Test omex

[stellaprins]

To test whether update to github actions works as expected.

[robertvi]

@stellaprins looks like the "Test test_suite output regeneration" action is now failing because we have deleted the test above it in the yml and therefore pymetadata module is no longer installed when the test is run. To fix this you could reorder the tests so that the new "test omex file creation" test is above the "Test test_suite output regeneration" test, then pymetadata module should be available.

[stellaprins]

The new "test omex file creation" test still gives a Docker error

• docker.errors.ContainerError: Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/tellurium' returned non-zero exit status 1

There are two Biosimulators warnings

• The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\x1b[0m\r\n\r\n/root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex is not a valid COMBINE/OMEX archive.\n
• The format of the archive must be [http://identifiers.org/combine.specifications/omex,](http://identifiers.org/combine.specifications/omex%60,) not [http://identifiers.org/combine.specifications:omex.\n](http://identifiers.org/combine.specifications:omex%60./n)'

File "/home/runner/work/SBMLShowcase/SBMLShowcase/SBML/../utils/init.py", line 267, in biosimulators_core
client.containers.run(f"ghcr.io/biosimulators/{engine}",
File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/docker/models/containers.py", line 905, in run
raise ContainerError(
docker.errors.ContainerError: Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/tellurium' returned non-zero exit status 1: b'/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning:\r\n\r\n\x1b[33mCOMBINE/OMEX archive has warnings.\r\n - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\x1b0m\r\n\r\n/root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex is not a valid COMBINE/OMEX archive.\n - The format of the archive must be [http://identifiers.org/combine.specifications/omex, not [http://identifiers.org/combine.specifications:omex.\n](http://identifiers.org/combine.specifications:omex%60./n)'
Error: Process completed with exit code 1.

[robertvi]

pymetadat 0.4.0 is probably an old version https://github.com/OpenSourceBrain/SBMLShowcase/actions/runs/9498644739/job/26177817122?pr=25#step:8:15 I reported this bug to the owner and he fixed it so the url generated will be correct if you can get pip to install the latest version of pymetadata matthiaskoenig/pymetadata#50

[robertvi]

i think the thing about the manifest is only a warning and will not cause it to fail by itself

[robertvi]

pymetadata 0.4.2 requires python >= 3.8 therefore we cannot test omex creation using this package on python 3.8 without supplying our own workaround for the ": instead of / in url" bug
see here

[robertvi]

maybe just skip this one test for v3.8?

[pgleeson]

@robertvi yes, certainly skip py3.8 if there is a package that doesn't work with it. It's nearing "end of life" anyway https://devguide.python.org/versions/

[robertvi]

If we're happy to skip python 3.8 from all the non-omv.yml checks then this should be ready to merge.

[pgleeson]

Is this method a duplication of the method below?

[stellaprins]

Yes, Rob split up the "add_xmlns_sbml_attribute_if_missing" I created into "add_xmlns_sbml_attribute" and "xmlns_sbml_attribute_missing". I think we can delete "add_xmlns_sbml_attribute_if_missing".