Check whether test_suite works after fixing issue with create_omex function

[stellaprins]

After fixing issues with the create_omex function #3, omex files that are accepted on https://run.biosimulations.org can be created (#2).

Try running the test_suite.

[stellaprins]

After fixing issues with create_omex function (see #3), allowing a minimal omex file to be generated (see #2) the same problems remain when trying to run the test_suite.

These are the error messages:

• /root/in/00001-sbml-l3v2-sedml.omexis not a valid COMBINE/OMEX archive.
• The SED-ML file at location./00001-sbml-l3v2-sedml.xmlis invalid.
• Data generatorS1_1is invalid.
• VariableS1_1_sis invalid.
• One or more namespaces required for target/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']are not defined. No namespaces are defined for the target.
• VariableS1_1_cis invalid.
• One or more namespaces required for target/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']are not defined. No namespaces are defined for the target.
• Data generatorS2_1is invalid.
• VariableS2_1_sis invalid.
• One or more namespaces required for target/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']are not defined. No namespaces are defined for the target.
• VariableS2_1_cis invalid.
• One or more namespaces required for target/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']` are not defined. No namespaces are defined for the target.

[stellaprins]

• [x] check whether the minimal omex file SBML\LEMS_NML2_Ex9_FN.omex can be run using run_biosimulators_docker

It fails. This is the resulting log.yml.

[stellaprins]

Try find an omex file to run using run_biosimulators_docker.

https://combinearchive.org/resources/:

• [x] COMBINE Archive Show Case broken link
• [x] examples of the SED-ML L1V3 specification as COMBINE archives

[stellaprins]

Test whether omex files found in examples of the SED-ML L1V3 specification as COMBINE archives run using run_biosimulators_docker.

• [ ] L1V3_vanderpol-sbml