From 16688f2a12a792b138f36233a28fd6726d89d294 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 9 Oct 2024 11:47:18 +0100
Subject: [PATCH 01/13] Add XFAIL for SBML incompatible engines
---
.../results_compatibility_biosimulators.md | 46 +++++++++----------
utils/__init__.py | 17 +++++--
2 files changed, 36 insertions(+), 27 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index c558cede..7894610c 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 amicipass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amiciDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```bionetgen
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 bionetgenXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```boolnet
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 boolnetXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
XFAIL
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 brian2XFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 copasiDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```gillespy2
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 gillespy2Details
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```ginsim
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 ginsimXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 libsbmlsimDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```masspy
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```neuron
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 neuronXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```opencor
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 opencorXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```pyneuroml
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 pyneuromlXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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/tmph18zw1q1/./LEMS_NML2_Ex9_FN.sbml could not be imported:
File /tmp/tmph18zw1q1/./LEMS_NML2_Ex9_FN.sbml.xml does not existDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```rbapy
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 rbapyXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```smoldyn
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. [] are compatible with smoldynXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 telluriumDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```vcell
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 xppXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```
{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
+ # pass / FAIL (if XFAIL no colour or img, if pass, green square)
results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'\
{x}' if x == 'FAIL' \
- else f' {x}')
+ else f' {x}' 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))
@@ -1121,7 +1122,15 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng
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))))
-
+ # list of sbml uncompatible engines fetched from engines dict
+ sbml_incompatible_engines = [e for e in engines.keys() if 'sbml' not in engines[e]['formats'][0]]
+ # change any fails for sbml incompatible engines to XFAIL, for both pass / FAIL and Compat colums
+ for engine in sbml_incompatible_engines:
+ results_table.loc[results_table['Engine'] == engine, 'pass / FAIL'] = 'XFAIL'
+ compatibility_content = check_file_compatibility_test(engine, types_dict, sbml_filepath, sedml_filepath)
+ results_table.loc[results_table['Engine'] == engine, 'Compat'] = collapsible_content(compatibility_content[1], title='XFAIL')
+ # results_table.loc[results_table['Engine'] == engine, 'Compat'] = 'XFAIL'
+
results_table['Engine'] = results_table['Engine'].apply(lambda x: collapsible_content(f'{engines[x]["url"]}
{engines[x]["status"]}', x))
return results_table
From 5309b3e78e713374ddfda122896d24044514b2f8 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 9 Oct 2024 13:19:05 +0100
Subject: [PATCH 02/13] update engines dict
---
utils/__init__.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/utils/__init__.py b/utils/__init__.py
index 7122a053..f007496a 100644
--- a/utils/__init__.py
+++ b/utils/__init__.py
@@ -29,7 +29,7 @@
'status': ""
},
'brian2': {
- 'formats': [('nml', 'sedml'), ('lems', 'sedml'), ('sbml', 'sedml')],
+ 'formats': [('nml', 'sedml'), ('lems', 'sedml')],
'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
'status': ""
},
@@ -79,7 +79,7 @@
'status': ""
},
'netpyne': {
- 'formats': [('sbml', 'sedml')],
+ 'formats': [('nml', 'sedml'), ('lems', 'sedml')],
'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/',
'status': ""
},
From e0f4f9a05185348789b202c93c25988de52f56fe Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 23 Oct 2024 10:28:40 +0100
Subject: [PATCH 03/13] add table with and without XFAIL to compare
---
.../results_compatibility_biosimulators.md | 46 +++++++++----------
...ts_compatibility_biosimulators_no_XFAIL.md | 23 ++++++++++
utils/__init__.py | 4 +-
3 files changed, 48 insertions(+), 25 deletions(-)
create mode 100644 SBML/tests/results_compatibility_biosimulators_no_XFAIL.md
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index 7894610c..e5e2dc58 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
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 amiciDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```bionetgen
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 bionetgenXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```boolnet
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 boolnetXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```brian2
https://docs.biosimulators.org/Biosimulators_pyNeuroML/
XFAIL
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 brian2XFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 copasiDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```gillespy2
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 gillespy2Details
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```ginsim
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 ginsimXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 libsbmlsimDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```masspy
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```neuron
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 neuronXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```opencor
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 opencorXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```pyneuroml
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 pyneuromlXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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/tmph18zw1q1/./LEMS_NML2_Ex9_FN.sbml could not be imported:
File /tmp/tmph18zw1q1/./LEMS_NML2_Ex9_FN.sbml.xml does not existDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```rbapy
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 rbapyXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```smoldyn
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. [] are compatible with smoldynXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 telluriumDetails
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```vcell
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 xppXFAIL
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
```Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.')```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 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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetXFAIL
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/
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 brian2XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', '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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimXFAIL
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/
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 netpyneXFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', '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/
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 neuronXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorXFAIL
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/
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 pyneuromlXFAIL
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/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```rbapy
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 rbapyXFAIL
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
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldynXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppXFAIL
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```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 amiciFAIL
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```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```FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', '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```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```pass
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```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 copasipass
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 gillespy2FAIL
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```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 libsbmlsimpass
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```FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', '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```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```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```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```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/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```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```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```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 telluriumpass
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```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 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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetXFAIL
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/
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 brian2XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', '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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimXFAIL
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/
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 netpyneXFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', '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/
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 neuronXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorXFAIL
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/
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 pyneuromlXFAIL
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/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```rbapy
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 rbapyXFAIL
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
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldynXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppXFAIL
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 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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetXFAIL
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/
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 brian2XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', '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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimXFAIL
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/
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 netpyneXFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', '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/
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 neuronXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorXFAIL
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/
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 pyneuromlXFAIL
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/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```rbapy
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 rbapyXFAIL
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
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldynXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppXFAIL
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```?B2>RrC=jb3kO
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delta 2243
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diff --git a/SBML/tests/d1_plots_local/gillespy2_d1.pdf b/SBML/tests/d1_plots_local/gillespy2_d1.pdf
index ab45e940fcc956e07527353b6111c7487d19b2ab..b91cda5143fc07e9d70f4199f9ed78f343b41e8f 100644
GIT binary patch
delta 23
fcmZ4My4H2W2RSZ710!QY17l-D%gw*!HZubNXH^I#
delta 23
fcmZ4My4H2W2RSYS3nK$VGZP~di_O2}HZubNXWj@g
diff --git a/SBML/tests/d1_plots_local/ginsim_d1.pdf b/SBML/tests/d1_plots_local/ginsim_d1.pdf
index a935f8ef5747c402b87737be58907e6b10d663f4..e32e94727fe97fc2feee26cdb261ba7ae223143e 100644
GIT binary patch
delta 23
ecmdm^w?}V7vfswJHfw8fX@#a*K>r4Pxw+8h9
delta 23
ecmdm^w?}V7vr4PyKnDQ;
diff --git a/SBML/tests/d1_plots_local/libsbmlsim_d1.pdf b/SBML/tests/d1_plots_local/libsbmlsim_d1.pdf
index 427e0d59cfc38895a6d521f57ff9e66c37bf244e..fcb7793a595ca5a6aeb8f3d10804e3d08cc66343 100644
GIT binary patch
delta 23
ecmdm7w7Ftwz3zz|EAqVCF
diff --git a/SBML/tests/d1_plots_local/masspy_d1.pdf b/SBML/tests/d1_plots_local/masspy_d1.pdf
index b292927cbe1661e92df99ced7b2b06d4c3c257b5..cffa17f0f80a1fc77d7227ae60eb3f652bf69364 100644
GIT binary patch
delta 23
ecmdm^w?}V7vfswJHfw8f%+2&M{>r4Px&<6Pc
delta 23
ecmdm^w?}V7vvm%>r4PyF$Vtt
diff --git a/SBML/tests/d1_plots_local/pysces_d1.pdf b/SBML/tests/d1_plots_local/pysces_d1.pdf
index db6aa474b8adfe794c7e06a0dde8b9f02df8629d..2a848d8cfdd50db752d83a5334ea68c3b946c581 100644
GIT binary patch
delta 57
zcmdm^w?}V7oCvd}p3&q)5qlLNt*M~zT$Gwvl9`|9l30?epy6U=WME`sXkcV)Xkct?
LYP9)?NCguB>^2Zd
delta 57
zcmdm^w?}V7oCvdpp2_4y5qlLNt*M~zT$Gwvl9`|9l30?epy6U=WME`sU}0onXl7z;
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diff --git a/SBML/tests/d1_plots_local/rbapy_d1.pdf b/SBML/tests/d1_plots_local/rbapy_d1.pdf
index 3281608ba150595812a0b218a65fe64a07967d57..45f3a5842a93ce196b156575a5f2b683f2041181 100644
GIT binary patch
delta 23
ecmdm^w?}V7vfswJHfw8fv+2&M{>r4Px-Uj;s
delta 23
ecmdm^w?}V7vr4PyGY0fswI+nX#d
diff --git a/SBML/tests/d1_plots_remote/boolnet_d1.pdf b/SBML/tests/d1_plots_remote/boolnet_d1.pdf
index 0e013d23552ed19f83cea397aeb3bed94989311e..02a96d5b1ebe767d1ed3a45ef344e34a51080009 100644
GIT binary patch
delta 23
ecmX@4cSvtTvfswI+nX#d<;pSA4yG#IC=LZP@
delta 23
ecmX@4cSvtTv
diff --git a/SBML/tests/d1_plots_remote/cbmpy_d1.pdf b/SBML/tests/d1_plots_remote/cbmpy_d1.pdf
index d9e3612911c5ae6f996ce062650d3c813992cc59..d9590df01fd8695ef2471f04200a9f7360ac862f 100644
GIT binary patch
delta 23
ecmX@4cSvtTvfswI+nX#d<@#a*KyG#IC^9Kt6
delta 23
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diff --git a/SBML/tests/d1_plots_remote/gillespy2_d1.pdf b/SBML/tests/d1_plots_remote/gillespy2_d1.pdf
index 7b208ee713cfa7c9b3e5be566a21b03572c5eb92..600e22f0044132c5ad28e717ef45d734f2064f82 100644
GIT binary patch
delta 23
fcmdn&y4iKZ2RSZ710!PtGh;(z%gw*!b}|D1XqX5*
delta 23
fcmdn&y4iKZ2RSYS3nK$VBNGEt^Uc5Hb}|D1XuAkK
diff --git a/SBML/tests/d1_plots_remote/ginsim_d1.pdf b/SBML/tests/d1_plots_remote/ginsim_d1.pdf
index 8f0b0dfe94c32a56b255918f1b56eab0e973a465..46b2b33c4b6e7b45400840c8f9b242e82d5ea3ba 100644
GIT binary patch
delta 23
ecmX@4cSvtTvfswI+nX#dX@#a*KyG#IC`UeaE
delta 23
ecmX@4cSvtTvfswI+nX#dX`Q}uSyG#ID5(f|f
delta 23
ecmX@4cSvtTv*o+l
delta 57
zcmX@4cSvtToCvdpp2_4y5qlLNt;wbDT$Gwvl9`|9l30?epy6U=WME`sU}0onXk=n&
LV7d8-NF5UZ>{k#@
diff --git a/SBML/tests/d1_plots_remote/rbapy_d1.pdf b/SBML/tests/d1_plots_remote/rbapy_d1.pdf
index b1afd78bbb8a7f5c1a0156c9dc5bdef4ba5aa685..1c4dc9853eb32fb029e343f432c8c3772ea1fc6f 100644
GIT binary patch
delta 23
ecmX@4cSvtTvfswI+nX#d%$>vm%yG#ID2L}!S
delta 23
ecmX@4cSvtTvamicihttps://docs.biosimulators.org/Biosimulators_AMICI/
| pass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicipass
The file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amicibionetgen
https://docs.biosimulators.org/Biosimulators_BioNetGen/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenXFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgenCAEE
CombineArchiveExecutionErrorDetails
The COMBINE/OMEX did not execute successfully:
The SED document did not execute successfully:
Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` 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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnetXFAIL
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/
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 brian2XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', '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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsimXFAIL
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/
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 netpyneXFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', '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/
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 neuronXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencorXFAIL
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/
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 pyneuromlXFAIL
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/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```rbapy
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 rbapyXFAIL
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
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldynXFAIL
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/
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xppXFAIL
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 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/
XFAIL
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/
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 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 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 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 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 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 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 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/
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 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/
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 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/
XFAIL
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/
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 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 pyscesCAEE
CombineArchiveExecutionErrorDetails
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?
Details
```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/
XFAIL
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
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] 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 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 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```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 amiciFAIL
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```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```FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with brian2FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with brian2. ['NeuroML', 'SED-ML', 'LEMS', '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```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```pass
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```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 copasipass
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 gillespy2FAIL
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```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 libsbmlsimpass
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```FAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with netpyneFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with netpyne. ['NeuroML', 'SED-ML', 'LEMS', '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```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```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```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```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/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```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```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```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 telluriumpass
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```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```
{engines[x]["status"]}', x))
From 13a2409495e7f8fe0ec34cba28e0cdb9afc632e4 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Wed, 23 Oct 2024 16:20:17 +0100
Subject: [PATCH 10/13] change colour coding, refactor table creation, update
results table
---
SBML/tests/d1_plots_local/amici_d1.pdf | Bin 13644 -> 13644 bytes
SBML/tests/d1_plots_local/bionetgen_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/boolnet_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/cbmpy_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/cobrapy_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/copasi_d1.pdf | Bin 14669 -> 14669 bytes
SBML/tests/d1_plots_local/gillespy2_d1.pdf | Bin 8877 -> 8877 bytes
SBML/tests/d1_plots_local/ginsim_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/libsbmlsim_d1.pdf | Bin 14643 -> 14643 bytes
SBML/tests/d1_plots_local/masspy_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/pysces_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/rbapy_d1.pdf | Bin 5948 -> 5948 bytes
SBML/tests/d1_plots_local/tellurium_d1.pdf | Bin 14664 -> 14664 bytes
SBML/tests/d1_plots_remote/amici_d1.pdf | Bin 13650 -> 13650 bytes
SBML/tests/d1_plots_remote/bionetgen_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/boolnet_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/cbmpy_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/cobrapy_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/copasi_d1.pdf | Bin 14675 -> 14675 bytes
SBML/tests/d1_plots_remote/gillespy2_d1.pdf | Bin 8883 -> 8883 bytes
SBML/tests/d1_plots_remote/ginsim_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/libsbmlsim_d1.pdf | Bin 14649 -> 14649 bytes
SBML/tests/d1_plots_remote/masspy_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/pysces_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/rbapy_d1.pdf | Bin 5954 -> 5954 bytes
SBML/tests/d1_plots_remote/tellurium_d1.pdf | Bin 14670 -> 14670 bytes
.../results_compatibility_biosimulators.md | 46 ++++----
SBML/tests/table.md | 6 -
SBML/tests/test_colour_coding_table.py | 11 --
utils/__init__.py | 111 +++++++++++-------
30 files changed, 92 insertions(+), 82 deletions(-)
delete mode 100644 SBML/tests/table.md
delete mode 100644 SBML/tests/test_colour_coding_table.py
diff --git a/SBML/tests/d1_plots_local/amici_d1.pdf b/SBML/tests/d1_plots_local/amici_d1.pdf
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diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index cfb92fad..fd1a3679 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compat | pass / FAIL (R) | pass / FAIL (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) |
-|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | 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 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/
XFAIL
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/
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 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 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 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 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 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 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 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/
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 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/
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 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/
XFAIL
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/
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 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 pyscesCAEE
CombineArchiveExecutionErrorDetails
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?
Details
```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/
XFAIL
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
XFAIL
The file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. ['Smoldyn', 'SED-ML'] 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 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 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 simulationspass
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:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```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
{engines[x]["status"]}', x))
+ results_table[indexname_engine] = results_table[indexname_engine].apply(lambda x: collapsible_content(f'{engines[x]["url"]}
{engines[x]["status"]}', x))
return results_table
@@ -1221,6 +1231,7 @@ def run_biosimulators_locally(sedml_file_name,
return results_local
+
def create_combined_results_table(results_remote,
results_local,
sedml_file_name,
@@ -1230,31 +1241,47 @@ def create_combined_results_table(results_remote,
engines=engines,
test_folder='tests'):
+ # Define constants inside the function
+ colname_error = 'Error'
+ colname_pass_fail = 'pass / FAIL'
+ colname_type = 'Type'
+ colname_compat = 'Compat'
+ colname_d1 = 'd1'
+ indexname_engine = 'Engine'
+
+ suffix_remote = ' (R)'
+ suffix_local = ' (L)'
+
+ # Create results tables for remote and local results
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:]))
- combined_results['Compat'] = combined_results['Compat (R)']
- combined_results.drop(columns=['Compat (R)', 'Compat (L)'], inplace=True)
-
- cols_order = ['Engine', \
- 'Compat', \
- 'pass / FAIL (R)', 'pass / FAIL (L)',\
- 'Type (R)', \
- 'Error (R)', 'Error (L)', \
- 'd1 (R)', 'd1 (L)']
+ # Rename columns to distinguish between local and remote results except for Engine column
+ results_table_remote.columns = [f"{col}{suffix_remote}" if col != indexname_engine else col for col in results_table_remote.columns]
+ results_table_local.columns = [f"{col}{suffix_local}" if col != indexname_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=indexname_engine, how='outer')
+ combined_results = combined_results.reindex(columns=[indexname_engine] + sorted(combined_results.columns[1:]))
+ combined_results[colname_compat] = combined_results[f"{colname_compat}{suffix_remote}"]
+ combined_results.drop(columns=[f"{colname_compat}{suffix_remote}", f"{colname_compat}{suffix_local}"], inplace=True)
+
+ # Define the order of columns
+ cols_order = [
+ indexname_engine,
+ colname_compat,
+ f"{colname_pass_fail}{suffix_remote}", f"{colname_pass_fail}{suffix_local}",
+ f"{colname_error}{suffix_remote}", f"{colname_error}{suffix_local}",
+ f"{colname_type}{suffix_remote}",
+ f"{colname_d1}{suffix_remote}", f"{colname_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))
From 39711822676c6a676b46c535240516bc219ef4e3 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 24 Oct 2024 18:58:10 +0100
Subject: [PATCH 11/13] refactor engines and types_dict to use constants from
utils and fix collapsible content xfail in compat col
---
.../results_compatibility_biosimulators.md | 22 +--
.../tests/test_compatibility_biosimulators.py | 6 +-
.../test_creation_combined_results_table.py | 3 +-
utils/__init__.py | 153 ++++++++----------
4 files changed, 86 insertions(+), 98 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index fd1a3679..f0658b5a 100644
--- a/SBML/tests/results_compatibility_biosimulators.md
+++ b/SBML/tests/results_compatibility_biosimulators.md
@@ -1,23 +1,23 @@
-| | Engine | Compat | pass / FAIL (R) | pass / FAIL (L) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) |
+| | Engine | Compatibility | pass / FAIL (R) | pass / FAIL (L) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) |
|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------|:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | 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 amiciamici
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 simulationspass
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 gillespy2cbmpy
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
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:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```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
CombineArchiveExecutionErrorpysces
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:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```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```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 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
{engines[x]["status"]}', x))
+ # 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"""
@@ -1155,7 +1155,7 @@ 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
@@ -1205,14 +1205,13 @@ 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)
@@ -1238,42 +1237,33 @@ def create_combined_results_table(results_remote,
sbml_file_name,
d1_plots_local_dir,
d1_plots_remote_dir,
- engines=engines,
test_folder='tests'):
-
- # Define constants inside the function
- colname_error = 'Error'
- colname_pass_fail = 'pass / FAIL'
- colname_type = 'Type'
- colname_compat = 'Compat'
- colname_d1 = 'd1'
- indexname_engine = 'Engine'
suffix_remote = ' (R)'
suffix_local = ' (L)'
# Create results tables for remote and local results
- 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)
+ 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 != indexname_engine else col for col in results_table_remote.columns]
- results_table_local.columns = [f"{col}{suffix_local}" if col != indexname_engine else col for col in results_table_local.columns]
+ 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=indexname_engine, how='outer')
- combined_results = combined_results.reindex(columns=[indexname_engine] + sorted(combined_results.columns[1:]))
- combined_results[colname_compat] = combined_results[f"{colname_compat}{suffix_remote}"]
- combined_results.drop(columns=[f"{colname_compat}{suffix_remote}", f"{colname_compat}{suffix_local}"], inplace=True)
+ 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 = [
- indexname_engine,
- colname_compat,
- f"{colname_pass_fail}{suffix_remote}", f"{colname_pass_fail}{suffix_local}",
- f"{colname_error}{suffix_remote}", f"{colname_error}{suffix_local}",
- f"{colname_type}{suffix_remote}",
- f"{colname_d1}{suffix_remote}", f"{colname_d1}{suffix_local}"
+ 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]
@@ -1295,17 +1285,17 @@ 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,
@@ -1313,7 +1303,6 @@ 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
From 0a3d29437544c1ac1cea4a89252454e7b9181d6a Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Thu, 24 Oct 2024 19:06:09 +0100
Subject: [PATCH 12/13] remove engines from input
---
SBML/tests/test_biosimulators_local.py | 5 +----
SBML/tests/test_biosimulators_remote.py | 5 +----
2 files changed, 2 insertions(+), 8 deletions(-)
diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py
index d3ddf1e5..0f59f7a5 100644
--- a/SBML/tests/test_biosimulators_local.py
+++ b/SBML/tests/test_biosimulators_local.py
@@ -12,9 +12,6 @@
import utils
import argparse
-engines = utils.engines
-types_dict = utils.types_dict
-
# Save the current working directory
cwd = os.getcwd()
print('Current working directory:', cwd)
@@ -44,5 +41,5 @@
results_local = utils.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)
\ No newline at end of file
diff --git a/SBML/tests/test_biosimulators_remote.py b/SBML/tests/test_biosimulators_remote.py
index 75b2b3ba..20896eb7 100644
--- a/SBML/tests/test_biosimulators_remote.py
+++ b/SBML/tests/test_biosimulators_remote.py
@@ -12,9 +12,6 @@
import utils
import argparse
-engines = utils.engines
-types_dict = utils.types_dict
-
# Save the current working directory
cwd = os.getcwd()
print('Current working directory:', cwd)
@@ -44,5 +41,5 @@
results_remote = utils.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)
\ No newline at end of file
From c82e511b6254da3e8a51b90b1e2b0b9bb14193b8 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 28 Oct 2024 10:00:13 +0000
Subject: [PATCH 13/13] add space after emoji, capitalise all pass, fail, xfail
and warning, add warning emoji for xfails
---
.../results_compatibility_biosimulators.md | 42 +++++++++----------
utils/__init__.py | 21 +++++-----
2 files changed, 32 insertions(+), 31 deletions(-)
diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md
index f0658b5a..1cf019a0 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) | Error (R) | Error (L) | Type (R) | d1 (R) | d1 (L) |
|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------|:------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------|
-| 0 | 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:
class 'AssertionError':
Unable to generate Stoichiometric Matrix! model has:
0 reactions
0 species
what did you have in mind?
Details
```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
ModuleNotFoundErroramici
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