[REVIEW]: A database of the healthy human spinal cord morphometry in the PAM50 template space #17
Comments
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Hello humans, I'm @roboneuro, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type: For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type: |
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Wordcount for |
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Failed to discover a |
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@valosekj I am working on a solution that will:
I'll let you know today when I confirm proper functionality. |
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@Valosek currently in your book the citations are in plaintext format, not linked to the bibliography you provided ( To fix this issue, I have made a few changes in the rrsg2020/paper repository, which can be reflected here for proper use of citations:
p {
text-align: justify;
}
a {
color: #870000!important;
}
a:hover {
color: brick!important;
}
a:visited {
color: #6f42c1!important;
}
body, h1, h2, h3, h4, h5 {
font-family: 'STIX Two Text';
}
h1 {
color: #342727!important;
}
.caption {
text-align:justify;
line-height:1.25;
font-size:80%
}
#site-navigation {
display: none;
}
#main-content{
margin: 0 auto;
}
.fa, .far, .fas {
color: red;
}
.header-article::after{
content: url('https://neurolibre.org/assets/joss2-b7ea8dd1f24ce2b0825db17e3495576253ba4c64df3384a66354713d76c40a75.svg');
width: 150px;
height: 80px;
position: absolute;
right: 10px;
}
.header-article::before{
content: url('https://raw.githubusercontent.com/neurolibre/brand/b5e10e051a0059824ca2f4204e1288927e551d49/svg/neurolibre_logo.svg');
width: 33px;
height: 33px;
position: absolute;
left: 10px;
}
sphinx:
recursive_update : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update
bibtex_reference_style: author_year
bibtex_default_style: plain
bibtex_tooltips: true
html_static_path: ['_static']
html_css_files: ['custom.css']
bibtex_bibfiles:
- ../paper.bib
🚨 Make sure that the reference directives are NOT between html tags, otherwise they won't be interpreted. Overall, keeping html tags to a minimum is good practice when writing a jupyter book. Unfortunately, there is currently no way to tag/link/reference interactive figures. So those will be followed by a markdown cell containing the caption text, and you'll need to manually enumerate the figures. Eventually, it should look like this: https://preview.neurolibre.org/book-artifacts/rrsg2020/github.com/paper/c0d7479f87cb0ef959ce87ba3a2bffe2ab44c330/_build/_page/index/singlehtml/ I am working on the last bit to automatically populate the PDF with the citations in context. Thank you for your patience! If you don't have it in you to deal with any of these, happy to send you a PR. |
Done in valosekj/PAM50-normalized-metrics-paper@c0cc15b and valosekj/PAM50-normalized-metrics-paper@4b1827f.
Okay! I tried the following syntax in my content/index.ipynb: but it doesn't seem to be working: 
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You should use the citation keys from the bibtex file. Let say for John Doe et al. 2017, the respective bibtex entry is article{doe2017-xy, Then in the text you {cite:p}'doe2017-xy' (quotes are gonna be the funky ones, can't find them on my phone). There are many examples in the rrsg notebook. You can use bibdesk to load and navigate your paper.bib, and to copy/paste cite commands. |
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Do you have any ideas why there is extra white space between the tables 2, 3, and 4 and their captions? 
Table 1 is rendered properly: 
Code for all tables is pretty similar; see here. |
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@roboneuro build book |
🟢 Successfully builtStatus: Success ℹ️ See details |
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🎊🎊🎊 |
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Regarding my previous comment about the white space below the tables, it should now be resolved by this recent commit. Can you rebuild the book one more time? |
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@roboneuro build book |
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👀 Looks like the reproducible preprint you requested has been already built: |
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@valosekj the book is already built at the latest commit, which includes the one you mention. You may want to try figure layout margins, |
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@roboneuro build book |
🟢 Successfully builtStatus: Success ℹ️ See details |
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🎊🎊🎊 |
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Ok great! Looks like the issue has been resolved. |
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@roboneuro build extended pdf |
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Done, data archive is now zenodo.10002180 |
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@roboneuro set 10.5281/zenodo.10002182 as docker archive |
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Done, docker archive is now 10.5281/zenodo.10002182 |
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@roboneuro recommend-accept |
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👋 @openjournals/executable-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in neurolibre/preprints#57, then you can now move forward with accepting the submission by compiling again with the command |
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@roboneuro recommend-accept |
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👋 @openjournals/executable-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in neurolibre/preprints#58, then you can now move forward with accepting the submission by compiling again with the command |
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@roboneuro sync pdf |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@roboneuro production sync pdf |
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🌱♻️📄 Synced the summary PDF from the source, should be now available at https://preprint.neurolibre.org/10.55458/neurolibre.00017.pdf?no-cache |
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@roboneuro publish |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@roboneuro accept |
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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository. If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file. You can copy the contents for your CITATION.cff file here: CITATION.cff
If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation. |
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🌰🌱🌺 THIS IS NOT A DRILL, YOU HAVE JUST PUBLISHED A NEUROLIBRE REPRODUCIBLE PREPRINT! 🌺🌸🍀 Here's what you must now do:
Any issues? Notify your editorial technical team... |
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@valosekj @jcohenadad @sandrinebedard thank you for this great submission, happy to see it on the front page of NeuroLibre! You can see that the DOI resolves into the publication page: https://doi.org/10.55458/neurolibre.00017 Above you can follow instructions to add For this submission, I had to edit the container archive, as repo2data was not called to download the data in the notebook. I updated the description so that people can download the data from zenodo and mount it to the container simply by following those instructions. As this is a beta release, each submission helps us identify and resolve issues, so thank you for your patience, and looking forward to more submissions! Instead of a PDF, you have 4 DOIs archiving reproducibility assets (including a 2.2GB Docker image), one reproducible preprint with interactive figures , all inter-linked through https://doi.org/10.55458/neurolibre.00017. You will be notified by ResearchGate by tomorrow, but it takes some more time for google scholar's web spiders to discover these. Either way, the content is officially registered by Crossref and you can cite it as you see fit. |
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This is so exciting! Thank you @agahkarakuzu and @roboneuro 😊 |
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🌰 🌱 🌺 Congratulations on your NeuroLibre Reproducible Preprint (NRP)! 🍀 🚀 ♻️By publishing this NRP, you've gone beyond simply posting another traditional preprint, demonstrating your commitment to transparency and reproducibility in presenting your new findings. This achievement is certainly something to take pride in, and if you wish to showcase it in your repository: This is how it will look in your, e.g., README: Note The DOI formatted badges are not rendering yet, please use the following: We need your help! NeuroLibre is a community-run reproducible preprint server and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
For details, please visit our documentation |
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Thank you @agahkarakuzu! 💯 |
Just a nitpick; the DOI in the above-mentioned code section should be |
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Thank you @agahkarakuzu! |
Submitting author: @valosekj (Jan Valošek)
Repository: https://github.com/valosekj/PAM50-normalized-metrics-paper
Branch with paper.md (empty if default branch): main
Version: r20230904
Editor: @agahkarakuzu
Reviewers: @mathieuboudreau
Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00017
Repository archive: 10.5281/zenodo.10002178
Data archive: 10.5281/zenodo.10002180
Book archive: 10.5281/zenodo.10002176
Docker archive: 10.5281/zenodo.10002182
Status
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Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@mathieuboudreau, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @agahkarakuzu know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
@mathieuboudreau, please create your checklist typing:
@roboneuro generate my checklistThe text was updated successfully, but these errors were encountered: