# Smoldyn provides the SFMT-1.3.3 (SIMD-oriented Fast Mersenne Twister) source code;

# currently unavailable on Fedora.

# http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/index.html

%global with_libs 0

# VTK support?

# See https://github.com/ssandrews/Smoldyn-official/issues/3

%global with_vtk 0

Name:  smoldyn

Summary: A particle-based spatial stochastic simulator

Version: 2.58

Release: 1%{?dist}

# The rxnparam.c and SurfaceParam.c source code files are in the public domain.

#

# The Next Subvolume module is Copyright 2012 by Martin Robinson and is distributed

# under the Gnu LGPL license.

#

# The rest of the code is Copyright 2003-2018 by Steven Andrews and also

# distributed under the Gnu LGPL.

#

# source/lib/SFMT is licensed under the 'BSD 3-clause "New" or "Revised" License'

License: LGPLv3+ and Public Domain and BSD

URL:   http://www.smoldyn.org

Source0: %{url}/%{name}-%{version}.zip

# Fix library paths according to the Fedora Project guidelines

Patch0: %{name}-fix_libpaths.patch

BuildRequires: boost-devel

BuildRequires: cmake3

BuildRequires: gcc

BuildRequires: %{?dts}gcc-c++

%if 0%{?rhel} == 7

BuildRequires: devtoolset-7-toolchain, devtoolset-7-libatomic-devel

# Coming on epel7

#BuildRequires: boost169-devel

%endif

BuildRequires: freeglut-devel

BuildRequires: libXmu-devel

BuildRequires: libXi-devel

BuildRequires: libtiff-devel

BuildRequires: libglvnd-devel

BuildRequires: perl-macros

%if %{?with_vtk}

BuildRequires: vtk-devel

%endif

BuildRequires: zlib-devel

Requires: bionetgen-perl

Provides: bundled(SFMT) = 1.3.3 

%description

Smoldyn is a computer program for cell-scale biochemical simulations.

It simulates each molecule of interest individually to capture natural

stochasticity and to yield nanometer-scale spatial resolution.

It treats other molecules implicitly, enabling it to simulate hundreds

of thousands of molecules over several minutes of real time.

Simulated molecules diffuse, react, are confined by surfaces,

and bind to membranes much as they would in a real biological system.

It is more accurate and faster than other particle-based simulators.

Smoldyn's unique features include: a "virtual experimenter" who can

manipulate or measure the simulated system, support for spatial compartments,

molecules with excluded volume, and simulations in 1, 2, or 3 dimensions. 

%if %{?with_libs}

%package devel

Summary: %{name} devel files 

Requires: %{name}%{?_isa} = %{version}-%{release}

Provides: %{name}-static = %{version}-%{release}

%description devel

This package provides the %{name} examples, header files and private libraries.

%endif

%package doc

Summary: %{name} PDF documentation

Requires: %{name} = %{version}-%{release}

BuildArch: noarch

%description doc

%{name} PDF documentation.

%prep

%setup -q -n %{name}-%{version}

%patch0 -p0 -b .fix_libpaths

# Copy license file

mv source/lib/SFMT/LICENSE.txt source/lib/SFMT/SFMT-LICENSE.txt

mv source/lib/SFMT/README.txt source/lib/SFMT/SFMT-README.txt

# Remove pre-built archives

rm -rf Linux

# Remove bundled libraries

rm -rf source/BioNetGen source/MinGWlibs Toolchain-mingw32.cmake

rm -rf source/vcell/* source/NextSubVolume/Eigen

rm -rf source/NextSubVolume/boost_include

%if !%{?with_vtk}

rm -f source/vtk/*

%endif

#Fix permissions

find . -type f -name "*.h" -exec chmod 0644 '{}' \;

find . -type f -name "*.c" -exec chmod 0644 '{}' \;

find . -type f -name "*.pdf" -exec chmod 0644 '{}' \;

find . -type f -name "*.txt" -exec chmod 0644 '{}' \;

find . -type f -name "*.txt" -exec sed -i 's/\r$//' '{}' \;

# Set system path to BNG2.pl

sed -e 's|../../../source/BioNetGen/BNG2.pl|%{perl_vendorlib}/BioNetGen/BNG2.pl|g' -i examples/S95_regression/lrmsim.txt \

 examples/S12_bionetgen/lrm/lrmsim.txt \

 examples/S12_bionetgen/abba/abbasim.txt \

 examples/S94_archive/Andrews_2016/BioNetGen/lrm/lrmsim.txt \

 examples/S94_archive/Andrews_2016/BioNetGen/abba/abbasim.txt

%build

mkdir -p build && pushd build

%if 0%{?rhel} == 7

. /opt/rh/devtoolset-7/enable

%endif

%cmake3 -Wno-dev \

 -DCPACK_BINARY_STGZ:BOOL=OFF \

 -DCPACK_BINARY_TGZ:BOOL=OFF \

 -DCPACK_BINARY_TZ:BOOL=OFF \

 -DCPACK_SOURCE_TBZ2:BOOL=OFF \

 -DCPACK_SOURCE_TGZ:BOOL=OFF \

 -DCPACK_SOURCE_TXZ:BOOL=OFF \

 -DCPACK_SOURCE_TZ:BOOL=OFF \

 -DOPTION_VCELL:BOOL=OFF \

%if %{?with_vtk}

 -DOPTION_VTK:BOOL=ON \

%else

 -DOPTION_VTK:BOOL=OFF \

%endif

%if %{?with_libs}

 -DOPTION_TARGET_LIBSMOLDYN:BOOL=ON \

%else

 -DOPTION_TARGET_LIBSMOLDYN:BOOL=OFF \

%endif

 -DOPTION_USE_ZLIB:BOOL=ON \

 -DOPTION_PDE:BOOL=ON \

 -DPERL_VENDORLIB:PATH=%{perl_vendorlib} \

 -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_INSTALL_LIBDIR:PATH=%{_libdir} \

 -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \

 -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_COLOR_MAKEFILE:BOOL=ON \

 -DCMAKE_SKIP_RPATH:BOOL=YES ..

%make_build V=1

popd

%install

%make_install -C build

%files

%doc source/lib/SFMT/SFMT-README.txt

%license License.txt source/lib/SFMT/SFMT-LICENSE.txt

%{_bindir}/%{name}

%if %{?with_libs}

%files devel

%doc examples

%{_includedir}/%{name}/

%{_libdir}/%{name}/

%endif

%files doc

%doc documentation/*

%changelog

* Fri Mar 29 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.58-1

- Release 2.58

* Sun Feb 03 2019 Antonio Trande <sagitter@fedoraproject.org> - 2.56-1

- First package

- Unbundle zlib, boost and BioNetGen

- Remove unused header files

- Fix file permissions

- Add License file provided by upstream