Merging refget docs.

[andrewyatz]

Taken the docs from Beth and integrated with previous PR request. Major changes

• Fixed error concerning coordinates with refget and Ensembl. Refget is 0-based
• Added more information about different types of retrieval
• Added a python notebook example (need to know how to link this)
• Moved docs to a peer of GraphQL
• Added information about odd things when using refget and alternative 3rd party clients
• Added more metadata examples

[azangru]

@bethflint

[bethflint]

@bethflint

This should be fixed now

[azangru]

I am confused about the expected fate of this Jupyter notebook file. We don't have any provisions for such files in the help&docs system. We can't show them as an interactive notebook; we don't register them during the build process, which means that we can't even link to them from a help page. You could transform it into a separate markdown file with a huge code block and link to it if you want users to see it. Or we could add a link from a help page to the ipynb file directly in the repo — GitHub runs Jupyter notebooks.

[andrewyatz]

The second option was my feeling as the right way forward. I didn't think GitHub could run a notebook, but could render the notebook. I had assumed once on the main branch, we could create a Binder link which their website seems good at generating.

Main thing is to get it into the repo so we can generate the link. At the moment it will be dead unless we can inject URLs into Markdown files which can have the current build branch injected into the URL

[azangru]

I didn't think GitHub could run a notebook, but could render the notebook.

Yes, you are right. Sorry; I assumed when I saw the actual checksums in the bottom of the rendered file here that Github actually executed the notebook code 🙂

I had assumed once on the main branch, we could create a Binder link which their website seems good at generating.

Got it! Good idea.