scottgigante-immunai commented 1 year ago

This PR begins to convert paper references to bibtex.

~Not ready to be merged yet~, as we need to handle:

[X] sending the bib to openproblems/website and rendering it;
[X] linking to the references from READMEs;
[ ] rendering the references in the results tables (will need to be fixed in website after results are updated)

Tests passing at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/5RkdFp3K7yuQOi

scottgigante-immunai commented 1 year ago

First attempt is up and running.

Example behaviour: https://deploy-preview-64--openproblems-sca.netlify.app/bibliography/#stuart2019comprehensive takes us direct to the citation

Stuart, T., Butler, A., Hoffman, P., et al., "Comprehensive Integration of Single-Cell Data". Cell, vol. 177, no. 7, pp. 1888-1902.e21, 2019. doi:10.1016/j.cell.2019.05.031.

Open to thoughts, input on style, etc.

See https://github.com/openproblems-bio/website/pull/64

scottgigante-immunai commented 1 year ago

@rcannood @LuckyMD this is ready for review now

LuckyMD commented 1 year ago

I currently don't see how references are linked from the READMEs in the website. Whenever I click on a reference in a README it sends me to the paper link instead (i.e. BioRxiv or nature methods...)

scottgigante-immunai commented 1 year ago

I currently don't see how references are linked from the READMEs in the website. Whenever I click on a reference in a README it sends me to the paper link instead (i.e. BioRxiv or nature methods...)

Here is an example (in the batch integration README).

Note that I didn't update references in the API section of the READMEs as those don't ever make it to the website, but we could change those too if we think it appropriate / preferable.

codecov[bot] commented 1 year ago

Codecov Report

Base: 94.80% // Head: 94.79% // Decreases project coverage by -0.01% :warning:

Coverage data is based on head (5403ecc) compared to base (413aebd). Patch coverage: 97.10% of modified lines in pull request are covered.

Additional details and impacted files

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Convert references to bib #720

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