- `
+ **Default:** `[]` (no limit)
+
+
- `--suite-path`
**Description:** Specifies the path to the directory containing the test suite files.
**Usage:** `--suite-path
amici
https://docs.biosimulators.org/Biosimulators_AMICI/
pass | pass | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amiciunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenCAEE
CombineArchiveExecutionErrorDetails
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`).
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetCAEE
CombineArchiveExecutionErrorDetails
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).
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2MNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpyunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpyCAEE
CombineArchiveExecutionErrorDetails
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
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```cobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/Only allows steady state simulations
FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapyunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapyCAEE
CombineArchiveExecutionErrorDetails
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
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/ pass | pass | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasiunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/ pass | pass | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimCAEE
CombineArchiveExecutionErrorDetails
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
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/ pass | pass | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsimunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspyunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspyCAEE
CombineArchiveExecutionErrorDetails
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 .
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyneunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyneMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencorunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencorMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/ pass | pass | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pyscesunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pyscesrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapyunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapyCAEE
CombineArchiveExecutionErrorDetails
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`).
Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldynunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldynMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/ pass | pass | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with telluriumunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell None | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellDetails
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/ FAIL | FAIL | unsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xppunsure
The file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xppMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```AMICI
https://docs.biosimulators.org/Biosimulators_AMICI/✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
BioNetGen
https://docs.biosimulators.org/Biosimulators_BioNetGen/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
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
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
BoolNet
https://docs.biosimulators.org/Biosimulators_BoolNet/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
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
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
Brian 2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
CBMPy
https://docs.biosimulators.org/Biosimulators_CBMPy/✅ PASS
The 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.
❌ FAIL
viewdownload
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
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
COBRApy
https://docs.biosimulators.org/Biosimulators_COBRApy/Only allows steady state simulations
✅ PASS
The 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.
❌ FAIL
viewdownload
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
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
COPASI
https://docs.biosimulators.org/Biosimulators_COPASI/✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
GillesPy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
GINsim
https://docs.biosimulators.org/Biosimulators_GINsim/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
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
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
LibSBMLSim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
MASSpy
https://docs.biosimulators.org/Biosimulators_MASSpy/✅ PASS
The 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.
❌ FAIL
viewdownload
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
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
NetPyNE
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
NEURON
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
OpenCOR
https://docs.biosimulators.org/Biosimulators_OpenCOR/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
pyNeuroML
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
PySCeS
https://docs.biosimulators.org/Biosimulators_PySCeS/✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
RBApy
https://docs.biosimulators.org/Biosimulators_RBApy/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
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
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
Smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
Tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
VCell
https://github.com/virtualcell/vcell✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
XPP
https://docs.biosimulators.org/Biosimulators_XPP/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
+ Maximize single objective function, hard bounds. +
+ +subsystem: C3
+ +subsystem: C3
+ +subsystem: C3
+ +subsystem: L
+ +subsystem: C2
+ +subsystem: C3
+ +subsystem: L
+ +subsystem: C3
+ +subsystem: C1
+ +subsystem: C1
+ +subsystem: L
+ +subsystem: C1
+ +subsystem: C2
+ +subsystem: C2
+ +subsystem: C2
+ +subsystem: C2
+ +subsystem: C2
+ +subsystem: C3
+ +subsystem: C3
+ +subsystem: L
+ +subsystem: L
+ +subsystem: C4
+ +subsystem: C4
+ +subsystem: L
+ +subsystem: C3
+ +subsystem: C3
+ +AMICI
https://docs.biosimulators.org/Biosimulators_AMICI/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp962614` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
BioNetGen
https://docs.biosimulators.org/Biosimulators_BioNetGen/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp55567` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
BoolNet
https://docs.biosimulators.org/Biosimulators_BoolNet/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp446179` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
Brian 2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
CBMPy
https://docs.biosimulators.org/Biosimulators_CBMPy/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp721457` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
COBRApy
https://docs.biosimulators.org/Biosimulators_COBRApy/Only allows steady state simulations
✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp482300` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
COPASI
https://docs.biosimulators.org/Biosimulators_COPASI/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp932942` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
GillesPy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp452671` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
GINsim
https://docs.biosimulators.org/Biosimulators_GINsim/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp292854` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
LibSBMLSim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp293403` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
MASSpy
https://docs.biosimulators.org/Biosimulators_MASSpy/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp256213` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
NetPyNE
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
NEURON
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
OpenCOR
https://docs.biosimulators.org/Biosimulators_OpenCOR/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
pyNeuroML
https://docs.biosimulators.org/Biosimulators_pyNeuroML/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
PySCeS
https://docs.biosimulators.org/Biosimulators_PySCeS/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp921920` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
RBApy
https://docs.biosimulators.org/Biosimulators_RBApy/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp24088` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
Smoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
Tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/✅ PASS
The 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.
❌ FAIL
viewdownload
logs
ERROR MESSAGE:
`/root/archive.omex` is not a valid COMBINE/OMEX archive.
- The SED-ML file at location `./tmp603270` is invalid.
- Data generator `OBJF_1` is invalid.
- Variable `OBJF` is invalid.
- One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.
ERROR TYPE:
ValueError
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
VCell
https://github.com/virtualcell/vcell✅ PASS
The 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.
❌ FAIL
ERROR MESSAGE:Error unknown. The log.yml containing error information was not found.
XPP
https://docs.biosimulators.org/Biosimulators_XPP/⚠ XFAIL
EXPECTED FAILThe 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.
⚠ XFAIL
EXPECTED FAILview
download
logs
ERROR MESSAGE:
No module named 'libsbml'
ERROR TYPE:
ModuleNotFoundError
⚠ XFAIL
EXPECTED FAILERROR MESSAGE:
Error unknown. The log.yml containing error information was not found.
BioSimulatorsWarning:
') text = text.replace('warnings.warn(termcolor.colored(message, Colors.warning.value), category)', '
') - # if text includes The COMBINE/OMEX did not execute successfully: make everyhting from that point red - text = text.replace('The COMBINE/OMEX did not execute successfully:', 'The COMBINE/OMEX did not execute successfully:') - return text + return text def check_file_compatibility_test(engine, model_filepath, experiment_filepath): ''' Check if the file extensions suggest the file types are compatible with the engine. - This is done by comparing the file extensions of the model and experiment files with the file types supported by the engine. - For SED-ML files, the expected file extension is '.sedml'. For SBML files, the expected file extension is '.sbml'. + Only .sedml and .sbml files, and .xml files with 'sedml' and/or 'sbml' in their filename + are considered at this moment. It can be extended to other cases if needed in the future. ''' - input_filetypes_tuple = get_filetypes(model_filepath, experiment_filepath) + file_extensions = get_filetypes(model_filepath, experiment_filepath) engine_filetypes_tuple_list = ENGINES[engine]['formats'] 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())] - if input_filetypes_tuple in engine_filetypes_tuple_list: - file_types = [TYPES[i] for i in input_filetypes_tuple] - return 'pass', (f"The file extensions {input_filetypes_tuple} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}") - if 'xml' in input_filetypes_tuple: - return 'unsure', (f"The file extensions of the input files are '{input_filetypes_tuple}'. These may be compatible with {engine}. {compatible_filetypes} are compatible with {engine}") + 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}.") + if 'xml' in file_extensions: + if 'sbml' in model_filepath and 'sedml' not in model_filepath: + if 'sbml' in experiment_filepath and 'sedml' in experiment_filepath: + file_types = ('sbml', 'sedml') + if file_types in engine_filetypes_tuple_list: + return 'pass', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is compatible with {engine}.
{compatible_filetypes} are compatible with {engine}.") + else: + return 'unsure', (f"The filenames '{model_filepath}' and '{experiment_filepath}' suggest the input files are {[TYPES[i] for i in file_types]} which is not compatible with {engine}.
{compatible_filetypes} are compatible with {engine}.") else: - return 'FAIL', (f"The file extensions {input_filetypes_tuple} suggest the input file types are not compatibe 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}.
{compatible_filetypes} are compatible with {engine}.") def collapsible_content(content, title='Details'): @@ -484,7 +483,7 @@ def collapsible_content(content, title='Details'): return f'
{title}
{content}{ENGINES[x]["status"]}', x)) - + results_table.loc[results_table[ENGINE] == e, "name"] = collapsible_content(content=f'{ENGINES[e]["url"]}
{ENGINES[e]["status"]}', title=f'{ENGINES[e]["name"]}') + return results_table def process_log_yml_dict(log_yml_dict): @@ -1256,6 +1263,15 @@ def create_combined_results_table(results_remote, suffix_remote = ' (R)' suffix_local = ' (L)' + + # save results_remote and results_local as json files with dicts + path_to_results_remote = os.path.join(test_folder, 'results_remote.json') + path_to_results_local = os.path.join(test_folder, 'results_local.json') + + with open(path_to_results_remote, 'w') as f: + json.dump(results_remote, f, indent=4) + with open(path_to_results_local, 'w') as f: + json.dump(results_local, f, indent=4) # Create results tables for remote and local results results_table_remote = create_results_table(results_remote, sbml_file_name, sedml_file_name, d1_plots_remote_dir)