add deprecation protocol for GSC

[mslarae13]

Copying what Sierra Moxen did for NMDC to add deprecation protocol to the GSC.

[mslarae13]

@turbomam @sujaypatil96 Would appreciate your review. I've kept this is draft as i'm expecting some additional updates will be needed or that I missed something!

[sujaypatil96]

This is a great start to implementing a deprecation protocol in MIxS @mslarae13 🚀

I left the above review comments with help from @sierra-moxon 😁 who helped implement the deprecation protocol in NMDC.

Do let me know if you would like me to help with modifications to this PR/branch to appropriate the changes similar to the deprecation guide implementation PR here: https://github.com/microbiomedata/berkeley-schema-fy24/pull/165

[mslarae13]

Thanks @sujaypatil96 !

• Much like the nmdc-schema repo, mixs also has custom jinja templates here: https://github.com/GenomicsStandardsConsortium/mixs/tree/main/src/doc-templates which need to be modified to include the ability to show the "DEPRECATED" text in bright red on documentation pages.

@sujaypatil96 I think I found Sierra's changes but I am not at all familiar with this file... so I've no idea where to put it.. does it matter?

• Add # Class: {{ title }} {% if element.deprecated %} <span style="color: red;"><strong> (DEPRECATED) </strong> {% endif %} to src/doc-templates/class.md.jinja2

• I edited src/doc-templates/enum.md.jinja2 hopefully correctly!

• I need to edit src/doc-templates/slot.md.jinja2.. does it matter where I pasted that chunk of code in? Before or after what you have in that file?

• It is mandatory that every LinkML schema YAML file have an id, which also includes deprecated.yaml: https://github.com/GenomicsStandardsConsortium/mixs/blob/d0590bad7858fa83ab543b18c01f980077e023ce/src/mixs/schema/deprecated.yaml

• Can do! I see mixs.yaml it's id: https://w3id.org/mixs .. How do I make id: https://w3id.org/mixs-deprecated