/include_schema

Primary LanguagePython

INCLUDE schema

Test LinkML-based schema for INCLUDE project

What is this?

This is a GitHub template for a LinkML project.

It allows you to create a project for your schema as quickly as possible. It takes care of generating a beautiful readthedocs themed site, as well as downstream artefacts, including:

  • JSON-Schema
  • ShEx
  • OWL
  • RDF (direct mapping)
  • SQL DDL (TODO)
  • TSV/CSV reports

Quickstart

  1. Click the big green "Use this template" button on this page
  2. Name your repo according to your schema, e.g. my_awesome_schema, and clone it
  3. Modify this file (README.md) to have a brief description of your project (keep your core docs in schema)
  4. Rename the schema file in src/schema. Keep the .yaml suffix
  5. Modify the schema, add your own classes and slots.
  6. Type make install all to build your downstream artefacts (jsonschema, owl, etc)
  7. Type make gh-deploy to make a github pages website

Minor tweak: for now you must pass in the name of your schema on the command line, e.g.

make all SCHEMA_NAME=my_awesome_schema

How it works

This repo is a GitHub "template" repo. When you "Use this template" it will make a copy for your project.

Everything is orchestrated by a generic single Makefile. For this to work you should follow certain conventions:

  • Keep your schema in src/schema
  • Use the .yaml suffix for all schema files
  • Use the suggested directory layout here.

To run the Makefile you will need Python (>=3.7), and biolinkml. You can type:

make install

or equivalently

. environment.sh
pip install -r requirements.txt

You can make specific targets, e.g

make stage-jsonschema

Use the all target to make everything

Note to redeploy documentation all you need to do is:

make gh-deploy

That's it!

The Makefile takes care of dependencies. Downstream files are only rebuilt if source files change.

Documentation framework

You can change the theme by editing mkdocs.yml

Do not edit docs in place. They are placed in the docs dir by make stage-docs.

You can add your own docs to `src/docs/

Note that docs are actually deployed on the gh-pages branch, but you don't need to worry about this. Just type:

make gh-deploy

The template site is deployed on

http://cmungall.github.io/linkml-template

But this is not very interesting as it is a toy schema

TODO

  • GitHub actions
  • Making separate modules for each import