# This is a serial build of NEURON
%global _description %{expand:
NEURON is a simulation environment for modeling individual neurons and networks
of neurons. It provides tools for conveniently building, managing, and using
models in a way that is numerically sound and computationally efficient. It is
particularly well-suited to problems that are closely linked to experimental
data, especially those that involve cells with complex anatomical and
biophysical properties.

This package does not include MPI support.

Please install the %{name}-devel package to compile nmodl files and so on.
}

%global tarname nrn

# fails somehow, disabled by default
%bcond_with metis

# Music support
%bcond_with music

%bcond_without mpich
%bcond_without openmpi

Name:       neuron
Version:    7.8.1
Release:    %autorelease
Summary:    A flexible and powerful simulator of neurons and networks

License:    GPLv3+
URL:        http://www.neuron.yale.edu/neuron/
Source0:    https://github.com/neuronsimulator/%{tarname}/archive/%{version}/%{name}-%{version}.tar.gz

Patch0:     0001-Unbundle-Random123.patch
# libstdc++ bundled is from 1988: seems heavily modified. Headers from there
# are not present in the current version
# https://github.com/neuronsimulator/nrn/issues/145

# Use system copy of Catch
Patch1:     0002-Unbundle-catch.patch
# We install the python bits ourselves
Patch2:     0003-Disable-python-build-and-install.patch
# Set soversions for all shared objects
Patch3:     0004-Set-soversions-for-libs.patch
# Set the right path for libdir
# Upstreamable
Patch4:     0005-Correct-librxdmath-path-for-64bit.patch
# stop build scripts from generating version during build
Patch5:     0006-Do-not-generate-version-info-at-buildtime.patch
# Remove rpaths
Patch6:     0007-Remove-rpaths.patch

# Quite a lot of files have been dropped in 7.8.1
# https://github.com/neuronsimulator/nrn/issues/719

# Random123 does not build on these, so neither can NEURON
# https://github.com/neuronsimulator/nrn/issues/114
ExcludeArch:    mips64r2 mips32r2

BuildRequires: make
BuildRequires:  autoconf
BuildRequires:  automake
BuildRequires:  bison
BuildRequires:  bison-devel
BuildRequires:  cmake
BuildRequires:  catch-devel
# Needs to be packaged separately
# BuildRequires:  coreneuron-devel
BuildRequires:  flex
BuildRequires:  (flex-devel or libfl-devel)
BuildRequires:  gcc
BuildRequires:  gcc-c++
BuildRequires:  git-core
# the cmake build requires iv with cmake too
BuildRequires:  iv-devel >= 0.1
BuildRequires:  libX11-devel
BuildRequires:  libXext-devel
BuildRequires:  libtool
%if %{with metis}
BuildRequires:  metis-devel
%endif
BuildRequires:  ncurses-devel
BuildRequires:  readline-devel
BuildRequires:  Random123-devel

# Bundles sundials. WIP
# https://github.com/neuronsimulator/nrn/issues/113
# BuildRequires:  sundials-devel
Provides: bundled(sundials) = 2.0.1

%description %_description

%package devel
Summary:    Development files for %{name}
Requires: %{name}%{?_isa} = %{version}-%{release}
Requires:  ncurses-devel
Requires:  readline-devel
Requires:  gcc-c++
Requires:  libtool
Requires:  libX11-devel
Requires:  libXext-devel

%description devel
Headers and development shared libraries for the %{name} package

%package doc
Summary:    Documentation for %{name}
BuildArch:  noarch

%description doc
Documentation for %{name}

%package -n python3-%{name}
Summary:   Python3 interface to %{name}
Requires:  %{name}%{?_isa} = %{version}-%{release}
BuildRequires:  python3-devel
BuildRequires:  python3-setuptools
BuildRequires:  python3-Cython
BuildRequires:  python3-pytest

%description -n python3-%{name} %_description

%if %{with mpich}
%package mpich
Summary:   %{name} built with MPICH support
BuildRequires:  mpich-devel
BuildRequires:  rpm-mpi-hooks
BuildRequires:  python3-mpi4py-mpich

Requires:       mpich
Requires:       python3-mpi4py-mpich


%description mpich %_description

%package mpich-devel
Summary:    Development files for %{name}
Requires: %{name}-mpich%{?_isa} = %{version}-%{release}

%description mpich-devel
Headers and development shared libraries for the %{name} package

%package -n python3-%{name}-mpich
Summary:    Python3 interface to %{name}-mpich
Requires:  %{name}-mpich%{?_isa} = %{version}-%{release}

%description -n python3-%{name}-mpich
%endif

%if %{with openmpi}
%package openmpi
Summary:   %{name} built with OpenMPI support
BuildRequires:  openmpi-devel
BuildRequires:  rpm-mpi-hooks
BuildRequires:  python3-mpi4py-openmpi

Requires:       openmpi
Requires:       python3-mpi4py-openmpi


%description openmpi %_description

%package openmpi-devel
Summary:    Development files for %{name}
Requires: %{name}-openmpi%{?_isa} = %{version}-%{release}

%description openmpi-devel
Headers and development shared libraries for the %{name} package

%package -n python3-%{name}-openmpi
Summary:    Python3 interface to %{name}-openmpi
Requires:  %{name}-openmpi%{?_isa} = %{version}-%{release}

%description -n python3-%{name}-openmpi
%endif

%prep
%autosetup -n %{tarname}-%{version} -S git

# Remove executable perms from source files
find src -type f -executable ! -name '*.sh' -exec chmod -x {} +

# fix collections import: not needed in new versions
sed -i 's/collections.Callable/collections.abc.Callable/'  share/lib/python/neuron/rxd/node.py
sed -i 's/collections.Callable/collections.abc.Callable/'  share/lib/python/neuron/rxd/species.py

# Remove bundled Random123
rm -rf src/Random123
rm -rf src/readline

# Create version file ourselves
# To create this, we run the git2version.sh script in a checked out copy of neuron
export TIMESTAMP=$(date +%Y-%m-%d)
cat > src/nrnoc/nrnversion.h << EOF
#define GIT_DATE "$TIMESTAMP"
#define GIT_BRANCH "master"
#define GIT_CHANGESET "da13bb7c"
#define GIT_DESCRIBE "7.8.1-1-gda13bb7c (Fedora %{fedora})"
EOF

# Use system libtool instead of a local copy that neuron tries to install
for f in bin/*_makefile.in; do
    sed -r -i 's|(LIBTOOL.*=.*)\$\(pkgdatadir\)(.*)|\1$(bindir)\2|' $f
done

# Stop system from using hard coded flags
sed -i '/CompilerFlagsHelpers/ d' cmake/ReleaseDebugAutoFlags.cmake

%build
# Not yet to be used
# export SUNDIALS_SYSTEM_INSTALL="yes"
%global do_build %{expand:
echo
echo "*** BUILDING %{name}-%{version}$MPI_COMPILE_TYPE ***"
echo
%set_build_flags
    cmake \\\
        -DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
        -DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
        -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\\
        -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\\
        -DCMAKE_INSTALL_INCLUDEDIR:PATH=$MPI_INCLUDE \\\
        -DCMAKE_INSTALL_LIBDIR:PATH=$MPI_LIB \\\
        -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\\
        -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\
        -DCMAKE_SKIP_RPATH:BOOL=ON \\\
        -DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\\
        -DBUILD_SHARED_LIBS:BOOL=ON \\\
        -DNRN_ENABLE_SHARED=ON \\\
        -DNRN_ENABLE_INTERVIEWS=ON \\\
        -DNRN_ENABLE_PYTHON=ON \\\
        -DNRN_ENABLE_PYTHON_DYNAMIC=OFF \\\
        -DNRN_ENABLE_THREADS=ON \\\
        -DNRN_ENABLE_MEMACS=ON \\\
        -DNRN_ENABLE_RX3D=ON \\\
        -DNRN_ENABLE_CORENEURON=OFF \\\
        -DNRN_ENABLE_TESTS=ON \\\
        -DNRN_ENABLE_REL_RPATH=OFF \\\
        -DNRN_ENABLE_MODULE_INSTALL=ON \\\
        -DNRN_ENABLE_INTERNAL_READLINE=OFF \\\
        -DNRN_ENABLE_MPI=$MPI_YES \\\
        -DMPI_INCLUDE_PATH=$MPI_INCLUDE \\\
        -DMPI_LIBRARY=$MPI_LIBFILE \\\
%if "%{_lib}" == "lib64" \
        -DLIB_SUFFIX=64 -B $MY_CMAKE_BUILDDIR && \
%else                      \
        -DLIB_SUFFIX="" -B $MY_CMAKE_BUILDDIR && \
%endif
%make_build -C $MY_CMAKE_BUILDDIR \

%if %{with music}
pushd $MY_CMAKE_BUILDDIR/src/neuronmusic
%make_build
%{py3_build}
popd
%endif
}


# Serial version
export MPI_COMPILER=serial
export MPI_SUFFIX=""
export MPI_HOME=%{_prefix}
export MPI_BIN=%{_bindir}
export MPI_INCLUDE=%{_includedir}
export MPI_LIB="%{_libdir}"
export MPI_LIBFILE=""
export MPI_YES=OFF
# Python 3
export MPI_COMPILE_TYPE=""
export MPI_SITEARCH="%{python3_sitearch}"
export MY_CMAKE_BUILDDIR="%_vpath_builddir"
%{do_build}

# MPICH
%if %{with mpich}
%{_mpich_load}
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
export MPI_YES=ON
# Python 3
export MPI_COMPILE_TYPE="-mpich"
export MY_CMAKE_BUILDDIR="%_vpath_builddir""-mpich"
export MPI_LIBFILE="$MPI_LIB/libmpi.so"
%{do_build}
%{_mpich_unload}
%endif

# OpenMPI
%if %{with openmpi}
%{_openmpi_load}
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
export MPI_YES=ON
# Python 3
export MPI_COMPILE_TYPE="-openmpi"
export MY_CMAKE_BUILDDIR="%_vpath_builddir""-openmpi"
export MPI_LIBFILE="$MPI_LIB/libmpi.so"
%{do_build}
%{_openmpi_unload}
%endif

%install
# Install everything

%global do_install %{expand:
echo
echo "*** INSTALLING %{name}-%{version}$MPI_COMPILE_TYPE ***"
echo
%make_install -C $MY_CMAKE_BUILDDIR

%if %{with music}
pushd $MY_CMAKE_BUILDDIR/src/neuronmusic
%{py3_install}
popd
%endif

# Python bits from the post install hook
# It requires the libraries before to be installed, not just built, so it must
# be done here. The only alternative is a different package that requires this,
# but this is simpler
RPM_LD_FLAGS="%{?__global_ldflags} -L$RPM_BUILD_ROOT/$MPI_LIB"
pushd $MY_CMAKE_BUILDDIR/src/nrnpython/
%{py3_build}
%{py3_install "--install-lib" "$MPI_PYTHON3_SITEARCH"}
popd

# set up second symlink for shared objects
pushd $RPM_BUILD_ROOT/$MPI_LIB/
    ln -sv ./libnrniv.so.0.0.0 libnrniv.so.0
    ln -sv ./librxdmath.so.0.0.0 librxdmath.so.0
popd
}

%global do_post_install_tweaks %{expand:
# Remove installed libfiles
rm -rfv $RPM_BUILD_ROOT/$MPI_HOME/lib/python/neuron/
# Post install clean up: remove stray object files
# Must be done at end, otherwise it deletes object files required for other builds
find . $RPM_BUILD_ROOT/$MPI_LIB/ -name "*.o" -exec rm -f '{}' \\;
# Remove libtool archives
find . $RPM_BUILD_ROOT/$MPI_LIB/ -name "*.la" -exec rm -f '{}' \\;
# Remove installed copy of libtool
# Remove iv header provided by iv package
rm -rf $RPM_BUILD_ROOT/$MPI_HOME/include/ivstream.h
# Delete installed libtool
rm -fv $RPM_BUILD_ROOT/$MPI_HOME/share/%{tarname}/libtool

# remove package note flag from nrnmech_makefile
pushd $RPM_BUILD_ROOT/$MPI_BIN/
    sed -i "s|-Wl,-dT,.*\.ld||" nrnmech_makefile
popd
# Only needed for MPI builds
if [ x"$MPI_SUFFIX" != "x" ]
then
# Do not install demo files for MPI packages
rm -rf $RPM_BUILD_ROOT/$MPI_HOME/share/%{tarname}/demo
# Renaming MPI bits
pushd $RPM_BUILD_ROOT/$MPI_BIN/
# Rename file references to use MPI_SUFFIX before renaming them
sed -i "s/nrniv\"/nrniv$MPI_SUFFIX\"/g" nrngui
sed -i -e "s/nrniv\"/nrniv$MPI_SUFFIX\"/g" -e "s/nrnmech_makefile/nrnmech_makefile$MPI_SUFFIX/g" -e "s/nocmodl/nocmodl$MPI_SUFFIX/g" nrnivmodl
sed -i -e "s/nocmodl/nocmodl$MPI_SUFFIX/g" nrnmech_makefile
sed -i -e "s/nocmodl/nocmodl$MPI_SUFFIX/g" mkthreadsafe

# Rename files to include $MPI_SUFFIX
for f in modlunit neurondemo nrngui nrniv sortspike mkthreadsafe nocmodl nrnivmodl nrnmech_makefile
do
    mv -v "$f"{,$MPI_SUFFIX}
done
mv -v nrnpyenv{,$MPI_SUFFIX}.sh
mv -v set_nrnpyenv{,$MPI_SUFFIX}.sh
popd
fi
}

# Serial
export MPI_LIB="%{_libdir}"
export MPI_COMPILE_TYPE=""
export MPI_PYTHON3_SITEARCH=%{python3_sitearch}
export MY_CMAKE_BUILDDIR="%_vpath_builddir"
export MPI_HOME="%{_prefix}"
export MPI_BIN="%{_bindir}"
export MPI_SUFFIX=""
%do_install
%do_post_install_tweaks
# Remove duplicate files. These are installed in the correct python locations already
# rm -rf $RPM_BUILD_ROOT/%%{_datadir}/%%{tarname}/lib/python/%%{name}



# mpich
%if %{with mpich}
%{_mpich_load}
export MPI_COMPILE_TYPE="-mpich"
export MY_CMAKE_BUILDDIR="%_vpath_builddir""-mpich"
%do_install
%do_post_install_tweaks
%{_mpich_unload}
%endif

# OpenMPI
%if %{with openmpi}
%{_openmpi_load}
export MPI_COMPILE_TYPE="-openmpi"
export MY_CMAKE_BUILDDIR="%_vpath_builddir""-openmpi"
%do_install
%do_post_install_tweaks
%{_openmpi_unload}
%endif

# The makefiles do not have shebangs
%files
%license Copyright
%{_bindir}/modlunit
%{_bindir}/neurondemo
%{_bindir}/nrngui
%{_bindir}/nrniv
%{_bindir}/sortspike
# Not needed but I'll include them for completeness anyway
%{_bindir}/nrnpyenv.sh
%{_bindir}/set_nrnpyenv.sh
# Libs
%{_libdir}/libnrniv.so.0.0.0
%{_libdir}/libnrniv.so.0
%{_libdir}/librxdmath.so.0.0.0
%{_libdir}/librxdmath.so.0
# other hoc files and data
%dir %{_datadir}/%{tarname}
%{_datadir}/%{tarname}/lib

# Python bits
%files -n python3-%{name}
# A data file resides here
%{python3_sitelib}/%{name}
# The libraries are here
%{python3_sitearch}/%{name}
# Egg info
%{python3_sitearch}/NEURON-7.8-py%{python3_version}.egg-info

%files devel
%license Copyright
%doc README.md
%{_bindir}/mkthreadsafe
%{_bindir}/nocmodl
%{_bindir}/nrnivmodl
%{_bindir}/nrnmech_makefile
# Headers
%{_includedir}/*.h
%{_includedir}/nrncvode/
# Shared objects
%{_libdir}/libnrniv.so
%{_libdir}/librxdmath.so
# required by neuron
# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890
%{_datadir}/%{tarname}/nrnmain.cpp

%files doc
%license Copyright
%{_datadir}/%{tarname}/demo

%if %{with mpich}
%files mpich
%license Copyright
%{_libdir}/mpich/bin/modlunit_mpich
%{_libdir}/mpich/bin/neurondemo_mpich
%{_libdir}/mpich/bin/nrngui_mpich
%{_libdir}/mpich/bin/nrniv_mpich
%{_libdir}/mpich/bin/sortspike_mpich
# Not needed but I'll include them for completeness anyway
%{_libdir}/mpich/bin/nrnpyenv_mpich.sh
%{_libdir}/mpich/bin/set_nrnpyenv_mpich.sh
# Libs
%{_libdir}/mpich/lib/libnrniv.so.0.0.0
%{_libdir}/mpich/lib/libnrniv.so.0
%{_libdir}/mpich/lib/librxdmath.so.0.0.0
%{_libdir}/mpich/lib/librxdmath.so.0
# 
%dir %{_libdir}/mpich/share/%{tarname}
%{_libdir}/mpich/share/%{tarname}/lib

# Python bits
%files -n python3-%{name}-mpich
# The libraries are here
%{python3_sitearch}/mpich/%{name}
# Egg info
%{python3_sitearch}/mpich/NEURON-7.8-py%{python3_version}.egg-info

%files mpich-devel
%license Copyright
%doc README.md
%{_libdir}/mpich/bin/mkthreadsafe_mpich
%{_libdir}/mpich/bin/nocmodl_mpich
%{_libdir}/mpich/bin/nrnivmodl_mpich
%{_libdir}/mpich/bin/nrnmech_makefile_mpich
# Headers
%{_libdir}/mpich/include/*.h
%{_libdir}/mpich/include/nrncvode/
# Shared objects
%{_libdir}/mpich/lib/libnrniv.so
%{_libdir}/mpich/lib/librxdmath.so
# required by neuron
# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890
%{_libdir}/mpich/share/%{tarname}/nrnmain.cpp
%endif

%if %{with openmpi}
%files openmpi
%license Copyright
%{_libdir}/openmpi/bin/modlunit_openmpi
%{_libdir}/openmpi/bin/neurondemo_openmpi
%{_libdir}/openmpi/bin/nrngui_openmpi
%{_libdir}/openmpi/bin/nrniv_openmpi
%{_libdir}/openmpi/bin/sortspike_openmpi
# Not needed but I'll include them for completeness anyway
%{_libdir}/openmpi/bin/nrnpyenv_openmpi.sh
%{_libdir}/openmpi/bin/set_nrnpyenv_openmpi.sh
# Libs
%{_libdir}/openmpi/lib/libnrniv.so.0.0.0
%{_libdir}/openmpi/lib/libnrniv.so.0
%{_libdir}/openmpi/lib/librxdmath.so.0.0.0
%{_libdir}/openmpi/lib/librxdmath.so.0
# 
%dir %{_libdir}/openmpi/share/%{tarname}
%{_libdir}/openmpi/share/%{tarname}/lib

# Python bits
%files -n python3-%{name}-openmpi
# The libraries are here
%{python3_sitearch}/openmpi/%{name}
# Egg info
%{python3_sitearch}/openmpi/NEURON-7.8-py%{python3_version}.egg-info

%files openmpi-devel
%license Copyright
%doc README.md
%{_libdir}/openmpi/bin/mkthreadsafe_openmpi
%{_libdir}/openmpi/bin/nocmodl_openmpi
%{_libdir}/openmpi/bin/nrnivmodl_openmpi
%{_libdir}/openmpi/bin/nrnmech_makefile_openmpi
# Headers
%{_libdir}/openmpi/include/*.h
%{_libdir}/openmpi/include/nrncvode/
# Shared objects
%{_libdir}/openmpi/lib/libnrniv.so
%{_libdir}/openmpi/lib/librxdmath.so
# required by neuron
# https://github.com/neuronsimulator/nrn/issues/719#issuecomment-677501890
%{_libdir}/openmpi/share/%{tarname}/nrnmain.cpp
%endif

%changelog
%autochangelog