[PRE REVIEW]: A database of the healthy human spinal cord morphometry in the PAM50 template space

[roboneuro]

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
Managing EiC: Agah Karakuzu

Status

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Markdown: [![status](https://neurolibre.org/papers/764a9031ba7a9108dc07a0da1c09dfbb/status.svg)](https://neurolibre.org/papers/764a9031ba7a9108dc07a0da1c09dfbb)

Author instructions

Thanks for submitting your paper to NeuroLibre @valosekj. Currently, there isn't a NeuroLibre editor assigned to your paper.

The AEiC suggestion for the handling editor is @agahkarakuzu.

@valosekj if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for NeuroLibre and may be suitable for this submission (please start at the bottom of the list).

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[agahkarakuzu]

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[agahkarakuzu]

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[roboneuro]

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[agahkarakuzu]

@roboneuro preview server status

[roboneuro]

Can't perform this without reviewers

[roboneuro]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[agahkarakuzu]

@roboneuro add @mathieuboudreau as reviewer

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Can't add reviewers: There is no editor assigned yet

[agahkarakuzu]

@roboneuro assign @agahkarakuzu as editor

[roboneuro]

Assigned! @agahkarakuzu is now the editor

[agahkarakuzu]

@roboneuro add @mathieuboudreau as reviewer

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@roboneuro preview server status

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[agahkarakuzu]

@roboneuro build book

[roboneuro]

Requested branch/SHA does not exist for https://github.com/valosekj/PAM50-normalized-metrics-paper/

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🟢 Successfully built

Status: Success 78a047ee
Last updated: 2023-09-07 06:49:45 PDT

ℹ️ See details

The next comment will forward the logs

[roboneuro]

https://preview.neurolibre.org/book-artifacts/valosekj/github.com/PAM50-normalized-metrics-paper/786f9a3aa69365b57f42174356bb9918951542db/_build/_page/index/singlehtml/

[agahkarakuzu]

@valosekj thank you so much for the submission!

I started some tasks to check the status of the PDF build (succeeds, there's an issue with the template on our end, I'll revert the funny author names section) as well as the jupyter book build (in progress).

I see that the GitHub action to build jupyter book is never triggered, I guess because you have not pushed to main since you added main.yml.

Also, I deleted the trailing / from the repository URL you provided during submission. I'll add a check to the submission system to deal with that automatically in future submissions neurolibre/neurolibre-neo#10, thanks!

The book is built and served in the link above, but looks like figures etc. are not rendered, yet these are not captured as errors. I'll look into it and let you know.

[agahkarakuzu]

@valosekj

OK, looks like the data location and the code are functional! I was able to generate tables and figures on Binder. To render plotly outputs in Jupyter Book, you need something like the following

from IPython.display import display, HTML
from plotly.offline import plot

my_table = table_demographic_characteristics(path_csv)
plot(my_table, filename = 'table1.html')
display(HTML('table1.html'))

I guess the function table_demographic_characteristics is not returning a plotly object, but the same pattern should work for create_subplot(df).

[valosekj]

To render plotly outputs in Jupyter Book, you need something like the following

from IPython.display import display, HTML
from plotly.offline import plot

my_table = table_demographic_characteristics(path_csv)
plot(my_table, filename = 'table1.html')
display(HTML('table1.html'))

Good catch! Thanks! I fixed this in spinalcordtoolbox/PAM50-normalized-metrics@192d0af and valosekj/PAM50-normalized-metrics-paper@e62f9ea.

[valosekj]

I see that the GitHub action to build jupyter book is never triggered, I guess because you have not pushed to main since you added main.yml.

Okay, after the last push to main, the GitHub action has been triggered but failed on the permission issue during cloning of the https://github.com/valosekj/PAM50-normalized-metrics-paper.git/ repo, which is strange because the repo is public and the link works for me.

[valosekj]

Also, I do not know if this is relevant, but I specified a particular release (r20230904) during the submission, which is no longer applicable after the recent commit.

[valosekj]

Do you know how to include chapter headings in the left sidebar? Currently, only Abstract is included, but I use # also for all other headings in my content/index.ipynb.

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[agahkarakuzu]

@valosekj in single page format we would like to get rid of the sidebar as in https://rrsg2020.github.io/paper/.

To do that, it takes a tiny modification. IIRC:

only_build_toc_files: true

Pinging @mathieuboudreau to confirm.

Also in the summary PDF, looks like there are some WIP sections, can you please go through them?

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[valosekj]

@valosekj in single page format we would like to get rid of the sidebar as in https://rrsg2020.github.io/paper/.

To do that, it takes a tiny modification. IIRC:

only_build_toc_files: true

Okay! Done in valosekj/PAM50-normalized-metrics-paper@d5459f8.

Also in the summary PDF, looks like there are some WIP sections, can you please go through them?

Thanks for pointing this out! The WIP sections (TODOs) are about adding a link to the interactive preprint to paper.md and content/index.ipynb. Is there already a permanent link that won't change in the future that I could use?

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🟢 Successfully built

Status: Success a22a27a7
Last updated: 2023-09-28 10:29:32 PDT

ℹ️ See details

The next comment will forward the logs

[agahkarakuzu]

Thanks for pointing this out! The WIP sections (TODOs) are about adding a link to the interactive preprint to paper.md and content/index.ipynb. Is there already a permanent link that won't change in the future that I could use?

@valosekj The PDF template itself has already a link to the reproducible preprint (on the left column): https://github.com/neurolibre/preprints/blob/neurolibre.00016/neurolibre.00016/10.55458.neurolibre.00016.pdf

They will resolve into DOI-formatted proper URLs upon publishing. So no need to duplicate it unless you want to. In that case the URL will be: https://preprint.neurolibre.org/10.55458/neurolibre.00016

[roboneuro]

https://preview.neurolibre.org/book-artifacts/valosekj/github.com/PAM50-normalized-metrics-paper/d5459f80d4bac97d7f1ff21437d0013af018e053/_build/_page/index/singlehtml/

[agahkarakuzu]

@valosekj the book build succeeds and the interactive figures are now rendered, thank you!!

Can you tag the code cells as described below so that they become collapsable in the jupyter book:

https://jupyterbook.org/en/stable/content/metadata.html#jupyter-cell-tags

Also, can you change the jupyter-book requirement version to jupyter-book==0.13.0 and I'll see if it gets rid of that sidebar.

[valosekj]

Thanks for pointing this out! The WIP sections (TODOs) are about adding a link to the interactive preprint to paper.md and content/index.ipynb. Is there already a permanent link that won't change in the future that I could use?

@valosekj The PDF template itself has already a link to the reproducible preprint (on the left column): https://github.com/neurolibre/preprints/blob/neurolibre.00016/neurolibre.00016/10.55458.neurolibre.00016.pdf

They will resolve into DOI-formatted proper URLs upon publishing. So no need to duplicate it unless you want to. In that case the URL will be: https://preprint.neurolibre.org/10.55458/neurolibre.00016

Okay! Resolved in valosekj/PAM50-normalized-metrics-paper@818b217.

Can you tag the code cells as described below so that they become collapsable in the jupyter book:

Done in valosekj/PAM50-normalized-metrics-paper@c24057c.

Also, can you change the jupyter-book requirement version to jupyter-book==0.13.0 and I'll see if it gets rid of that sidebar.

Sure! Done in valosekj/PAM50-normalized-metrics-paper@4094a08.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🟢 Successfully built

Status: Success 0ae2896b
Last updated: 2023-09-28 13:05:44 PDT

ℹ️ See details

The next comment will forward the logs

[roboneuro]

https://preview.neurolibre.org/book-artifacts/valosekj/github.com/PAM50-normalized-metrics-paper/4871821464f73a6cc7662cbf4b8f55a46535106c/_build/_page/index/singlehtml/

[agahkarakuzu]

Perfect! Now I'll move this to actual review.

[agahkarakuzu]

@roboneuro start review

[roboneuro]

OK, I've started the review over in openjournals/joss-reviews#17.