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@@ -0,0 +1 @@ +/bionetgen-0.8.0.tar.gz diff --git a/python-bionetgen.spec b/python-bionetgen.spec new file mode 100644 index 0000000..46197f0 --- /dev/null +++ b/python-bionetgen.spec @@ -0,0 +1,398 @@ +%global _empty_manifest_terminate_build 0 +Name: python-bionetgen +Version: 0.8.0 +Release: 1 +Summary: A simple CLI and library for BioNetGen modelling language +License: unlicensed +URL: https://github.com/RuleWorld/PyBioNetGen +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/4d/1e/32dd08837b4a182b364a9d961d7a36dbd953eb68f98600c3b93fe8d1b9ca/bionetgen-0.8.0.tar.gz +BuildArch: noarch + +Requires: python3-cement +Requires: python3-nbopen +Requires: python3-numpy +Requires: python3-pyyaml +Requires: python3-colorlog +Requires: python3-xmltodict +Requires: python3-seaborn +Requires: python3-libroadrunner +Requires: python3-sympy +Requires: python3-lxml +Requires: python3-networkx +Requires: python3-libsbml +Requires: python3-pylru +Requires: python3-pyparsing + +%description +# A simple CLI for BioNetGen + +[](https://github.com/RuleWorld/PyBioNetGen/actions) +[](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/RuleWorld/PyBioNetGen) + +This is a simple CLI and a library for [BioNetGen modelling language](http://bionetgen.org/). PyBioNetGen also includes a heavily updated version of [Atomizer](https://github.com/RuleWorld/atomizer) which allows for conversion of models written in [Systems Biology Markup Language (SBML)](https://synonym.caltech.edu/) into BioNetGen language (BNGL) format. + +Please see the [documentation](https://pybionetgen.readthedocs.io/en/latest/) to learn how to use PyBioNetGen. + +## Installation + +You will need both python (3.7 and above) and perl installed. Once both are available you can use the following pip command to install the package + +``` +$ pip install bionetgen +``` + +### Features + +PyBioNetGen comes with a command line interface (CLI), based on [cement framework](https://builtoncement.com/), as well as a functional library that can be imported. The CLI can be used to run BNGL models, generate Jupyter notebooks and do rudimentary plotting. + +The library side provides a simple BNGL model runner as well as a model object that can be manipulated and used to get libRoadRunner simulators for the model. + +PyBioNetGen also includes a heavily updated version of [Atomizer](https://github.com/RuleWorld/atomizer) which allows for conversion of SBML models into BNGL format. Atomizer can also be used to automatically try to infer the internal structure of SBML species during the conversion, see [here](https://pybionetgen.readthedocs.io/en/latest/atomizer.html) for more information. Please note that this version of Atomizer is the main supported version and the version distributed with BioNetGen will eventually be deprecated. + +The model object requires a system call to BioNetGen so the initialization can be relatively costly, in case you would like to use it for parallel applications, use the [libRoadRunner](http://libroadrunner.org/) simulator instead, unless you are doing NFSim simulations. + +### Usage + +Sample CLI usage + +``` +$ bionetgen -h # help on every subcommand +$ bionetgen run -h # help on run subcommand +$ bionetgen run -i mymodel.bngl -o output_folder # this runs the model in output_folder +``` + +Sample library usage + +``` +import bionetgen + +ret = bionetgen.run("/path/to/mymodel.bngl", out="/path/to/output/folder") +# out keyword is optional, if not given, +# generated files will be deleted after running +res = ret.results['mymodel'] +# res will be a numpy record array of your gdat results + +model = bionetgen.bngmodel("/path/to/mymodel.bngl") +# model will be a python object that contains all model information +print(model.parameters) # this will print only the parameter block in BNGL format +print(model) # this will print the entire BNGL +model.parameters.k = 1 # setting parameter k to 1 +with open("new_model.bngl", "w") as f: + f.write(str(model)) # writes the changed model to new_model file + +# this will give you a libRoadRunner instance of the model +librr_sim = model.setup_simulator() +``` + +You can find more tutorials [here](https://pybionetgen.readthedocs.io/en/latest/tutorials.html). + +### Environment Setup + +The following demonstrates setting up and working with a development environment: + +``` +### create a virtualenv for development + +$ make virtualenv + +$ source env/bin/activate + + +### run bionetgen cli application + +$ bionetgen --help + + +### run pytest / coverage + +$ make test +``` + +### Docker + +Included is a basic `Dockerfile` for building and distributing `BioNetGen CLI`, +and can be built with the included `make` helper: + +``` +$ make docker + +$ docker run -it bionetgen --help +``` + +### Publishing to PyPI + +You can use `make dist` command to make the distribution and push to PyPI with + +``` +python -m twine upload dist/* +``` + +You'll need to have a PyPI API token created, see [here](https://packaging.python.org/tutorials/packaging-projects/) for more information. + + +%package -n python3-bionetgen +Summary: A simple CLI and library for BioNetGen modelling language +Provides: python-bionetgen +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-bionetgen +# A simple CLI for BioNetGen + +[](https://github.com/RuleWorld/PyBioNetGen/actions) +[](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/RuleWorld/PyBioNetGen) + +This is a simple CLI and a library for [BioNetGen modelling language](http://bionetgen.org/). PyBioNetGen also includes a heavily updated version of [Atomizer](https://github.com/RuleWorld/atomizer) which allows for conversion of models written in [Systems Biology Markup Language (SBML)](https://synonym.caltech.edu/) into BioNetGen language (BNGL) format. + +Please see the [documentation](https://pybionetgen.readthedocs.io/en/latest/) to learn how to use PyBioNetGen. + +## Installation + +You will need both python (3.7 and above) and perl installed. Once both are available you can use the following pip command to install the package + +``` +$ pip install bionetgen +``` + +### Features + +PyBioNetGen comes with a command line interface (CLI), based on [cement framework](https://builtoncement.com/), as well as a functional library that can be imported. The CLI can be used to run BNGL models, generate Jupyter notebooks and do rudimentary plotting. + +The library side provides a simple BNGL model runner as well as a model object that can be manipulated and used to get libRoadRunner simulators for the model. + +PyBioNetGen also includes a heavily updated version of [Atomizer](https://github.com/RuleWorld/atomizer) which allows for conversion of SBML models into BNGL format. Atomizer can also be used to automatically try to infer the internal structure of SBML species during the conversion, see [here](https://pybionetgen.readthedocs.io/en/latest/atomizer.html) for more information. Please note that this version of Atomizer is the main supported version and the version distributed with BioNetGen will eventually be deprecated. + +The model object requires a system call to BioNetGen so the initialization can be relatively costly, in case you would like to use it for parallel applications, use the [libRoadRunner](http://libroadrunner.org/) simulator instead, unless you are doing NFSim simulations. + +### Usage + +Sample CLI usage + +``` +$ bionetgen -h # help on every subcommand +$ bionetgen run -h # help on run subcommand +$ bionetgen run -i mymodel.bngl -o output_folder # this runs the model in output_folder +``` + +Sample library usage + +``` +import bionetgen + +ret = bionetgen.run("/path/to/mymodel.bngl", out="/path/to/output/folder") +# out keyword is optional, if not given, +# generated files will be deleted after running +res = ret.results['mymodel'] +# res will be a numpy record array of your gdat results + +model = bionetgen.bngmodel("/path/to/mymodel.bngl") +# model will be a python object that contains all model information +print(model.parameters) # this will print only the parameter block in BNGL format +print(model) # this will print the entire BNGL +model.parameters.k = 1 # setting parameter k to 1 +with open("new_model.bngl", "w") as f: + f.write(str(model)) # writes the changed model to new_model file + +# this will give you a libRoadRunner instance of the model +librr_sim = model.setup_simulator() +``` + +You can find more tutorials [here](https://pybionetgen.readthedocs.io/en/latest/tutorials.html). + +### Environment Setup + +The following demonstrates setting up and working with a development environment: + +``` +### create a virtualenv for development + +$ make virtualenv + +$ source env/bin/activate + + +### run bionetgen cli application + +$ bionetgen --help + + +### run pytest / coverage + +$ make test +``` + +### Docker + +Included is a basic `Dockerfile` for building and distributing `BioNetGen CLI`, +and can be built with the included `make` helper: + +``` +$ make docker + +$ docker run -it bionetgen --help +``` + +### Publishing to PyPI + +You can use `make dist` command to make the distribution and push to PyPI with + +``` +python -m twine upload dist/* +``` + +You'll need to have a PyPI API token created, see [here](https://packaging.python.org/tutorials/packaging-projects/) for more information. + + +%package help +Summary: Development documents and examples for bionetgen +Provides: python3-bionetgen-doc +%description help +# A simple CLI for BioNetGen + +[](https://github.com/RuleWorld/PyBioNetGen/actions) +[](https://vscode.dev/redirect?url=vscode://ms-vscode-remote.remote-containers/cloneInVolume?url=https://github.com/RuleWorld/PyBioNetGen) + +This is a simple CLI and a library for [BioNetGen modelling language](http://bionetgen.org/). PyBioNetGen also includes a heavily updated version of [Atomizer](https://github.com/RuleWorld/atomizer) which allows for conversion of models written in [Systems Biology Markup Language (SBML)](https://synonym.caltech.edu/) into BioNetGen language (BNGL) format. + +Please see the [documentation](https://pybionetgen.readthedocs.io/en/latest/) to learn how to use PyBioNetGen. + +## Installation + +You will need both python (3.7 and above) and perl installed. Once both are available you can use the following pip command to install the package + +``` +$ pip install bionetgen +``` + +### Features + +PyBioNetGen comes with a command line interface (CLI), based on [cement framework](https://builtoncement.com/), as well as a functional library that can be imported. The CLI can be used to run BNGL models, generate Jupyter notebooks and do rudimentary plotting. + +The library side provides a simple BNGL model runner as well as a model object that can be manipulated and used to get libRoadRunner simulators for the model. + +PyBioNetGen also includes a heavily updated version of [Atomizer](https://github.com/RuleWorld/atomizer) which allows for conversion of SBML models into BNGL format. Atomizer can also be used to automatically try to infer the internal structure of SBML species during the conversion, see [here](https://pybionetgen.readthedocs.io/en/latest/atomizer.html) for more information. Please note that this version of Atomizer is the main supported version and the version distributed with BioNetGen will eventually be deprecated. + +The model object requires a system call to BioNetGen so the initialization can be relatively costly, in case you would like to use it for parallel applications, use the [libRoadRunner](http://libroadrunner.org/) simulator instead, unless you are doing NFSim simulations. + +### Usage + +Sample CLI usage + +``` +$ bionetgen -h # help on every subcommand +$ bionetgen run -h # help on run subcommand +$ bionetgen run -i mymodel.bngl -o output_folder # this runs the model in output_folder +``` + +Sample library usage + +``` +import bionetgen + +ret = bionetgen.run("/path/to/mymodel.bngl", out="/path/to/output/folder") +# out keyword is optional, if not given, +# generated files will be deleted after running +res = ret.results['mymodel'] +# res will be a numpy record array of your gdat results + +model = bionetgen.bngmodel("/path/to/mymodel.bngl") +# model will be a python object that contains all model information +print(model.parameters) # this will print only the parameter block in BNGL format +print(model) # this will print the entire BNGL +model.parameters.k = 1 # setting parameter k to 1 +with open("new_model.bngl", "w") as f: + f.write(str(model)) # writes the changed model to new_model file + +# this will give you a libRoadRunner instance of the model +librr_sim = model.setup_simulator() +``` + +You can find more tutorials [here](https://pybionetgen.readthedocs.io/en/latest/tutorials.html). + +### Environment Setup + +The following demonstrates setting up and working with a development environment: + +``` +### create a virtualenv for development + +$ make virtualenv + +$ source env/bin/activate + + +### run bionetgen cli application + +$ bionetgen --help + + +### run pytest / coverage + +$ make test +``` + +### Docker + +Included is a basic `Dockerfile` for building and distributing `BioNetGen CLI`, +and can be built with the included `make` helper: + +``` +$ make docker + +$ docker run -it bionetgen --help +``` + +### Publishing to PyPI + +You can use `make dist` command to make the distribution and push to PyPI with + +``` +python -m twine upload dist/* +``` + +You'll need to have a PyPI API token created, see [here](https://packaging.python.org/tutorials/packaging-projects/) for more information. + + +%prep +%autosetup -n bionetgen-0.8.0 + +%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-bionetgen -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.8.0-1 +- Package Spec generated @@ -0,0 +1 @@ +d64785c37813d482c42fb25d306528ee bionetgen-0.8.0.tar.gz |