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diff --git a/SBML/tests/d1_plots_remote/rbapy_d1.pdf b/SBML/tests/d1_plots_remote/rbapy_d1.pdf
index b1afd78b..0e0efcf5 100644
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diff --git a/SBML/tests/d1_plots_remote/tellurium_d1.pdf b/SBML/tests/d1_plots_remote/tellurium_d1.pdf
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diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index c558cede..1cf019a0 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | amici
https://docs.biosimulators.org/Biosimulators_AMICI/
pass | pass | pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicipass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
FAIL | FAIL | FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe 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 `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`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```boolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe 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 `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2MNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```cbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpypass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpyCAEE
CombineArchiveExecutionErrorDetails
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:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.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 simulationspass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapypass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapyCAEE
CombineArchiveExecutionErrorDetails
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:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```copasi
https://docs.biosimulators.org/Biosimulators_COPASI/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasipass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe 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 `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: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```libsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimpass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspypass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['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/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```netpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpynepass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyneMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```neuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```opencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```pyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```pysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscespass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesCAEE
CombineArchiveExecutionErrorDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Model at /tmp/tmpod71_ka_/./LEMS_NML2_Ex9_FN.sbml could not be imported:
File /tmp/tmpod71_ka_/./LEMS_NML2_Ex9_FN.sbml.xml does not existDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```rbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapyFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe 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 `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`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.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
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldynFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldynMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```tellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumpass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellpass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppMNFE
ModuleNotFoundErrorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.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 file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenDetails
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`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorboolnet
https://docs.biosimulators.org/Biosimulators_BoolNet/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetDetails
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).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorbrian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2Details
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorcbmpy
https://docs.biosimulators.org/Biosimulators_CBMPy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpyDetails
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:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcobrapy
https://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapyDetails
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:
- SteadyStateSimulationDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorcopasi
https://docs.biosimulators.org/Biosimulators_COPASI/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasigillespy2
https://docs.biosimulators.org/Biosimulators_GillesPy2/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2ginsim
https://docs.biosimulators.org/Biosimulators_GINsim/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimDetails
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: 20000Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorlibsbmlsim
https://docs.biosimulators.org/Biosimulators_LibSBMLSim/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsimmasspy
https://docs.biosimulators.org/Biosimulators_MASSpy/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspyDetails
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/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrornetpyne
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorneuron
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuronDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```MNFE
ModuleNotFoundErroropencor
https://docs.biosimulators.org/Biosimulators_OpenCOR/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpyneuroml
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuromlDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```MNFE
ModuleNotFoundErrorpysces
https://docs.biosimulators.org/Biosimulators_PySCeS/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pyscesDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Model at /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml could not be imported:
File /tmp/tmp1bq_quiv/./LEMS_NML2_Ex9_FN.sbml.xml does not existDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorrbapy
https://docs.biosimulators.org/Biosimulators_RBApy/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapyDetails
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`).Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```CAEE
CombineArchiveExecutionErrorsmoldyn
https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] are compatible with smoldynDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```MNFE
ModuleNotFoundErrortellurium
https://docs.biosimulators.org/Biosimulators_tellurium/
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with telluriumvcell
https://github.com/virtualcell/vcell
✅ PASS
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcellDetails
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```xpp
https://docs.biosimulators.org/Biosimulators_XPP/
⚠ XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppDetails
No module named 'libsbml'Details
```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```MNFE
ModuleNotFoundError
{x}' if 'FAIL' in x else
- f'{x}' if 'xml' in x or 'unsure' in x else
- f'
{x}' if 'pass' in x else x)
- # pass / FAIL
- results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'\
- {x}' if x == 'FAIL' \
- else f' {x}')
+ results_table[ERROR] = results_table.apply(lambda x: None if x[PASS_FAIL] == x[ERROR] else x[ERROR], axis=1)
+ results_table[PASS_FAIL] = results_table[PASS_FAIL].replace('other', 'FAIL')
+
+ results_table[ERROR] = results_table[ERROR].apply(lambda x: ansi_to_html(x))
+ results_table[ERROR] = results_table[ERROR].apply(lambda x: collapsible_content(x))
+ results_table[PASS_FAIL] = results_table[PASS_FAIL].apply(lambda x: f'{fail_html}' if x == 'FAIL' \
+ else f'{pass_html}' if x == 'pass' else x)
+
# d1 plot clickable link
- results_table['d1'] = results_table['Engine'].apply(lambda x: d1_plots_dict(engines, output_dir).get(x, None))
- results_table['d1'] = results_table['d1'].apply(lambda x: create_hyperlink(x,title='plot'))
-
- # if Type is in the table add message with collapsible content
- if 'Type' in results_table.columns:
- results_table['Type'] = results_table['Type'].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x))))
+ results_table[D1] = results_table[ENGINE].apply(lambda x: d1_plots_dict(output_dir).get(x, None))
+ results_table[D1] = results_table[D1].apply(lambda x: create_hyperlink(x,title='plot'))
+ if TYPE in results_table.columns:
+ results_table[TYPE] = results_table[TYPE].apply(lambda x: collapsible_content(x,"".join(re.findall(r'[A-Z]', x))))
- results_table['Engine'] = results_table['Engine'].apply(lambda x: collapsible_content(f'{engines[x]["url"]}
{engines[x]["status"]}', x))
+ for e in ENGINES.keys():
+ compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath)
- return results_table
+ print(e, compatibility_content[0] )
+ if compatibility_content[0] == 'pass':
+ results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{pass_html}')
+ elif compatibility_content[0] == 'unsure':
+ results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{warning_html}')
+ else:
+ results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{fail_html}')
+
+ # add xfail to engines that do not support sbml
+ sbml_incompatible_ENGINES = [e for e in ENGINES.keys() if 'sbml' not in ENGINES[e]['formats'][0]]
+ for e in sbml_incompatible_ENGINES:
+ compatibility_content = check_file_compatibility_test(e, sbml_filepath, sedml_filepath)
+ results_table.loc[results_table[ENGINE] == e, COMPAT] = collapsible_content(compatibility_content[1], title=f'{xfail_html}')
+ results_table.loc[results_table[ENGINE] == e, PASS_FAIL] = f'{xfail_html}'
+
+
+ # add status message defined in ENGINES
+ results_table[ENGINE] = results_table[ENGINE].apply(lambda x: collapsible_content(f'{ENGINES[x]["url"]}
{ENGINES[x]["status"]}', x))
+ return results_table
def run_biosimulators_remotely(sedml_file_name,
sbml_file_name,
- d1_plots_remote_dir,
- engines=engines,
+ d1_plots_remote_dir,
test_folder='tests'):
""" run with directory pointing towards the location of the sedml and sbml files"""
@@ -1140,7 +1156,7 @@ def run_biosimulators_remotely(sedml_file_name,
remote_output_dir = os.path.join(test_folder, remote_output_dir)
download_links_dict = dict()
- for e in engines.keys():
+ for e in ENGINES.keys():
download_link = run_biosimulators_remote(e, sedml_file_name, sbml_file_name)
download_links_dict[e] = download_link
@@ -1190,14 +1206,13 @@ def run_biosimulators_remotely(sedml_file_name,
def run_biosimulators_locally(sedml_file_name,
sbml_file_name,
d1_plots_local_dir,
- engines=engines,
test_folder='tests'):
results_local = {}
output_folder = 'local_results'
local_output_dir = os.path.join(test_folder, output_folder)
- for e in engines.keys():
+ for e in ENGINES.keys():
print('Running ' + e)
local_output_dir_e = os.path.abspath(os.path.join(local_output_dir, e))
print(local_output_dir_e)
@@ -1216,37 +1231,48 @@ def run_biosimulators_locally(sedml_file_name,
return results_local
+
def create_combined_results_table(results_remote,
results_local,
sedml_file_name,
sbml_file_name,
d1_plots_local_dir,
d1_plots_remote_dir,
- engines=engines,
test_folder='tests'):
-
- results_table_remote = create_results_table(results_remote, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_remote_dir)
- results_table_local = create_results_table(results_local, types_dict, sbml_file_name, sedml_file_name, engines, d1_plots_local_dir)
-
- # rename cols to distinguish between local and remote results except for Engine column
- results_table_remote.columns = [str(col) + ' (R)' if col != 'Engine' else str(col) for col in results_table_remote.columns]
- results_table_local.columns = [str(col) + ' (L)' if col != 'Engine' else str(col) for col in results_table_local.columns]
- # combine remote and local results
- combined_results = pd.merge(results_table_remote, results_table_local, on='Engine', how='outer')
- combined_results = combined_results.reindex(columns=['Engine'] + sorted(combined_results.columns[1:]))
-
- cols_order = ['Engine', 'pass / FAIL (R)', 'pass / FAIL (L)',\
- 'Compat (R)', 'Compat (L)', \
- 'Type (R)', \
- 'Error (R)', 'Error (L)', \
- 'd1 (R)', 'd1 (L)']
+ suffix_remote = ' (R)'
+ suffix_local = ' (L)'
+
+ # 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)
+ results_table_local = create_results_table(results_local, sbml_file_name, sedml_file_name, d1_plots_local_dir)
+
+ # Rename columns to distinguish between local and remote results except for Engine column
+ results_table_remote.columns = [f"{col}{suffix_remote}" if col != ENGINE else col for col in results_table_remote.columns]
+ results_table_local.columns = [f"{col}{suffix_local}" if col != ENGINE else col for col in results_table_local.columns]
+
+ # Combine remote and local results
+ combined_results = pd.merge(results_table_remote, results_table_local, on=ENGINE, how='outer')
+ combined_results = combined_results.reindex(columns=[ENGINE] + sorted(combined_results.columns[1:]))
+ combined_results[COMPAT] = combined_results[f"{COMPAT}{suffix_remote}"]
+ combined_results.drop(columns=[f"{COMPAT}{suffix_remote}", f"{COMPAT}{suffix_local}"], inplace=True)
+
+ # Define the order of columns
+ cols_order = [
+ ENGINE,
+ COMPAT,
+ f"{PASS_FAIL}{suffix_remote}", f"{PASS_FAIL}{suffix_local}",
+ f"{ERROR}{suffix_remote}", f"{ERROR}{suffix_local}",
+ f"{TYPE}{suffix_remote}",
+ f"{D1}{suffix_remote}", f"{D1}{suffix_local}"
+ ]
combined_results = combined_results[cols_order]
+ # Save the results to a Markdown file with utf-8 encoding
path_to_results = os.path.join(test_folder, 'results_compatibility_biosimulators.md')
print('Saving results to:', path_to_results)
- with open(path_to_results, 'w') as f:
+ with open(path_to_results, 'w', encoding='utf-8') as f:
f.write(combined_results.to_markdown())
print('Number of columns in md table:', len(combined_results.columns))
@@ -1260,17 +1286,17 @@ def run_biosimulators_remotely_and_locally(sedml_file_name,
sbml_file_name,
d1_plots_remote_dir,
d1_plots_local_dir,
- engines=engines, test_folder='tests'):
+ test_folder='tests'):
results_remote = run_biosimulators_remotely(sedml_file_name=sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_remote_dir=d1_plots_remote_dir,
- engines=engines, test_folder=test_folder)
+ test_folder=test_folder)
results_local = run_biosimulators_locally(sedml_file_name=sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_local_dir=d1_plots_local_dir,
- engines=engines, test_folder=test_folder)
+ test_folder=test_folder)
results_table = create_combined_results_table(results_remote,
results_local,
@@ -1278,7 +1304,6 @@ def run_biosimulators_remotely_and_locally(sedml_file_name,
sbml_file_name=sbml_file_name,
d1_plots_local_dir=d1_plots_local_dir,
d1_plots_remote_dir=d1_plots_remote_dir,
- engines=engines,
test_folder=test_folder)
return results_table
\ No newline at end of file