def test_error(self):
def exec_sedml_docs_in_combine_archive(archive_filename,
outputs_dirname):
pass
with self.assertRaises(ValueError):
self.App = build_cli(None, '4.5.6', 'Test Simulator', '1.2.3',
'https://test-simulator.org',
exec_sedml_docs_in_combine_archive)
with self.assertRaises(ValueError):
self.App = build_cli('test-simulator', '4.5.6', None, '1.2.3',
'https://test-simulator.org',
exec_sedml_docs_in_combine_archive)
with self.assertRaises(ValueError):
self.App = build_cli('test-simulator', '4.5.6', 'Test Simulator',
'1.2.3', 'https://test-simulator.org', None)
def setUp(self):
def exec_sedml_docs_in_combine_archive(archive_filename,
outputs_dirname,
config=None):
if archive_filename:
print(archive_filename)
if outputs_dirname:
raise Exception(outputs_dirname)
return None, CombineArchiveLog()
self.App = build_cli(
'test-simulator',
'4.5.6',
'Test Simulator',
'1.2.3',
'https://test-simulator.org',
exec_sedml_docs_in_combine_archive,
environment_variables=ENVIRONMENT_VARIABLES.values())
''' BioSimulators-compliant command-line interface '''
__author__ = 'Jonathan Karr'
__email__ = '*****@*****.**'
__all__ = [
'App',
'main',
]
from . import __version__, get_simulator_version
from .combine import exec_sedml_docs_in_combine_archive
from biosimulators_utils.simulator.cli import build_cli
App = build_cli('smoldyn', __version__,
'Smoldyn', get_simulator_version(), 'http://www.smoldyn.org',
exec_sedml_docs_in_combine_archive)
def main():
with App() as app:
app.run()
if __name__ == '__main__':
main()
""" BioSimulators-compliant command-line interface to the `BioNetGen <https://bionetgen.org/>`_ simulation program.
:Author: Jonathan Karr <*****@*****.**>
:Date: 2021-01-05
:Copyright: 2020-2021, BioSimulators
:License: MIT
"""
from . import get_simulator_version
from ._version import __version__
from .core import exec_sedml_docs_in_combine_archive
from biosimulators_utils.simulator.cli import build_cli
App = build_cli('bionetgen', __version__,
'BioNetGen', get_simulator_version(), 'https://bionetgen.org',
exec_sedml_docs_in_combine_archive)
def main():
with App() as app:
app.run()
""" BioSimulators-compliant command-line interface to the `LibSBMLsim <http://fun.bio.keio.ac.jp/software/libsbmlsim/>`_ library.
:Author: Jonathan Karr <*****@*****.**>
:Date: 2021-03-27
:Copyright: 2021, BioSimulators Team
:License: MIT
"""
from ._version import __version__
from .core import exec_sedml_docs_in_combine_archive
from biosimulators_utils.simulator.cli import build_cli
from biosimulators_utils.simulator.data_model import AlgorithmSubstitutionPolicy
from biosimulators_utils.simulator.environ import ENVIRONMENT_VARIABLES
import libsbmlsim
App = build_cli(
'libsbmlsim',
__version__,
'LibSBMLsim',
libsbmlsim.__version__,
'http://fun.bio.keio.ac.jp/software/libsbmlsim/',
exec_sedml_docs_in_combine_archive,
environment_variables=[ENVIRONMENT_VARIABLES[AlgorithmSubstitutionPolicy]])
def main():
with App() as app:
app.run()
""" BioSimulators-compliant command-line interface to the `GillesPy2 <https://github.com/StochSS/GillesPy2>`_ simulation program.
:Author: Jonathan Karr <*****@*****.**>
:Author: Bilal Shaikh <*****@*****.**>
:Date: 2020-12-13
:Copyright: 2020, BioSimulators Team
:License: MIT
"""
from . import get_simulator_version
from ._version import __version__
from .core import exec_sedml_docs_in_combine_archive
from biosimulators_utils.simulator.cli import build_cli
App = build_cli('biosimulators-gillespy2', __version__, 'GillesPy2',
get_simulator_version(),
'https://github.com/StochSS/GillesPy2',
exec_sedml_docs_in_combine_archive)
def main():
with App() as app:
app.run()
""" BioSimulators-compliant command-line interface to the `MySimulator <https://url.for.my.simulator>`_ simulation program.
:Author: Author name <email@organization>
:Date: YYYY-MM-DD
:Copyright: YYYY, Owner
:License: <License, e.g., MIT>
"""
from ._version import __version__
from .core import get_simulator_version, exec_sedml_docs_in_combine_archive
from biosimulators_utils.simulator.cli import build_cli
App = build_cli('biosimulators-my-simulator', __version__, 'My Simulator',
get_simulator_version(), 'https://url.for.my.simulator',
exec_sedml_docs_in_combine_archive)
def main():
with App() as app:
app.run()