[SCHEMA] Reorganize schema code into a package

[tsalo]

This stems from #885 (comment). The idea is to make the schema code operate as a proper Python package, so we can also start writing tests for it.

We still may want to move schema-related code into a different repository at some point (e.g., bids-schema, pybids), but for now I'd just like to have the code organized nicely within this repo.

Changes proposed:

• Reorganize schemacode into a Python package, so that it can be installed and tests can be written for it.
  • This involves symlinking the schema files in src/schema to tools/schemacode/schemacode/data/schema. Thanks to @effigies for that.
• Write a few initial tests for schemacode. These can be improved in future PRs.
• Add a GitHub Action to run continuous integration for the new package and upload a coverage report to CodeCov.
• Add new schema-related folders to the CODEOWNERS file with myself listed.

[tsalo]

I'm not sure why mkdocs has such a hard time tracking down the schema files in CircleCI. It works fine locally...

EDIT: Of course, it's because, now that schemacode is a package, it's stored in site-packages, away from the rest of the repo!

[tsalo]

My main blocker at the moment is that, as a package, schemacode will end up in site-packages instead of with the bids-specification files. As a result, relative paths to the schema files (which are in src/schema and not tools/schemacode) will break when schemacode is installed. I don't know how to work around that without creating a copy of the schema files in schemacode, which would make it hard to test out changes to the schema.

[effigies]

@tsalo Made several updates. RTD is fixed. The PDF build looks like it needs updating to new modules. I assume you'll be able to figure that out faster than me, but let me know if you want me to tackle it.

[tsalo]

Thanks @effigies! How does it work? It looks like the schema files are duplicated in tools/schemacode/schemacode/data/schema/. Are those files updated automatically when the files in src/schema/ are updated?

[effigies]

It's just a symlink, so they will be copied into the package. If you're going to develop, it probably makes sense to pip install -e so you can keep using the symlink, rather than a frozen snapshot from install time. But from a CI build perspective, it's all based on the current commit, so fine to freeze.

[tsalo]

Awesome! I fixed the module paths, so I think everything is good to go.

[tsalo]

@bendhouseart sorry for not requesting your review earlier. I know you wanted to take a look, though we didn't end up trying out poetry.

[sappelhoff]

I believe that the messed up links only appear in HTML comments in the built site.

I see :| but it's still annoying to have linkchecker now fail until we release ...

But that's not a blocker for this PR, which I approve of!

[yarikoptic]

just some minor comments/suggestions - ok to ignore

[sappelhoff]

I believe that the messed up links only appear in HTML comments in the built site.

I see :| but it's still annoying to have linkchecker now fail until we release ...

We could add a small Python script that checks whether the current commit is tagged (=stable), or not (=dev), and then in CI before building with mkdocs, that Python scripts changes stable to latest in the following line:

bids-specification/mkdocs.yml

Line 2 in 98ca3fa

site_url: https://bids-specification.readthedocs.io/en/stable/

🤔 or would we screw up search engine results with that? I am not very familiar with "canonical URL" metadata in HTML headers.

[tsalo]

We could add a small Python script that checks whether the current commit is tagged (=stable), or not (=dev), and then in CI before building with mkdocs, that Python scripts changes stable to latest

I have no clue if that's possible, but having the ability to update content files with Python scripts within CI would be really useful for adding tooltips (#954). The problem I have been bumping into for that is that the macros-generated content is not available for the auto-linked tooltips to grab onto. Generating the glossary within CI would circumvent that issue, I believe.

That said, I don't even know where to start to do it.

[bendhouseart]

Looked over the changed files and managed to build and install locally w/ setup.py 👍. I'd call it good to go.

Python 3.9.9 (main, Nov 21 2021, 03:22:47)
[Clang 12.0.0 (clang-1200.0.32.29)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import schemacode
>>>

[bendhouseart]

CircleCI disagrees, but eh.

[effigies]

Looks good. A couple bits of code caught my eye as likely able to be simplified. I haven't tested though...

[tsalo]

The built site looks good to me, as does the PDF. Now that we have two approvals, is this alright to merge or do we want to wait 5 days?

Also, thank you to @effigies and @bendhouseart for your reviews!

[effigies]

The 5 days is more for semantic changes than infrastructure.