Quick and dirty markdown

[gaurav]

A quick-and-dirty implementation of Markdown generation (to https://www.ggvaidya.com/ga4gh-va-spec/).

This PR includes:

• Some fixes to the schema to ensure that Markdown generation succeeds.
• A Makefile with some targets for locally serving documentation (make docserve) and for publishing documentation to GitHub Pages (make gh-pages).
• An update to the mkdocs and pyproject.toml to add support for the Material theme.

[gaurav]

@sujaypatil96 Here's a list of changes I needed to make to get mkdocs working in this repo:

• Replaced assets/spreadsheets/ga4gh_schemasheets.tsv with the latest spreadsheet.
• Make some changes to schema/ga4gh.yaml
  • Corrections needed in the spreadsheet:
  • exact_mappings sometimes comma separates values, e.g. IAO:0000030, FRBR:Work. This confuses the CURIE parser. A pipe delimiter appears to work (e.g. IAO:0000030 | FRBR:Work), but I'm not sure what the right way to represent multiple IDs in LinkML is.
  • Several slots (e.g. Data Item, hasEvidence Line) or class names (e.g. Information Entity, Research Study) have spaces in their name, which are not allowed by LinkML.
  • Corrections need to be made to schemasheets or LinkML:
  • Types like string, dateTime and so on are created as Classes, which is incorrect -- they should be created as types.
  • Types like string, dateTime and so on conflict with the LinkML types. Either (1) the LinkML types should be used directly, in which case these types should be removed from the spreadsheet, or (2) the ga4gh types should have a different name, such as ga4ghString.
  • Types like string, dateTime and so on don't use is_a to determine if a type has a parent
  • Several slots (e.g. Data Item, hasEvidence Line) or class names (e.g. Information Entity, Research Study) have spaces in their name, which are not allowed by LinkML. schemasheets should either produce an error or replace spaces with underscores.
• Made some changes to mkdocs.yml:
  • docs_dir: docs -> target/docs (this is the directory where Markdown files are generated by gen-markdown)
  • site_dir: mkdocs_html -> site (this is the directory where the HTML files are generated for Google Pages to use)
• Changed theme to material.

[sujaypatil96]

Thank you so much for this comment @gaurav. It was super helpful. I implemented most of the fixes you've recommended above in the latest code on the main branch. Hope you don't mind me closing this PR?

[gaurav]

I think closing this PR is exactly the right call. Thanks, Sujay!