%global pretty_name STEPS

%global module_name steps

# Switch them off if you want

# Best to start with the serial version

%bcond_without mpich

%bcond_without openmpi

%if 0%{?fedora} >= 33 || 0%{?rhel} >= 9

%global blaslib flexiblas

%else

%global blaslib openblas

%endif

# Do not currently use system sundials

# https://bugzilla.redhat.com/show_bug.cgi?id=1820991

%global system_sundials  0

%global _description %{expand:

STEPS is a package for exact stochastic simulation of reaction-diffusion

systems in arbitrarily complex 3D geometries. Our core simulation algorithm is

an implementation of Gillespie's SSA, extended to deal with diffusion of

molecules over the elements of a 3D tetrahedral mesh.

While it was mainly developed for simulating detailed models of neuronal

signaling pathways in dendrites and around synapses, it is a general tool and

can be used for studying any biochemical pathway in which spatial gradients and

morphology are thought to play a role.

STEPS also supports accurate and efficient computational of local membrane

potentials on tetrahedral meshes, with the addition of voltage-gated channels

and currents. Tight integration between the reaction-diffusion calculations and

the tetrahedral mesh potentials allows detailed coupling between molecular

activity and local electrical excitability.

We have implemented STEPS as a set of Python modules, which means STEPS users

can use Python scripts to control all aspects of setting up the model,

generating a mesh, controlling the simulation and generating and analyzing

output. The core computational routines are still implemented as C/C++

extension modules for maximal speed of execution.

STEPS 3.0.0 and above provide early parallel solution for stochastic spatial

reaction-diffusion and electric field simulation.

Documentation can be found here:

http://steps.sourceforge.net/manual/manual_index.html

}

Name:           python-%{module_name}

Version:        3.5.0

Release:        6%{?dist}

Summary:        STochastic Engine for Pathway Simulation

License:        GPLv2

URL:            http://steps.sourceforge.net/

Source0:        https://github.com/CNS-OIST/STEPS/archive/%{version}/%{module_name}-%{version}.tar.gz

# Header only library, needs cc file

# https://raw.githubusercontent.com/amrayn/easyloggingpp/master/src/easylogging%2B%2B.cc

Source1:        easylogging++.cc

# https://raw.githubusercontent.com/amrayn/easyloggingpp/master/src/easylogging%2B%2B.h

Source2:        easylogging++.h

# Patches generated from: https://github.com/sanjayankur31/STEPS/tree/fedora-3.5.0

# use system gtest

Patch0:         0001-Unbundle-gtest.patch

%if "%{system_sundials}" == "1"

# Tweak cmake file to stop looking for SUNDIALS_DIR

Patch1:         0002-Update-sundials-cmake.patch

%endif

# Remove flags they set

Patch2:         0003-Remove-flags-set-by-project.patch

# Remove pysteps flags

Patch3:         0004-Remove-pysteps-flags.patch

# We'll install manually, much easier and cleaner

Patch4:         0005-Disable-pyinstall.patch

BuildRequires: make

BuildRequires:  cmake

BuildRequires:  gcc-c++

BuildRequires:  git-core

BuildRequires:  gtest-devel

BuildRequires:  petsc-devel

BuildRequires:  python3-devel

BuildRequires:  %{py3_dist Cython}

BuildRequires:  %{py3_dist numpy}

BuildRequires:  %{py3_dist setuptools}

BuildRequires:  %{blaslib}-devel

BuildRequires:  Random123-devel

%if "%{system_sundials}" == "1"

BuildRequires:  sundials2-devel

%endif

%description

%{_description}

%package -n python3-%{module_name}

Summary:        STochastic Engine for Pathway Simulation

Provides:       %{module_name} = %{version}-%{release}

%description -n python3-%{module_name}

%{_description}

%if %{with openmpi}

%package -n python3-%{module_name}-openmpi

Summary:        %{module_name} built with openmpi

BuildRequires:  openmpi-devel

BuildRequires:  petsc-openmpi-devel

BuildRequires:  rpm-mpi-hooks

BuildRequires:  sundials-openmpi-devel

Requires:       openmpi

%description -n python3-%{module_name}-openmpi

%{_description}

%endif

%if %{with mpich}

%package -n python3-%{module_name}-mpich

Summary:        %{module_name} built with mpich

BuildRequires:  mpich-devel

BuildRequires:  petsc-mpich-devel

BuildRequires:  rpm-mpi-hooks

BuildRequires:  sundials-mpich-devel

Requires:       mpich

%description -n python3-%{module_name}-mpich

%{_description}

%endif

%prep

%autosetup -n %{pretty_name}-%{version} -S git

# Easyloggingpp

mkdir -pv src/third_party/easyloggingpp/src/

cp %{SOURCE1} src/third_party/easyloggingpp/src/ -v

cp %{SOURCE2} src/third_party/easyloggingpp/src/ -v

# Correct for sundials2

# sed -i.orig 's|^#include.*

# Build directories

mkdir build

%if %{with openmpi}

mkdir build-openmpi

%endif

%if %{with mpich}

mkdir build-mpich

%endif

%build

# Best to use && so that if anything in the chain fails, the build also fails

# straight away

%global do_cmake_config %{expand: \

echo

echo "*** BUILDING %{module_name}-%{version}$MPI_COMPILE_TYPE ***"

echo

%set_build_flags

pushd build$MPI_COMPILE_TYPE  &&

    cmake \\\

        -DUSE_BUNDLE_EASYLOGGINGPP:BOOLEAN="ON" \\\

        -DUSE_BUNDLE_RANDOM123:BOOLEAN="OFF" \\\

%if "%{system_sundials}" == "1"

        -DUSE_BUNDLE_SUNDIALS:BOOLEAN="OFF" \\\

        -DSUNDIALS_DIR:PATH=%{_datadir} \\\

        -DSUNDIALS_INCLUDE_DIR:PATH=%{_includedir}/sundials2 \\\

        -DSUNDIALS_LIBRARY_DIR:PATH=%{_libdir} \\\

%endif

        -DCMAKE_C_FLAGS_RELEASE:STRING="-DNDEBUG" \\\

        -DCMAKE_CXX_FLAGS_RELEASE:STRING="-DNDEBUG" \\\

        -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" \\\

        -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \\\

        -DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \\\

        -DLIB_INSTALL_DIR:PATH=%{_libdir} \\\

        -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \\\

        -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \\\

        -DPYTHON_INSTALL_PREFIX:PATH=$MPI_PYTHON3_SITEARCH \\\

        -DCMAKE_SKIP_RPATH:BOOL=ON \\\

        -DUSE_MPI:BOOL=$MPI_YES \\\

        -DUSE_PETSC:BOOL=False \\\

        -DBLAS_LIBRARIES=-l%{blaslib} \\\

        -DCMAKE_INSTALL_PREFIX:PATH=$MPI_HOME \\\

        -DBUILD_SHARED_LIBS:BOOL=ON \\\

%if "%{_lib}" == "lib64"

        -DLIB_SUFFIX=64 ../ &&

%else

        -DLIB_SUFFIX=""  ../ &&

%endif

popd || exit -1;

}

%global do_make_build %{expand: \

make %{?_smp_mflags} -C build$MPI_COMPILE_TYPE &&

pushd pysteps &&

    CFLAGS="%{optflags}" LDFLAGS="%{__global_ldflags}" %{__python3}  ../build$MPI_COMPILE_TYPE/pysteps/cmake_setup.py build --executable="/usr/bin/python3 -s" --build-base=../build$MPI_COMPILE_TYPE/pysteps/build/  &&

popd || exit -1

}

# Build serial version, dummy arguments

export MPI_COMPILE_TYPE=""

export MPI_COMPILER=serial

export MPI_SUFFIX=""

export MPI_HOME=%{_prefix}

export MPI_BIN=%{_bindir}

export MPI_PYTHON3_SITEARCH=%{python3_sitearch}

export MPI_YES="False"

%{do_cmake_config}

%{do_make_build}

# Build mpich version

%if %{with mpich}

%{_mpich_load}

export CC=mpicc

export CXX=mpicxx

export FC=mpif90

export F77=mpif77

export MPI_YES="True"

export MPI_COMPILE_TYPE="-mpich"

%{do_cmake_config}

%{do_make_build}

%{_mpich_unload}

%endif

# Build OpenMPI version

%if %{with openmpi}

%{_openmpi_load}

export CC=mpicc

export CXX=mpicxx

export FC=mpif90

export F77=mpif77

export MPI_YES="True"

export MPI_COMPILE_TYPE="-openmpi"

%{do_cmake_config}

%{do_make_build}

%{_openmpi_unload}

%endif

%install

# Install everything

%global do_install %{expand: \

echo

echo "*** INSTALLING %{module_name}-%{version}$MPI_COMPILE_TYPE ***"

echo

    make install DESTDIR=$RPM_BUILD_ROOT INSTALL="install -p" CPPROG="cp -p" -C build$MPI_COMPILE_TYPE || exit -1

    pushd pysteps &&

        CFLAGS="%{optflags}" LDFLAGS="%{__global_ldflags}" %{__python3}  ../build$MPI_COMPILE_TYPE/pysteps/cmake_setup.py build --executable="/usr/bin/python3 -s" --build-base=../build$MPI_COMPILE_TYPE/pysteps/build/ install --install-lib=$MPI_PYTHON3_SITEARCH -O1 --skip-build --root $RPM_BUILD_ROOT &&

    popd || exit -1

}

# install serial version

export MPI_COMPILE_TYPE=""

export MPI_SUFFIX=""

export MPI_HOME=%{_prefix}

export MPI_BIN=%{_bindir}

export MPI_YES="False"

export MPI_COMPILE_TYPE=""

export MPI_PYTHON3_SITEARCH="%{python3_sitearch}"

%{do_install}

# Install MPICH version

%if %{with mpich}

%{_mpich_load}

export MPI_YES="True"

export MPI_COMPILE_TYPE="-mpich"

%{do_install}

%{_mpich_unload}

%endif

# Install OpenMPI version

%if %{with openmpi}

%{_openmpi_load}

export MPI_YES="True"

export MPI_COMPILE_TYPE="-openmpi"

%{do_install}

%{_openmpi_unload}

%endif

%files -n python3-%{module_name}

%license LICENSE.md

%{python3_sitearch}/%{module_name}

%{python3_sitearch}/%{module_name}-%{version}-py%{python3_version}.egg-info

%if %{with mpich}

%files -n python3-%{module_name}-mpich

%license LICENSE.md

%{python3_sitearch}/mpich/%{module_name}

%{python3_sitearch}/mpich/%{module_name}-%{version}-py%{python3_version}.egg-info

%endif

%if %{with openmpi}

%files -n python3-%{module_name}-openmpi

%license LICENSE.md

%{python3_sitearch}/openmpi/%{module_name}

%{python3_sitearch}/openmpi/%{module_name}-%{version}-py%{python3_version}.egg-info

%endif

%changelog

* Tue Oct 06 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.5.0-6

- Rebuild for sundials-5.4.0

* Thu Aug 27 2020 Iñaki Úcar <iucar@fedoraproject.org> - 3.5.0-5

- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager

* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 3.5.0-4

- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild

* Thu Jun 25 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.5.0-3

- Explicitly BR setuptools

* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 3.5.0-2

- Rebuilt for Python 3.9

* Sat Apr 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 3.5.0-1

- Initial rpmbuild