Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

🧑🏻‍🔬 Citations & bibliography #161

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
Open

🧑🏻‍🔬 Citations & bibliography #161

wants to merge 3 commits into from

Conversation

rowanc1
Copy link
Member

@rowanc1 rowanc1 commented Jun 23, 2023

Working on a first attempt to connect up citations.

citations-in-jupyter

Some things to think about for this PR:

  • figure out some state management for shared components
  • have a bibliography listed at the end of the notebook or article
  • pull out the citation transform, and into some shared library (maybe a new one, because citation-js is big)
  • link up DOIs
  • listen to more than just a single, root bibliography.bib

@rowanc1 rowanc1 added the enhancement New feature or request label Jun 23, 2023
@github-actions
Copy link
Contributor

Binder 👈 Launch a Binder on branch executablebooks/jupyterlab-myst/agoose77/wip-bibliography

rowanc1
rowanc1 commented Jun 23, 2023
View reviewed changes
Copy link
Member Author

@rowanc1 rowanc1 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Some notes!

src/index.ts
import { IRenderMimeRegistry } from '@jupyterlab/rendermime';

import { notebookCellExecuted } from './actions';
import { mystMarkdownRendererFactory } from './mime';
import { citationRenderers } from './myst';
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@agoose77 we need some way to share the citation renderer into the various places we use those renderer. I don't think they necessarily need to be "connected" (i.e. an update to a bib file doesn't really need to force a re-render, but the next render should bring in the right citation).

The way we have done this in the CLI is to have a state manager, that is indexed based on file name, and then we combine citation renderers before we render the markdown.

I think this could work, and maybe that works? Curious if you know of a better way to share state between the plugins?

src/index.ts
Comment on lines +96 to +100
if (renderer) {
citationRenderers[bibFile] = renderer;
} else {
delete citationRenderers[bibFile];
}
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

When the manager changes, we just update the shared state, which is then available next time we render markdown. I don't really think we need to go full: update-the bib when the markdown changes as it could potentially render every single cell.

src/citations.tsx
};
}

export function combineCitationRenderers(renderers: CitationRenderer[]) {
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

A bunch of this is copied from the CLI, we need to create a package, share this functionality and delete it here!

src/index.ts
activate: (app: JupyterFrontEnd) => {
console.log('Using jupyterlab-myst:bibliography');

const bibFile = 'bibliography.bib';
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Right now this only works for a single bib file in the root.

@rowanc1 rowanc1 mentioned this pull request Jun 23, 2023
Open
@rowanc1 rowanc1 force-pushed the agoose77/wip-bibliography branch from 105e29b to f9a0137 Compare July 4, 2023 22:00
@agoose77 agoose77 force-pushed the agoose77/wip-bibliography branch from f9a0137 to 19beaa3 Compare January 22, 2024 13:57
@alanlujan91 alanlujan91 mentioned this pull request Mar 28, 2024
Open
37 tasks
@srprca
Copy link

srprca commented Jul 13, 2024

Hello!

I wanted to try out this preliminary version of citations & bibliography, and so I tried building this extension from this pull request.

When I run pip install -e ".[test]", the build process fails with:

File "/usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 167, in prepare_metadata_for_build_editable
    hook = backend.prepare_metadata_for_build_editable
AttributeError: module 'hatchling.build' has no attribute 'prepare_metadata_for_build_editable'

I Googled for this error, and found the following suggestion: pypa/hatch#1114 (comment)

However, it didn't work for me.

I wonder if this problem is indicative of some mistake on my side...?

Thank you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
enhancement New feature or request
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@rowanc1 @srprca @agoose77