3
%if 0%{?fedora}
Requires: python3-protobuf
%endif

%description python3
This package contains wrappers for Python 3 (the base package already
includes Python 2 wrappers).
%endif

%define MPI_MODULES mpi spb

%if 0%{?with_mpich}
%package mpich
Group:         Applications/Engineering
Summary:       MPI module and dependents, for mpich
Requires:      %{name} = %{version}-%{release}
Requires:      mpich
%if 0%{?fedora}
Requires:      python2-mpich
%endif
BuildRequires: mpich-devel

%description mpich
This package contains an IMP.mpi module to add MPI support,
using the mpich library. It also includes all IMP modules that depend
on IMP.mpi (IMP.spb).

%package mpich-devel
Group:         Applications/Engineering
Summary:       MPI module and dependents development files, for mpich
Requires:      %{name}-mpich = %{version}-%{release}
Requires:      mpich

%description mpich-devel
Development files for IMP.mpi module (and dependents) with mpich.
%endif

%prep
%setup -n imp-%{version}

# Exclude bundled libraries from provides and requires
%if 0%{?fedora} > 22
# In newer Fedora, the old script-based dependency generation doesn't play
# nicely with the new mechanism for adding MPI dependencies
# (rpm-mpi-hooks package)
%if 0%{?with_mpich}
%global __provides_exclude ^libTAU\\.so.*|libimp_mpi\\.so.*|libimp_spb\\.so.*$
%global __requires_exclude ^libTAU\\.so.*|libmpi\\.so.*|libmpicxx\\.so.*|libimp_mpi\\.so.*|libimp_spb\\.so.*$
%else
%global __provides_exclude ^libTAU\\.so.*$
%global __requires_exclude ^libTAU\\.so.*$
%endif
%else
%define reqprog %{_builddir}/find-requires-%{name}
%define proprog %{_builddir}/find-provides-%{name}

cat <<EOF > %{reqprog}
#!/bin/bash
%{__find_requires} $@ | grep -v %{bundled}
exit $?
EOF
cat <<EOF > %{proprog}
#!/bin/bash
%{__find_provides} $@ | grep -v %{bundled}
exit $?
EOF
chmod a+x %{reqprog}
chmod a+x %{proprog}
%define _use_internal_dependency_generator 0
%define __find_requires %{reqprog}
%define __find_provides %{proprog}
%endif

%build
# For now, bundle RMF with IMP (long term, may be better to put in a separate
# RPM)
mkdir imp && mv * imp || :
mkdir build && cd build
%if 0%{?with_mpich}
module load %{mpiprefix}mpich-%{_arch}
%endif
%if 0%{?fedora} >= 29
# Help cmake to find CGAL
export CGAL_DIR=%{_libdir}/cmake/CGAL
%endif
cmake ../imp -DCMAKE_BUILD_TYPE=Release \
             -DCMAKE_INSTALL_PREFIX=%{_prefix} \
             -DCMAKE_INSTALL_DOCDIR=%{_prefix}/share/doc/%{name}-%{version} \
             -DIMP_TIMEOUT_FACTOR=4 \
             -DIMP_DISABLED_MODULES=scratch %{cmake_opts}

# Normally make will stop at the first error. Since an RPM cannot be built
# if the build did not complete successfully, this is the default here too.
# Pass '-D "keep_going 1"' to your rpmbuild invocation if you want it to
# keep going; we use this in nightly builds to see every broken module,
# not just the first one.
%if 0%{?keep_going}
mkdir logs
../imp/tools/nightly-tests/build_all.py --run-tests=fast --ctest="ctest --output-on-failure" --outdir=logs --summary=logs/summary.pck "make -k"
%else
make
%endif
%if 0%{?with_mpich}
module purge
%endif

%install
cd build
make DESTDIR=${RPM_BUILD_ROOT} install

%if 0%{?with_python3}
# Build Python 3 wrappers
py2_ver=`python2 -c "import sys; print('%d.%d' % sys.version_info[:2])"`
py3_ver=`python3 -c "import sys; print('%d.%d' % sys.version_info[:2])"`
py3_lib=`echo %{_libdir}/libpython3.*.so`
py3_inc=`echo /usr/include/python3.*`
%if 0%{?with_mpich}
module load %{mpiprefix}mpich-%{_arch}
%endif
cmake ../imp \
      -DCMAKE_INSTALL_PREFIX=%{_prefix} \
      -DCMAKE_INSTALL_PYTHONDIR=%{_libdir}/python${py3_ver}/site-packages \
      -DSWIG_PYTHON_LIBRARIES=${py3_lib} \
      -DPYTHON_INCLUDE_DIRS=${py3_inc} \
      -DPYTHON_INCLUDE_PATH=${py3_inc} \
      -DPYTHON_LIBRARIES=${py3_lib}
make DESTDIR=${RPM_BUILD_ROOT} install
%if 0%{?with_mpich}
module purge
%endif

# Don't build Python 3 MPI for now
for mod in %{MPI_MODULES}; do
  rm -rf ${RPM_BUILD_ROOT}%{_libdir}/python${py3_ver}/site-packages/IMP/${mod}
  rm -f ${RPM_BUILD_ROOT}%{_libdir}/python${py3_ver}/site-packages/_IMP_${mod}.so
done

# Replace .py files with symlinks to Python 2 files (since they are the same)
(cd ${RPM_BUILD_ROOT}%{_libdir}/python${py3_ver} \
 && find site-packages -name '*.py' \
      -exec ln -sf ${RPM_BUILD_ROOT}%{_libdir}/python${py2_ver}/\{\} \{\} \; \
 && symlinks -rc .)
%endif

# Put MPI-dependent libraries and binaries in mpich directories
%if 0%{?with_mpich}
(cd ${RPM_BUILD_ROOT}%{_libdir}/python2*/site-packages/ && mkdir mpich)
(cd ${RPM_BUILD_ROOT}%{_libdir} && mkdir -p mpich/bin mpich/lib)
(cd ${RPM_BUILD_ROOT}%{_bindir} && mv spb* ${RPM_BUILD_ROOT}%{_libdir}/mpich/bin)
for mod in %{MPI_MODULES}; do
  (cd ${RPM_BUILD_ROOT}%{_libdir}/python2*/site-packages/ \
   && mv _IMP_${mod}.so mpich/)
  (cd ${RPM_BUILD_ROOT}%{_libdir} && mv libimp_${mod}.so.* mpich/lib/)
  (cd ${RPM_BUILD_ROOT}%{_libdir} && rm libimp_${mod}.so \
   && ln -sf mpich/lib/libimp_${mod}.so.* libimp_${mod}.so)
done

# Add MPI-dependent directory to Python search path
%if 0%{?rhel} == 6
(cd ${RPM_BUILD_ROOT}%{_libdir}/python2*/site-packages && cat > imp-mpi.pth <<END)
# Set MPI implementation-specific Python search path, for IMP.
# On Fedora this is handled by the python2-mpich package, while in RHEL7
# the mpich modulefile sets PYTHONPATH, but nothing appears to handle it
# in RHEL6, so we'll do it ourselves.
import sys, os; s = os.getenv('MPI_PYTHON_SITEARCH'); s and (s in sys.path or sys.path.append(s))
END
%endif
%endif

# Note that we currently don't include the documentation in the RPM, since
#      a) it takes a long time to run doxygen
#      b) doxygen isn't installed on all of our build systems
#      c) it is really big
#  and d) only certain versions of doxygen work correctly
# You can build the documentation by running "make IMP-doc"
# on the IMP source code.
README=${RPM_BUILD_ROOT}%{_prefix}/share/doc/%{name}-%{version}/README
echo "For full IMP documentation, please go to" > ${README}
# Direct nightly build users to most recent nightly build docs
if echo ${version} | grep -q git; then
  echo "https://integrativemodeling.org/nightly/doc/manual/" >> ${README}
else
  echo "https://integrativemodeling.org/%{version}/doc/manual/" >> ${README}
fi
# Bundle libTAU from build machine so users don't have to get it separately
# (can't use %_libdir here since that is dependent on whatever we redefined
# %_prefix to be, but dependent libraries are always in /usr)
mkdir ${RPM_BUILD_ROOT}%{_libdir}/IMP
cp /usr/%{_lib}/libTAU.so.1 ${RPM_BUILD_ROOT}%{_libdir}/IMP/

%if 0%{?rhel} && 0%{?RHEL_SALI_LAB}
# Bundle OpenCV and CGAL libraries
%if 0%{?rhel} < 7
for cvlib in cv cxcore highgui; do
  cp /usr/%{_lib}/lib${cvlib}.so.2.1 ${RPM_BUILD_ROOT}%{_libdir}/IMP/
done
%endif
cp /usr/%{_lib}/libCGAL.so.10 ${RPM_BUILD_ROOT}%{_libdir}/IMP/
%endif

# Don't distribute example application, dependency, or system
pydir=${RPM_BUILD_ROOT}%{_libdir}/python2*/site-packages
rm -rf ${RPM_BUILD_ROOT}%{_prefix}/bin/example \
       ${RPM_BUILD_ROOT}%{_libdir}/libimp_example_system* \
       ${RPM_BUILD_ROOT}%{_libdir}/libexample* \
       ${RPM_BUILD_ROOT}%{_prefix}/include/example* \
       ${pydir}/IMP/example_system_local \
       ${pydir}/_IMP_example_system_local.so

# Make sure all Python applications use the same Python we built with
perl -pi -e 's^#!.*python.*^#!/usr/bin/python^' ${RPM_BUILD_ROOT}%{_prefix}/bin/*

%files
%defattr(-,root,root)
%doc %{_prefix}/share/doc/%{name}-%{version}
%{_prefix}/share/IMP
%{_prefix}/bin/*
%{_libdir}/libimp*.so.*
%{_libdir}/libRMF*.so
%{_libdir}/IMP
%{_libdir}/python2*/site-packages/IMP
%{_libdir}/python2*/site-packages/_IMP*so
%{_libdir}/python2*/site-packages/RMF*
%{_libdir}/python2*/site-packages/_RMF*so
%{_libdir}/python2*/site-packages/ihm
%if 0%{?with_mpich}
%exclude %{_prefix}/share/doc/%{name}-%{version}/examples/mpi
%exclude %{_prefix}/share/IMP/swig/IMP_mpi.*
%exclude %{_prefix}/share/IMP/swig/IMP_spb.*
%exclude %{_prefix}/share/IMP/build_info/MPI
%exclude %{_prefix}/share/IMP/build_info/IMP.mpi
%exclude %{_prefix}/share/IMP/build_info/IMP_mpi.pck
%exclude %{_prefix}/share/IMP/build_info/IMP.spb
%exclude %{_prefix}/share/IMP/build_info/IMP_spb.pck
%exclude %{_libdir}/python2*/site-packages/IMP/mpi
%exclude %{_libdir}/python2*/site-packages/IMP/spb
%endif

%if 0%{?with_python3}
%files python3
%defattr(-,root,root)
%{_libdir}/python3*/site-packages/IMP
%{_libdir}/python3*/site-packages/_IMP*so
%{_libdir}/python3*/site-packages/RMF*
%{_libdir}/python3*/site-packages/_RMF*so
%{_libdir}/python3*/site-packages/ihm
%{_libdir}/python3*/site-packages/__pycache__
%endif

%if 0%{?with_mpich}
%files mpich
%defattr(-,root,root)
%doc %{_prefix}/share/doc/%{name}-%{version}/examples/mpi
%{_prefix}/share/IMP/swig/IMP_mpi.*
%{_prefix}/share/IMP/swig/IMP_spb.*
%{_prefix}/share/IMP/build_info/MPI
%{_prefix}/share/IMP/build_info/IMP.mpi
%{_prefix}/share/IMP/build_info/IMP_mpi.pck
%{_prefix}/share/IMP/build_info/IMP.spb
%{_prefix}/share/IMP/build_info/IMP_spb.pck
%{_libdir}/python2*/site-packages/IMP/mpi
%{_libdir}/python2*/site-packages/IMP/spb
%if 0%{?rhel} == 6
%{_libdir}/python2*/site-packages/imp-mpi.pth
%endif
%{_libdir}/python2*/site-packages/mpich/_IMP_mpi.so
%{_libdir}/python2*/site-packages/mpich/_IMP_spb.so
%{_libdir}/mpich/lib/libimp_mpi.so.*
%{_libdir}/mpich/lib/libimp_spb.so.*
%{_libdir}/mpich/bin/spb*

%files mpich-devel
%defattr(-,root,root)
%{_libdir}/libimp_mpi.so
%{_libdir}/libimp_spb.so
%{_prefix}/include/IMP/mpi
%{_prefix}/include/IMP/spb
%endif

%files devel
%defattr(-,root,root)
%{_prefix}/include/IMP
%{_prefix}/include/IMP.h
%{_prefix}/include/RMF
%{_libdir}/libimp*.so
%if 0%{?with_mpich}
%exclude %{_prefix}/include/IMP/mpi
%exclude %{_prefix}/include/IMP/spb
%exclude %{_libdir}/libimp_mpi.so
%exclude %{_libdir}/libimp_spb.so
%endif

%changelog
* Tue Jan 08 2019 Ben Webb <ben@salilab.org>   2.10.0-1
- 2.10.0 release.

* Mon Jul 02 2018 Ben Webb <ben@salilab.org>   2.9.0-1
- 2.9.0 release.

* Wed Aug 16 2017 Ben Webb <ben@salilab.org>   2.8.0-1
- 2.8.0 release.

* Thu Apr 13 2017 Ben Webb <ben@salilab.org>   2.7.0-1
- 2.7.0 release.

* Wed May 25 2016 Ben Webb <ben@salilab.org>   2.6.2-1
- 2.6.2 release.

* Thu Apr 14 2016 Ben Webb <ben@salilab.org>   2.6.1-1
- 2.6.1 release.

* Mon Mar 28 2016 Ben Webb <ben@salilab.org>   2.6.0-1
- 2.6.0 release.

* Tue Jun 30 2015 Ben Webb <ben@salilab.org>   2.5.0-1
- 2.5.0 release.

* Fri Feb 27 2015 Ben Webb <ben@salilab.org>   2.4.0-1
- 2.4.0 release.

* Tue Dec 09 2014 Ben Webb <ben@salilab.org>   2.3.1-1
- 2.3.1 release.

* Fri Oct 24 2014 Ben Webb <ben@salilab.org>   2.3.0-1
- 2.3.0 release.

* Mon Aug 11 2014 Ben Webb <ben@salilab.org>   2.2.1-1
- 2.2.1 release.

* Wed Apr 09 2014 Ben Webb <ben@salilab.org>   2.2.0-1
- 2.2.0 release.

* Mon Nov 04 2013 Ben Webb <ben@salilab.org>   2.1.1-1
- 2.1.1 release.

* Thu Oct 24 2013 Ben Webb <ben@salilab.org>   2.1.0-1
- 2.1.0 release.

* Thu May 02 2013 Ben Webb <ben@salilab.org>   2.0.1-1
- 2.0.1 release.

* Mon Apr 29 2013 Ben Webb <ben@salilab.org>   2.0.0-1
- 2.0.0 release.

* Mon Mar 08 2010 Ben Webb <ben@salilab.org>   1.0-1
- 1.0 release.

* Thu May 07 2009 Ben Webb <ben@salilab.org>
- Initial build.