rkcook312
commented
1 year ago maths equation on eLife preprint displayed OK?
Open nlisgo opened 1 year ago
rkcook312
commented
1 year ago maths equation on eLife preprint displayed OK?
fred-atherden
commented
1 year ago Nice spot @rkcook312.
In short - no, but we have to live with it.
The main problem is that bioRxiv capture equations as images. When these are inline it's quite difficult without knowing the content of the image what size to display them (it's also difficult when not inline, but less so).
The best way around this would be for bioRxiv to capture these in a machine readable format - something we hope they will in the near future (we can also look into ways to OCR these images).
In the meantime, we can expect some poorly sized inline equations - and we may be able to do more on the platform side of things to get these rendered in a more legible way. Since that's a platform based solution (e.g. CSS) it doesn't really affect the content, so I think we should proceed as is.
Hope that makes sense, but LMK if not!
"msas": "Evolutionary Biology" "msid": "86899" "preprintDoi": "10.1101/2023.01.28.525977" "Reviewed Preprint posted": "2023-09-01" "Sent for peer review": "2023-03-23" "Posted to bioRxiv": "2023-01-30" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.01.28.525977v1/")
[PLACE PDF URL HERE WHEN AVAILABLE] See step 7
Step 1. Inform bioRxiv
Who can help: @QueenKraken, @nlisgo, @scottaubrey
Step 2. Create preview of manuscript
Who can help: @fred-atherden, @nlisgo, @scottaubrey
Pull request: [PLACE LINK TO PULL REQUEST HERE]
Detailed instructions: https://github.com/elifesciences/enhanced-preprints-data#add-a-manuscript
Step 3: Awaiting public reviews and QC
Who can help: Production team
Who can help: Editorial team
Example
``` "msas": "Genetics and Genomics", "Neuroscience" "msid": "84628" "version": "1" "preprintDoi": "10.1101/2022.10.28.514241" "articleType": "Reviewed Preprint" "status": "Published from the original preprint after peer review and assessment by eLife." "Reviewed Preprint posted": "2023-01-02" "Sent for peer review": "2022-10-28" "Posted to bioRxiv": "2022-11-21" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2022.10.28.514241v1") Editors: Reviewing Editor Michael B Eisen University of California, Berkeley, United States Senior Editor Michael B Eisen University of California, Berkeley, United States ```Step 4: Modify manuscripts.json (no PDF)
Pull request: [PLACE LINK TO PULL REQUEST HERE] #enhanced-preprint comment thread: [PLACE LINK TO COMMENT HERE]
Instructions to modify manuscripts.json
- Visit: https://github.com/elifesciences/enhanced-preprints-client/actions/workflows/publish-manuscript.yaml - Click: Run workflow - Complete the form and click "Run workflow" - A successful run should result in a new pull request at https://github.com/elifesciences/enhanced-preprints-client/pulls - Open the pull request and click the "Ready for review" button to trigger tests - Once the tests pass and you are happy with the changes the PR can be merged Example pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/334/files Once the pull request is merged in it should be available a few minutes later.Request that a doi
Post the following in #enhanced-preprint:
Step 5: Awaiting search reindex
The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.
Additional info
If needed, the jenkins pipeline to reindex search can be triggered sooner. https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/Step 6: Published! Request PDF generation
#enhanced-preprint comment thread: [PLACE LINK TO COMMENT HERE]
Post the following to the #enhanced-preprint on slack:
Step 7: Introduce PDF to data folder and git repo
Detailed instructions: https://github.com/elifesciences/enhanced-preprints-data#add-a-pdf
Step 8: Add PDF url to manuscripts.json
[PLACE LINK TO PULL REQUEST HERE]
Instructions to add PDF url to manuscripts.json
- Visit: https://github.com/elifesciences/enhanced-preprints-client/actions/workflows/add-pdf-url-to-manuscript.yaml - Click: Run workflow - Complete the form and click "Run workflow" - A successful run should result in a new pull request at https://github.com/elifesciences/enhanced-preprints-client/pulls - Open the pull request and click the "Ready for review" button to trigger tests - Once the tests pass and you are happy with the changes the PR can be merged Example pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/397/files Once the pull request is merged in it should be available a few minutes later.Step 9: Done!