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Create a JOSS paper #260

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olevs opened this issue Dec 15, 2023 · 3 comments
Open

Create a JOSS paper #260

olevs opened this issue Dec 15, 2023 · 3 comments
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enhancement New feature or request

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@olevs
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olevs commented Dec 15, 2023

Create and submit a code paper to Journal of Open Source Software (JOSS)
@olevs olevs added the enhancement New feature or request label Dec 15, 2023
@olevs olevs self-assigned this Dec 15, 2023
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Dec 15, 2023
@olevs
DOC: Added JOSS example paper and bib file templates. ALive-research#260
23eadfa
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Dec 15, 2023
@olevs
DOC: Added JOSS example text in paper.md. ALive-research#260
6089891
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Dec 20, 2023
@olevs
WIP: Added some more text, references and figures to the initial vers…
f05a6de 
…ion of the JOSS paper. ALive-research#260
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 10, 2024
@olevs
WIP: Added a short overview section to the paper. ALive-research#260
fc7d4e2
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 12, 2024
@olevs
WIP: Added more text from the EUVIP paper, and references to current …
a2e101c 
…ALive papers. ALive-research#260
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 12, 2024
@olevs
WIP: Added github action for compiling JOSS paper. ALive-research#260
482f3bb
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 12, 2024
@olevs
WIP: Minor fixes of the JOSS paper. ALive-research#260
201c673
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 15, 2024
@olevs
WIP: Added figures to the JOSS paper: ALive-research#260
1a1e0f5
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 15, 2024
@olevs
WIP: Fixed figure file names. ALive-research#260
6990f93
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 15, 2024
@olevs
WIP: Minor text changes. ALive-research#260
3ca77a7
gatangen added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 16, 2024
@gatangen
WIP: Some text updates. ALive-research#260
e2de5d8
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 18, 2024
@olevs
WIP: Fixed reference. ALive-research#260
423c140
olevs added a commit to SINTEFMedtek/Slicer-Liver that referenced this issue Jan 23, 2024
@olevs
WIP: Scale image. ALive-research#260
8e1ddb6
RafaelPalomar pushed a commit that referenced this issue Apr 10, 2024
@olevs @RafaelPalomar
DOC: Added JOSS example paper and bib file templates. #260
2808508
RafaelPalomar pushed a commit that referenced this issue Apr 10, 2024
@olevs @RafaelPalomar
DOC: Added JOSS example text in paper.md. #260
57f97cc
@olevs
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olevs commented Jun 6, 2024

After the last merge the paper draft no longer builds. It seems like the code for converting *.svg files no longer functions correctly.
This is an issue with the JOSS script for github actions, and the github runners (github seems to update runners regularly).
It seems like the error is with rsvg-convert, and I tried to change draft-pdf.yml to install this explicitly, but it still fails. I also tried to change ubuntu runner from ubuntu-latest (22.04) to ubuntu-20.04, but I still get the same error.

The solution is either to try to fix the JOSS script(s), wait for JOSS to fix them, or manually convert the .svg images to another format (like .png).
@RafaelPalomar The simplest solution is probably to just convert the .svg images to another format.

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olevs commented Jun 6, 2024

I tested my previous suggestion in my separate test branch (with the first draft), and that worked fine.
On Ubuntu the conversion can be done with "rsvg-convert resectograms-overview.svg > resectograms-overview.png".
@RafaelPalomar Will you do it, or should I?

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@olevs I can do it. I'm checking the develop branch already

RuoyanMeng added a commit that referenced this issue Oct 18, 2024
@RuoyanMeng @olevs
@gatangen @RafaelPalomar @dalbenzioG
Feature/joss paper (#271)
5ecfee2 
* DOC: Added JOSS example paper and bib file templates. #260

* DOC: Added JOSS example text in paper.md. #260

* DOC: Add paper content

* DOC: Move pape to own folder

This moves the paper files to its own folder and modifies the github
workflow files to adjust for this

* DOC: Update paper conten

Co-authored-by: Ole Vegard Solberg <[email protected]>
Co-authored-by: Geir Arne Tangen <[email protected]>
Co-authored-by: Gabriella d'Albenzio <[email protected]>
Co-authored-by: Ruoyan Meng <[email protected]>

* COMP: Fix paper pdf generation workflow

* DOC: Add atypical vs. anatomical figure to paper

* DOC: Fix typos in paper

* DOC: Fix figures

* DOC: Minor changes and typo fixes

* Add GdA ORCID

* Add Couinaud segments figure

* Add bib reference

* Paper revision GdA

* Fix typo in the text

* Remove { width=100% } under resectogram figure

* Revert "Remove { width=100% } under resectogram figure"

This reverts commit 3985a4e.

* DOC: Fixed ref to fig 4

* DOC: Minor additions to text.

* DOC: Minor text changes

* DOC: update pdf generator

* DOC: Changed Liver Volumetry description

* DOC: Update reference

* DOC: revise reference

---------

Co-authored-by: Ole Vegard Solberg <[email protected]>
Co-authored-by: Geir Arne Tangen <[email protected]>
Co-authored-by: Rafael Palomar <[email protected]>
Co-authored-by: Gabriella d'Albenzio <[email protected]>
Co-authored-by: Ole Vegard Solberg <[email protected]>
Co-authored-by: Gabriella d' Albenzio <[email protected]>
Co-authored-by: Rafael Palomar <[email protected]>
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