def createReadmeString(self, outputPath):
""" README.md added to the archive.
:return: readme information
:rtype: str
"""
readme = """
# Tellurium {} experiment
This COMBINE archive stores an tellurium experiment.
http://tellurium.analogmachine.org/
## Run Experiment
To reproduce the experiment and to create the figures and data run
```
import tellurium as te
omexPath = '{}'
te.executeSEDML(omexPath)
```
in tellurium, with `omexPath` the path to this archive file.
""".format(te.getTelluriumVersion(), os.path.basename(outputPath))
return readme
def createReadmeString(self, outputPath):
""" README.md added to the archive.
:return: readme information
:rtype: str
"""
readme = """
# Tellurium {} experiment
This COMBINE archive stores an tellurium experiment.
http://tellurium.analogmachine.org/
## Run Experiment
To reproduce the experiment and to create the figures and data run
```
import tellurium as te
omexPath = '{}'
te.executeSEDML(omexPath)
```
in tellurium, with `omexPath` the path to this archive file.
""".format(te.getTelluriumVersion(),
os.path.basename(outputPath))
return readme
__imports += "Imported RoadRunner %s" % roadrunner.__version__.split(
';')[0]
if __has_libantimony:
__imports += ", antimony %s" % antimony.__version__
if __has_sbml2matlab:
__imports += ", sbml2matlab %s" % sbml2matlab.__version__
if __has_teplugins:
__imports += ", TePlugins %s" % teplugins.__version__
if __has_numpy:
__imports += ", NumPy %s" % np.__version__
if __has_scipy:
__imports += ", SciPy %s" % sp.__version__
if __has_matplotlib:
__imports += ", Matplotlib %s" % mpl.__version__
if __has_tellurium:
__imports += ', and Tellurium %s as "te"' % te.getTelluriumVersion()
exec_print("")
if __imports:
exec_print(__imports)
#Not imported/ missing
__notimports = []
if not __has_roadrunner:
__notimports.append("roadrunner")
if not __has_libantimony:
__notimports.append("antimony")
if not __has_sbml2matlab:
__notimports.append("sbml2matlab")
if not __has_teplugins:
__notimports.append("teplugins")
def test_getTelluriumVersionInfo(self):
version = te.getTelluriumVersion()
self.assertTrue(isinstance(version, str))
self.assertTrue(len(version) > 0)
self.assertEqual(version, te.__version__)
from tellurium import sbmlToAntimony
from tellurium import sbmlToCellML
from tellurium import cellmlToAntimony
from tellurium import cellmlToSBML
from tellurium import getEigenvalues
from tellurium import plotArray
from tellurium import plotWithLegend
from tellurium import loadTestModel
from tellurium import getTestModel
from tellurium import listTestModels
# helper classes
from teio.latex import LatexExport
from analysis.parameterscan import ParameterScan, SteadyStateScan
# sedml & combine support
from sedml.tesedml import sedmlToPython, executeSEDML, executeOMEX
from sedml.tephrasedml import experiment
from tecombine import combine
import optimization
import visualization
try:
import temiriam
except ImportError:
pass
import notebooks
__version__ = getTelluriumVersion()
if __has_matplotlib:
__imports.append("Matplotlib {}".format(mpl.__version__))
if __has_guiqwt:
__imports.append("guidata {}".format(guidata.__version__))
__imports.append("guiqwt {}".format(guiqwt.__version__))
if __has_roadrunner:
__imports.append("libRoadRunner %s" % roadrunner.__version__.split(';')[0])
if __has_libantimony:
__imports.append("Antimony %s" % antimony.__version__)
if __has_sbml2matlab:
__imports.append("sbml2matlab %s" % sbml2matlab.__version__)
if __has_rrplugins:
__imports.append("RRPlugins %s" % rrplugins.__version__)
if __has_tellurium:
__imports.append('Tellurium %s as "te"' % te.getTelluriumVersion())
exec_print()
if __imports:
exec_print("Imported " + ", ".join(__imports))
exec_print()
#==============================================================================
# Add help about the "scientific" command
#==============================================================================
def setscientific():
"""Set 'scientific' in __builtin__"""
infos = ""
if __has_numpy:
# coding: utf-8
# Back to the main [Index](../index.ipynb)
# #### Version information
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
# to get the tellurium version use
print(te.getTelluriumVersion())
# to print the full version info use
print('-' * 80)
te.printVersionInfo()
print('-' * 80)
# #### Repeat simulation without notification
# In[2]:
# Load SBML file
r = te.loada("""
model test
J0: X0 -> X1; k1*X0;
X0 = 10; X1=0;
k1 = 0.2
end
from tellurium import sbmlToCellML
from tellurium import cellmlToAntimony
from tellurium import cellmlToSBML
from tellurium import getEigenvalues
from tellurium import plotArray
from tellurium import plotWithLegend
from tellurium import loadTestModel
from tellurium import getTestModel
from tellurium import listTestModels
# helper classes
from teio.latex import LatexExport
from analysis.parameterscan import ParameterScan, SteadyStateScan
# sedml & combine support
from sedml.tesedml import sedmlToPython, executeSEDML, executeOMEX
from sedml.tephrasedml import experiment
from tecombine import combine
import optimization
import visualization
try:
import temiriam
except ImportError:
pass
import notebooks
__version__ = getTelluriumVersion()
def test_getTelluriumVersionInfo(self):
version = te.getTelluriumVersion()
self.assertTrue(isinstance(version, str))
self.assertTrue(len(version) > 0)
self.assertEqual(version, te.__version__)
# coding: utf-8
# Back to the main [Index](../index.ipynb)
# #### Version information
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
# to get the tellurium version use
print(te.getTelluriumVersion())
# to print the full version info use
print('-' * 80)
te.printVersionInfo()
print('-' * 80)
# #### Repeat simulation without notification
# In[2]:
# Load SBML file
r = te.loada("""
model test
J0: X0 -> X1; k1*X0;
X0 = 10; X1=0;
if __has_roadrunner:
__imports += "Imported RoadRunner %s" % roadrunner.__version__.split(';')[0]
if __has_libantimony:
__imports += ", antimony %s" % antimony.__version__
if __has_sbml2matlab:
__imports += ", sbml2matlab %s" % sbml2matlab.__version__
if __has_teplugins:
__imports += ", TePlugins %s" % teplugins.__version__
if __has_numpy:
__imports += ", NumPy %s" % np.__version__
if __has_scipy:
__imports += ", SciPy %s" % sp.__version__
if __has_matplotlib:
__imports += ", Matplotlib %s" % mpl.__version__
if __has_tellurium:
__imports += ', and Tellurium %s as "te"' % te.getTelluriumVersion()
exec_print("")
if __imports:
exec_print(__imports)
#Not imported/ missing
__notimports = []
if not __has_roadrunner:
__notimports.append("roadrunner")
if not __has_libantimony:
__notimports.append("antimony")
if not __has_sbml2matlab:
__notimports.append("sbml2matlab")
if not __has_teplugins:
__notimports.append("teplugins")
