diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 0a977f5d..22b1eb79 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types may not be compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
Reached maximum number of steps

|
❌ FAILERROR MESSAGE:
Reached maximum number of steps

| plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BioNetGen.

BNGL and SED-ML are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with BoolNet.

SED-ML and SBML-qual are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with Brian 2.

NeuroML, LEMS and SED-ML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with GINsim.

SED-ML and SBML-qual are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with MASSpy.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NetPyNE.

NeuroML, LEMS and SED-ML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with NEURON.

NeuroML, LEMS and SED-ML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with OpenCOR.

CellML and SED-ML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with pyNeuroML.

NeuroML, LEMS and SED-ML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?


ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with RBApy.

RBApy and SED-ML are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

SBML and SED-ML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML.

BNGL, SBML and SED-ML are compatible with VCell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The file extensions ('sbml', 'sedml') suggest the input file types are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index 755a3c90..9cab69c5 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
❌ FAILview
download
logs

ERROR MESSAGE:
status: QUEUED

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BioNetGen.

SED-ML and BNGL are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BoolNet.

SBML-qual and SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Brian 2.

SED-ML, LEMS and NeuroML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with GINsim.

SBML-qual and SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

The following targets are not supported:
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']
- /sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']

Only following targets are supported:
- M_S1
- M_S2
- R_reaction1
- S1
- S2
- k1
- reaction1

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NetPyNE.

SED-ML, LEMS and NeuroML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NEURON.

SED-ML, LEMS and NeuroML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with pyNeuroML.

SED-ML, LEMS and NeuroML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with RBApy.

SED-ML and RBApy are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| plot | plot | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
✅ PASSview
download
logs

| ✅ PASS | plot | plot | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '00001-sbml-l3v2.xml' and '00001-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md index ca8741e2..6c2279b7 100644 --- a/test_suite/test_01186/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_01186/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | -|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| -|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with amici.

['SBML', 'SED-ML'] are compatible with amici.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with bionetgen.

['BNGL', 'SED-ML'] are compatible with bionetgen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with boolnet.

['SBML-qual', 'SED-ML'] are compatible with boolnet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with brian2.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cbmpy.

['SBML', 'SED-ML'] are compatible with cbmpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with cobrapy.

['SBML', 'SED-ML'] are compatible with cobrapy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with copasi.

['SBML', 'SED-ML'] are compatible with copasi.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with gillespy2.

['SBML', 'SED-ML'] are compatible with gillespy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with ginsim.

['SBML-qual', 'SED-ML'] are compatible with ginsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with libsbmlsim.

['SBML', 'SED-ML'] are compatible with libsbmlsim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with masspy.

['SBML', 'SED-ML'] are compatible with masspy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with netpyne.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyne.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with neuron.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with opencor.

['CellML', 'SED-ML'] are compatible with opencor.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with pyneuroml.

['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | -|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with pysces.

['SBML', 'SED-ML'] are compatible with pysces.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with rbapy.

['RBApy', 'SED-ML'] are compatible with rbapy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with smoldyn.

['Smoldyn', 'SED-ML'] are compatible with smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | -|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with tellurium.

['SBML', 'SED-ML'] are compatible with tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | -|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is compatible with vcell.

['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | -|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are ['SBML', 'SED-ML'] which is not compatible with xpp.

['XPP', 'SED-ML'] are compatible with xpp.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file +| Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | d1 (R) | d1 (L) | +|:-------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------|:---------| +|
AMICIhttps://docs.biosimulators.org/Biosimulators_AMICI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with AMICI.

SED-ML and SBML are compatible with AMICI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
BioNetGenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BioNetGen.

SED-ML and BNGL are compatible with BioNetGen.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
BoolNethttps://docs.biosimulators.org/Biosimulators_BoolNet/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with BoolNet.

SBML-qual and SED-ML are compatible with BoolNet.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
Brian 2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Brian 2.

SED-ML, LEMS and NeuroML are compatible with Brian 2.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
CBMPyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with CBMPy.

SED-ML and SBML are compatible with CBMPy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

'MLStripper' object has no attribute 'unescape'

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
COBRApyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COBRApy.

SED-ML and SBML are compatible with COBRApy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `cobra.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
COPASIhttps://docs.biosimulators.org/Biosimulators_COPASI/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with COPASI.

SED-ML and SBML are compatible with COPASI.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':No suitable equivalent for 'KISAO_0000437' could be found with the provided substitution policy

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
GillesPy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with GillesPy2.

SED-ML and SBML are compatible with GillesPy2.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
GINsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with GINsim.

SBML-qual and SED-ML are compatible with GINsim.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Namespaces must include 1 SBML qual namespace.

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
LibSBMLSimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with LibSBMLSim.

SED-ML and SBML are compatible with LibSBMLSim.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
MASSpyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with MASSpy.

SED-ML and SBML are compatible with MASSpy.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
NetPyNEhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NetPyNE.

SED-ML, LEMS and NeuroML are compatible with NetPyNE.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
NEURONhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with NEURON.

SED-ML, LEMS and NeuroML are compatible with NEURON.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
OpenCORhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with OpenCOR.

SED-ML and CellML are compatible with OpenCOR.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
pyNeuroMLhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with pyNeuroML.

SED-ML, LEMS and NeuroML are compatible with pyNeuroML.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | +|
PySCeShttps://docs.biosimulators.org/Biosimulators_PySCeS/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with PySCeS.

SED-ML and SBML are compatible with PySCeS.
|
❌ FAILview
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

class 'ValueError':SteadyStateSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `SteadyStateSimulation` is not supported. Simulation must be an instance of one of the following:
- UniformTimeCourseSimulation

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
RBApyhttps://docs.biosimulators.org/Biosimulators_RBApy/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with RBApy.

SED-ML and RBApy are compatible with RBApy.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
The COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
Smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with Smoldyn.

SED-ML and Smoldyn are compatible with Smoldyn.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.

| | | +|
Telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with Tellurium.

SED-ML and SBML are compatible with Tellurium.
|
❌ FAILview
download
logs

ERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
|
❌ FAILERROR MESSAGE:
flux balance analysis

ERROR TYPE:
CombineArchiveExecutionError
| | | +|
VCellhttps://github.com/virtualcell/vcell
|
✅ PASSThe filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is compatible with VCell.

SED-ML, BNGL and SBML are compatible with VCell.
|
✅ PASSview
download
logs

|
❌ FAILERROR MESSAGE:
Runtime Exception

| | | +|
XPPhttps://docs.biosimulators.org/Biosimulators_XPP/
|
⚠ XFAILEXPECTED FAIL

The filenames '01186-sbml-l3v2.xml' and '01186-sbml-l3v2-sedml.xml' suggest the input files are SBML and SED-ML which is not compatible with XPP.

SED-ML and XPP are compatible with XPP.
|
⚠ XFAILEXPECTED FAIL

view
download
logs

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
|
⚠ XFAILEXPECTED FAIL

ERROR MESSAGE:
No module named 'libsbml'

ERROR TYPE:
ModuleNotFoundError
| | | \ No newline at end of file diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py index d2a83f3b..189fe00c 100644 --- a/test_suite/test_test_suite_compatibility_biosimulators.py +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -148,6 +148,7 @@ def process_cases(args): print(f"Changed to {new_directory}") engine_list = list(engines.keys()) + # engine_list = engine_list[:5] utils.run_biosimulators_remotely_and_locally(engine_list, os.path.basename(sedml_file_path), diff --git a/utils/__init__.py b/utils/__init__.py index 8d150b26..deaf876a 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -278,7 +278,7 @@ def add_xmlns_fbc_attribute(sedml_filepath, sbml_filepath, temp_sedml_filepath=N if os.path.exists(temp_sedml_filepath): with open(temp_sedml_filepath, 'r') as file: sedstr = file.read() - + if sedstr == "": with open(sedml_filepath, 'r') as file: sedstr = file.read() @@ -296,10 +296,12 @@ def add_xmlns_fbc_attribute(sedml_filepath, sbml_filepath, temp_sedml_filepath=N missing_fbc_attribute = 'xmlns:fbc="' + fbc_xmlns + '"' sedstr = sedstr[:location] + ' ' + missing_fbc_attribute + sedstr[location:] + if temp_sedml_filepath == None: temp_sedml_filepath = sedml_filepath with open(temp_sedml_filepath,"w") as fout: + fout.write(sedstr) @@ -513,12 +515,21 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): ''' file_extensions = get_filetypes(model_filepath, experiment_filepath) engine_filetypes_tuple_list = ENGINES[engine]['formats'] + engine_name = ENGINES[engine]['name'] flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist if sublist != 'unclear'] compatible_filetypes = [TYPES[i] for i in flat_engine_filetypes_tuple_list if i in list(TYPES.keys())] + unique_compatible_filetpyes = list(set(compatible_filetypes)) + + unique_compatible_filetpyes_strings = ', '.join(unique_compatible_filetpyes[:-1]) + ' and ' + unique_compatible_filetpyes[-1] if len(unique_compatible_filetpyes) > 1 else unique_compatible_filetpyes[0] + + file_types = [TYPES[i] for i in file_extensions] + filetypes_strings = ', '.join(file_types[:-1]) + ' and ' + file_types[-1] if len(file_types) > 1 else file_types[0] + + if file_extensions == ('sbml', 'sedml') and file_extensions not in engine_filetypes_tuple_list: + return 'FAIL', (f"The file extensions {file_extensions} suggest the input file types are {filetypes_strings} which is not compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") if file_extensions in engine_filetypes_tuple_list: - file_types = [TYPES[i] for i in file_extensions] - return 'pass', (f"The file extensions {file_extensions} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}.") + return 'pass', (f"The file extensions {file_extensions} suggest the input file types are {filetypes_strings}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") if 'xml' in file_extensions: model_sbml = 'sbml' in model_filepath @@ -527,12 +538,15 @@ def check_file_compatibility_test(engine, model_filepath, experiment_filepath): experiment_sedml = 'sedml' in experiment_filepath if model_sbml and experiment_sbml and experiment_sedml and not model_sedml: - file_types = [TYPES[i] for i in ('sbml', 'sedml') ] - return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {file_types} which is compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") - else: - return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may be compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + file_types_tuple = ('sbml', 'sedml') + file_types = [TYPES[i] for i in file_types_tuple] + filetypes_strings = ', '.join(file_types[:-1]) + ' and ' + file_types[-1] if len(file_types) > 1 else file_types[0] + if file_types_tuple in engine_filetypes_tuple_list: + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {filetypes_strings} which is compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") + else: + return 'FAIL', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {filetypes_strings} which is not compatible with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") else: - return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatible with {engine}.

{compatible_filetypes} are compatible with {engine}.") + return 'unsure', (f"The file extensions {file_extensions} suggest the input file types may not be compatibe with {engine_name}.

{unique_compatible_filetpyes_strings} are compatible with {engine_name}.") def collapsible_content(content, title='Details'):