# 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

# 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: 2.72
Release: %autorelease

# 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/libSteve/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: https://github.com/ssandrews/Smoldyn/archive/refs/tags/v%{version}/Smoldyn-%{version}.tar.gz

# Fix library paths according to the Fedora Project guidelines
Patch0: %{name}-fix_libpaths.patch
Patch1: %{name}-freeglut.patch
Patch2: %{name}-create_soname.patch
Patch3: %{name}-avoid_automatic_wheel.patch

BuildRequires: cmake
BuildRequires: gcc
BuildRequires: gcc-c++
BuildRequires: boost-devel
BuildRequires: freeglut-devel
BuildRequires: libXmu-devel
BuildRequires: libXi-devel
BuildRequires: libtiff-devel
BuildRequires: libglvnd-devel
BuildRequires: make
BuildRequires: perl-macros
# For testing
BuildRequires: xorg-x11-server-Xvfb
%if %{?with_vtk}
BuildRequires: vtk-devel
%endif
BuildRequires: zlib-devel
BuildRequires: xorg-x11-server-Xvfb
Requires: %{name}-libs%{?_isa} = %{version}-%{release}

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 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. 

%package doc
Summary: %{name} documentation
Requires: %{name} = %{version}-%{release}
BuildArch: noarch
%description doc
%{name} documentation.

%package libs
Summary: %{name} libraries
%description libs
%{name} shared libraries.

%package libs-devel
Summary: %{name} libraries for development
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
Provides: %{name}-libs-static = 0:%{version}-%{release}
%description libs-devel
%{name} shared and static libraries for development.

%package -n python3-smoldyn
Summary: %{name} libraries for Python
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-wheel
BuildRequires: pybind11-devel
Requires: python3-numpy
# For testing
BuildRequires: python3-matplotlib
BuildRequires: python3-flaky
%{?python_provide:%python_provide python3-%{name}}
%description -n python3-smoldyn
%{name} libraries for Python.

%prep
%autosetup -n Smoldyn-%{version} -N
%patch -P 0 -p0 -b .fix_libpaths
%patch -P 1 -p0 -b .freeglut
%patch -P 2 -p0 -b .create_soname
%patch -P 3 -p0 -b .avoid_automatic_wheel

# Remove bundled archives
rm -rf source/MSVClibs
rm -rf source/pybind11

# 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
 
# Copy license file
cp -p source/libSteve/SFMT/LICENSE.txt source/libSteve/SFMT/SFMT-LICENSE.txt
cp -p source/libSteve/SFMT/README.txt source/libSteve/SFMT/SFMT-README.txt

# Remove Python byte cache from previous Python versions shipped in upstream tarball
find -name '*.pyc' -delete


%build
# Python binding needs shared libraries
%cmake -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
 -DBUILD_SHARED_LIBS:BOOL=ON \
 -DSMOLDYN_VERSION:STRING=%{version} \
 -DSMOLDYN_VERSION_MAJOR:STRING=2 \
 -DOPTION_TARGET_LIBSMOLDYN:BOOL=ON \
 -DOPTION_STATIC:BOOL=OFF \
 -DOPTION_PYTHON:BOOL=ON -DPYBIND11_FINDPYTHON:BOOL=ON -Dpybind11_DIR:PATH=%{_datadir}/cmake/pybind11 \
 -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 \
 -DHAVE_GL_FREEGLUT_H=TRUE -DOPTION_EXAMPLES:BOOL=OFF -DOPTION_DOCS:BOOL=OFF
%cmake_build

%install
%cmake_install
pushd %{__cmake_builddir}/py
mkdir -p %{buildroot}%{python3_sitearch}
cp -a smoldyn *.egg-info %{buildroot}%{python3_sitearch}/
popd

%check
# Most tests look not executable
pushd %{__cmake_builddir}
export LD_LIBRARY_PATH=%{buildroot}%{_libdir}
export PYTHONPATH=%{buildroot}%{python3_sitearch}
xvfb-run ctest -j1 -VV -R "test_api|test_sanity|test_biosimulator" --output-on-failure --debug
popd

%files
%{_bindir}/%{name}
%doc Using-Smoldyn-with-SED-ML-COMBINE-BioSimulators.md README.md

%files libs
%license License.txt source/libSteve/SFMT/SFMT-LICENSE.txt LICENSE
%{_libdir}/lib%{name}_shared.so.%{version}
%{_libdir}/lib%{name}_shared.so.2

%files libs-devel
%{_libdir}/lib%{name}_shared.so
%{_libdir}/lib%{name}_static.a
%{_includedir}/%{name}/

%files -n python3-smoldyn
%license License.txt source/libSteve/SFMT/SFMT-LICENSE.txt LICENSE
%{python3_sitearch}/%{name}/
%{python3_sitearch}/*.egg-info

%files doc
%doc docs/*

%changelog
%autochangelog