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diff --git a/python-apricopt.spec b/python-apricopt.spec new file mode 100644 index 0000000..cd28dd7 --- /dev/null +++ b/python-apricopt.spec @@ -0,0 +1,217 @@ +%global _empty_manifest_terminate_build 0 +Name: python-apricopt +Version: 0.0.2a3 +Release: 1 +Summary: A library for simulation-based parameter optimization +License: GNU General Public License v3 (GPLv3) +URL: http://mclab.di.uniroma1.it +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/04/39/3609e58dc6f7b024051535511d817c365063bf03954f5f993956cd2a8748/apricopt-0.0.2a3.tar.gz +BuildArch: noarch + +Requires: python3-attrs +Requires: python3-chaospy +Requires: python3-cycler +Requires: python3-future +Requires: python3-importlib-metadata +Requires: python3-kiwisolver +Requires: python3-libroadrunner +Requires: python3-matplotlib +Requires: python3-mpmath +Requires: python3-numpy +Requires: python3-Pillow +Requires: python3-pyparsing +Requires: python3-copasi +Requires: python3-dateutil +Requires: python3-libsbml +Requires: python3-PyYAML +Requires: python3-scipy +Requires: python3-seaborn +Requires: python3-six +Requires: python3-sympy +Requires: python3-tqdm +Requires: python3-zipp + +%description +# Apricopt # + +Apricopt is a python framework for simulation-based optimisation of dynamical systems. + +It is agnostic with respect to the optimiser and to the simulator. + +Apricopt supports the PEtab format for the definition of the optimisation problem. More info about PEtab [here](https://petab.readthedocs.io/en/latest/). + +Currently, we support the following simulators: + +* COPASI. A state-of-the-art simulator for models of biological processes. We support SBML models (any level and version). +* RoadRunner. A fast state-of-the-art simulator of biological models. + +Currently, we support the following black-box optimisers: + +* NOMAD. A state-of the art black-box solver that supports surrogate models. More info [here](https://www.gerad.ca/nomad/). +* SciPy.optimize. A python library that implements several algorithms for multivariate optimization. More info [here](https://docs.scipy.org/doc/scipy/reference/optimize.html). +* PySwarms. A python library that implements various forms of the Particle Swarm Optimization algorithm. More info [here](https://pyswarms.readthedocs.io/en/latest/). + +Currently, we support the following white-box optimisers: + +* COPASI. It supports several optimisation algorithms for biological processes. More info [here](http://copasi.org/Support/User_Manual/Methods/Optimization_Methods/) + +### Info ### + +WIP + +* Version 0.0.2a3 + + +### Who do I talk to? ### + +* Marco Esposito (author) - esposito@di.uniroma1.it +* Leonardo Picchiami (author) - picchiami.1643888@studenti.uniroma1.it + + +Copyright (C) 2020-2021 Marco Esposito, Leonardo Picchiami. + +Distributed under GNU General Public License v3. + + + + +%package -n python3-apricopt +Summary: A library for simulation-based parameter optimization +Provides: python-apricopt +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-apricopt +# Apricopt # + +Apricopt is a python framework for simulation-based optimisation of dynamical systems. + +It is agnostic with respect to the optimiser and to the simulator. + +Apricopt supports the PEtab format for the definition of the optimisation problem. More info about PEtab [here](https://petab.readthedocs.io/en/latest/). + +Currently, we support the following simulators: + +* COPASI. A state-of-the-art simulator for models of biological processes. We support SBML models (any level and version). +* RoadRunner. A fast state-of-the-art simulator of biological models. + +Currently, we support the following black-box optimisers: + +* NOMAD. A state-of the art black-box solver that supports surrogate models. More info [here](https://www.gerad.ca/nomad/). +* SciPy.optimize. A python library that implements several algorithms for multivariate optimization. More info [here](https://docs.scipy.org/doc/scipy/reference/optimize.html). +* PySwarms. A python library that implements various forms of the Particle Swarm Optimization algorithm. More info [here](https://pyswarms.readthedocs.io/en/latest/). + +Currently, we support the following white-box optimisers: + +* COPASI. It supports several optimisation algorithms for biological processes. More info [here](http://copasi.org/Support/User_Manual/Methods/Optimization_Methods/) + +### Info ### + +WIP + +* Version 0.0.2a3 + + +### Who do I talk to? ### + +* Marco Esposito (author) - esposito@di.uniroma1.it +* Leonardo Picchiami (author) - picchiami.1643888@studenti.uniroma1.it + + +Copyright (C) 2020-2021 Marco Esposito, Leonardo Picchiami. + +Distributed under GNU General Public License v3. + + + + +%package help +Summary: Development documents and examples for apricopt +Provides: python3-apricopt-doc +%description help +# Apricopt # + +Apricopt is a python framework for simulation-based optimisation of dynamical systems. + +It is agnostic with respect to the optimiser and to the simulator. + +Apricopt supports the PEtab format for the definition of the optimisation problem. More info about PEtab [here](https://petab.readthedocs.io/en/latest/). + +Currently, we support the following simulators: + +* COPASI. A state-of-the-art simulator for models of biological processes. We support SBML models (any level and version). +* RoadRunner. A fast state-of-the-art simulator of biological models. + +Currently, we support the following black-box optimisers: + +* NOMAD. A state-of the art black-box solver that supports surrogate models. More info [here](https://www.gerad.ca/nomad/). +* SciPy.optimize. A python library that implements several algorithms for multivariate optimization. More info [here](https://docs.scipy.org/doc/scipy/reference/optimize.html). +* PySwarms. A python library that implements various forms of the Particle Swarm Optimization algorithm. More info [here](https://pyswarms.readthedocs.io/en/latest/). + +Currently, we support the following white-box optimisers: + +* COPASI. It supports several optimisation algorithms for biological processes. More info [here](http://copasi.org/Support/User_Manual/Methods/Optimization_Methods/) + +### Info ### + +WIP + +* Version 0.0.2a3 + + +### Who do I talk to? ### + +* Marco Esposito (author) - esposito@di.uniroma1.it +* Leonardo Picchiami (author) - picchiami.1643888@studenti.uniroma1.it + + +Copyright (C) 2020-2021 Marco Esposito, Leonardo Picchiami. + +Distributed under GNU General Public License v3. + + + + +%prep +%autosetup -n apricopt-0.0.2a3 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-apricopt -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.0.2a3-1 +- Package Spec generated |