Fix MkDocs build warnings and CI job

[CasperWA]

Description:

Fixes #250

Add attr_list extension to accommodate the width specifications of images.

Remove unresolvable cross-references, re-create resources, or re-direct cross-references.

Update documentation, fixing retrieval and rendering.

Streamline create-api-reference-docs invoke task to be more EMMOntoPy-specific.

This also treats the emmopy/emmocheck.py file differently, when creating the API Reference MarkDown file for it, setting the handling of base/parent classes to False; meaning parent classes should not be considered for the documentation (as this results in warnings from the unittest.case.TestCase class).

Type of change:

• Bug fix.
• New feature.
• Documentation update.

Checklist:

This checklist can be used as a help for the reviewer.

• Is the code easy to read and understand?
• Are comments for humans to read, not computers to disregard?
• Does a new feature has an accompanying new test (in the CI or unit testing schemes)?
• Has the documentation been updated as necessary?
• Does this close the issue?
• Is the change limited to the issue?
• Are errors handled for all outcomes?
• Does the new feature provide new restrictions on dependencies, and if so is this documented?

Comments:

[francescalb]

Why do you want to remove all the links in the .md?

[CasperWA]

Why do you want to remove all the links in the .md?

I don't think I am? Which ones do you mean specifically?
The only links I'm actually removing is the ones to local "owl" files that don't exist?

[francescalb]

Yes, you are right. The should be .ttl files and not local. From: Casper Welzel Andersen ***@***.***> Sent: tirsdag 12. oktober 2021 16.30 To: emmo-repo/EMMO-python ***@***.***> Cc: Francesca Lønstad Bleken ***@***.***>; Review requested ***@***.***> Subject: Re: [emmo-repo/EMMO-python] Fix MkDocs build warnings and CI job (#254) Why do you want to remove all the links in the .md? I don't think I am? Which ones do you mean specifically? The only links I'm actually removing is the ones to local "owl" files that don't exist? - You are receiving this because your review was requested. Reply to this email directly, view it on GitHub<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Femmo-repo%2FEMMO-python%2Fpull%2F254%23issuecomment-941066903&data=04%7C01%7Cfrancesca.l.bleken%40sintef.no%7C0195caa00ba74115062408d98d8cb89a%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637696457799681331%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=8CXjCtlxh3uRx8nr5JZn03AxtbFL4z6pZbUAsJL4GiY%3D&reserved=0>, or unsubscribe<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALPGADYG5VYEQYJCRYHQGG3UGRA5BANCNFSM5F2O5BPQ&data=04%7C01%7Cfrancesca.l.bleken%40sintef.no%7C0195caa00ba74115062408d98d8cb89a%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637696457799681331%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1E54azfHNn7suVDip3ugHMQEfzHS7eofIvKIoXyvJ9U%3D&reserved=0>. Triage notifications on the go with GitHub Mobile for iOS<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7Cfrancesca.l.bleken%40sintef.no%7C0195caa00ba74115062408d98d8cb89a%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637696457799691291%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=cDv4tEJnlGBz8lCY5%2FdKBhs%2FRvZhM0BOeUpMNrY234g%3D&reserved=0> or Android<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7Cfrancesca.l.bleken%40sintef.no%7C0195caa00ba74115062408d98d8cb89a%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637696457799691291%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=yG21MiXh9eSQBmTcvTxTjTdYmXO4k%2F%2Fs%2FOrfwoCcf7I%3D&reserved=0>.

[CasperWA]

Yes, you are right. The should be .ttl files and not local.

Yeah - I was confused about these lines.

I think maybe they are there because this whole part of the example is taken "out of context" in a way? If it is generated as part of the full EMMO documentation, it might make sense :)

If you have some good alternative targets for the links here, feel free to add suggestions or perhaps direct me to the a base URL where I can find them?

[CasperWA]

This is ready to go with an accepting review.

[francescalb]

I agree, inthe README the only example is using emmo-inferred, which means that it is not using an ontology using the original structure. It is a little difficult to find the correct .ttl files on on the emmo official repository (emmo-repo.github.io). In this example we should point to the 'latest' here, so as not to have an outdated example from the start. Let's therefore skip it for now.