# 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: 2.67.3 Release: 6%{?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/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 Patch4: %{name}-bug121.patch Patch5: %{name}-bug123.patch %if 0%{?fedora} || 0%{?rhel} > 7 BuildRequires: cmake %else BuildRequires: cmake3 %endif 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 %patch0 -p0 -b .fix_libpaths %patch1 -p0 -b .freeglut %patch2 -p0 -b .create_soname %patch3 -p0 -b .avoid_automatic_wheel %patch4 -p1 -b .bug121 %patch5 -p1 -b .bug123 # 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 %cmake3 -Wno-dev -B build \ -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 %make_build -C build %install %make_install -C build pushd build/py mkdir -p %{buildroot}%{python3_sitearch} cp -a smoldyn *.egg-info %{buildroot}%{python3_sitearch}/ popd %check # Most tests look not executable cd build 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 %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 %{_includedir}/%{name}/ %files libs-devel %{_libdir}/lib%{name}_shared.so %{_libdir}/lib%{name}_static.a %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 * Sat Jul 22 2023 Fedora Release Engineering - 2.67.3-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild * Tue Jun 27 2023 Python Maint - 2.67.3-5 - Rebuilt for Python 3.12 * Sat Jan 21 2023 Fedora Release Engineering - 2.67.3-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Sat Jul 23 2022 Fedora Release Engineering - 2.67.3-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Mon Jun 13 2022 Python Maint - 2.67.3-2 - Rebuilt for Python 3.11 * Sat Mar 19 2022 Antonio Trande - 2.67.3-1 - Release 2.67.3 * Sat Jan 22 2022 Fedora Release Engineering - 2.66.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Fri Oct 29 2021 Antonio Trande - 2.66.1-1 - Release 2.66.1 * Fri Sep 10 2021 Miro Hrončok - 2.65-5 - Remove unused Python 3.9 byte cache * Fri Jul 23 2021 Fedora Release Engineering - 2.65-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Fri Jun 04 2021 Python Maint - 2.65-3 - Rebuilt for Python 3.10 * Fri Jun 04 2021 Antonio Trande - 2.65-2 - Add Provides for static libraries * Wed Jun 02 2021 Antonio Trande - 2.65-1 - Release 2.65 - Create Python binding - Create libraries * Sat Jan 30 2021 Antonio Trande - 2.63-2 - Exclude example files (strange permissions) * Fri Jan 29 2021 Antonio Trande - 2.63-1 - Release 2.63 * Wed Jan 27 2021 Fedora Release Engineering - 2.61-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild * Wed Jul 29 2020 Fedora Release Engineering - 2.61-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild * Fri Jul 24 2020 Jeff Law - 2.61-4 - Use __cmake_in_source_build * Mon May 25 2020 Antonio Trande - 2.61-3 - Fix patch for EPEL7 * Mon May 25 2020 Antonio Trande - 2.61-2 - Patched for using Boost169 on EPEL7 * Sun May 24 2020 Antonio Trande - 2.61-1 - Release 2.61 * Thu Jan 30 2020 Fedora Release Engineering - 2.58-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Tue Sep 17 2019 Gwyn Ciesla - 2.58-3 - Rebuilt for new freeglut * Fri Jul 26 2019 Fedora Release Engineering - 2.58-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * Fri Mar 29 2019 Antonio Trande - 2.58-1 - Release 2.58 * Sun Feb 03 2019 Antonio Trande - 2.56-1 - First package - Unbundle zlib, boost and BioNetGen - Remove unused header files - Fix file permissions - Add License file provided by upstream