[REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #3042

whedon · 2021-02-15T16:39:51Z

Submitting author: @fmatuschke (Felix Matuschke)
Repository: https://github.com/3d-pli/fastpli
Version: 1.1.0
Editor: @oliviaguest
Reviewers: @vigji, @glyg, @RealPolitiX
Archive: 10.5281/zenodo.4720075

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Review checklist for @glyg

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Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
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Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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Software paper

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Review checklist for @vigji

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I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@fmatuschke) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @RealPolitiX

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@fmatuschke) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

The text was updated successfully, but these errors were encountered:

whedon · 2021-02-15T16:39:54Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @vigji it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon · 2021-02-15T16:40:21Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-2-121 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-02-15T16:40:24Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.34 s (347.2 files/s, 110372.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              2              2          21804
Python                          49           1601           1480           4518
C++                             15            692            202           2978
C/C++ Header                    19            304             69           1451
Markdown                         4            115              0            275
CMake                            5             39             36            201
YAML                             3             16             21            180
Jupyter Notebook                 2              0            418            176
Bourne Shell                    10             30             14            165
make                             2             34             10            145
TeX                              1              8              0            100
reStructuredText                 3             17             80              9
-------------------------------------------------------------------------------
SUM:                           117           2858           2332          32002
-------------------------------------------------------------------------------


Statistical information for the repository '845d1dee56dd4b12c318a43e' was
gathered on 2021/02/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
fmatuschke                     658         30396          17112          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
fmatuschke                13295           43.7         11.1                6.30

whedon · 2021-02-15T16:41:01Z

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

oliviaguest · 2021-02-15T16:43:57Z

Thank you so much, @vigji for accepting to review this. I want to find at least one more reviewer, but since you started reviewing already, please feel free to indeed get started.

Please read the instructions above. If you have trouble ticking things off in the list above, remember you need to click to "accept" here: https://github.com/openjournals/joss-reviews/invitations! Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread, so we can all keep track of them. 🌸

For examples of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

oliviaguest · 2021-02-16T14:18:54Z

@whedon add @glyg as reviewer

whedon · 2021-02-16T14:18:59Z

OK, @glyg is now a reviewer

oliviaguest · 2021-02-16T14:20:30Z

👋 @glyg welcome! Make sure to read the instructions above, accept the invitation, etc.

vigji · 2021-02-16T15:21:17Z

I'll link here below all issues related to this review:

oliviaguest · 2021-02-18T18:14:03Z

@whedon add @RealPolitiX as reviewer

whedon · 2021-04-26T16:29:32Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-4-121-1 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK
- 10.1103/physreve.83.041804 is OK
- 10.3389/fninf.2017.00005 is OK
- 10.1016/j.neuroimage.2019.02.055 is OK
- 10.1364/opex.13.004420 is OK
- 10.1117/1.3241986 is OK
- 10.1016/j.optcom.2020.126113 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest · 2021-04-26T16:30:32Z

@whedon generate pdf

oliviaguest · 2021-04-26T16:30:57Z

@whedon accept

whedon · 2021-04-26T16:31:00Z

Attempting dry run of processing paper acceptance...

whedon · 2021-04-26T16:32:51Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-4-121-1 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK
- 10.1103/physreve.83.041804 is OK
- 10.3389/fninf.2017.00005 is OK
- 10.1016/j.neuroimage.2019.02.055 is OK
- 10.1364/opex.13.004420 is OK
- 10.1117/1.3241986 is OK
- 10.1016/j.optcom.2020.126113 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-04-26T16:33:51Z

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

whedon · 2021-04-26T16:34:24Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2262

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2262, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman · 2021-04-30T22:10:07Z

@fmatuschke I have proofread your paper and have some very minor comments which I hope you can address:

Please check It allows contrasting fibers and fiber tracts and ultimately reconstructing 3D nerve fiber orientations, some words seem missing. Should this be something like It provides image contrast for fibers and fiber tracts, and ultimately enables reconstruction of 3D nerve fiber orientations?
Please introduce the acronym dMRI for diffusion magnetic resonance imaging, when the terms are first used/introduced.
Consider changing Different types of simulation... to Different types of simulations...

Once you have considered the above please call @whedon generate pdf to update the paper. I will then review the changes and process acceptance when ready.

One more important note relates to the Zenodo archive

Please ensure that the meta-data for the Zenodo archive matches that of the paper in terms of the author list as well as the title. Currently the archive title read: Fiber Architecture Simulation Toolbox for 3D-PLI but this should match the paper and be changed to fastPLI: A Fiber Architecture Simulation Toolbox for3D-PLI. You can manually change this on Zenodo.

The version tag for the Zenodo archive is 1.1.0. I will therefore assume we should update the version tag here also. I will do this shortly below 👇.

Thanks.

Kevin-Mattheus-Moerman · 2021-04-30T22:10:34Z

@whedon set 1.1.0 as version

whedon · 2021-04-30T22:10:37Z

OK. 1.1.0 is the version.

fmatuschke · 2021-05-03T07:55:29Z

Dear @Kevin-Mattheus-Moerman,
I change all three of your comments. Thanks for your help.
Regarding the version number. Yes, it is now officially 1.1. Thanks to the reviewers I changed quite a bit, so I had to increase the minor version.
I have also corrected the title in the Zenodo archive.

fmatuschke · 2021-05-03T07:55:44Z

@whedon generate pdf

whedon · 2021-05-03T07:57:02Z

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

Kevin-Mattheus-Moerman · 2021-05-03T08:07:50Z

@whedon accept

whedon · 2021-05-03T08:07:54Z

Attempting dry run of processing paper acceptance...

whedon · 2021-05-03T08:08:21Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3389/fninf.2011.00034 is OK
- 10.3233/APC190017 is OK
- 10.1103/physrevx.10.021002 is OK
- 10.17815/jlsrf-4-121-1 is OK
- 10.3389/fnana.2018.00075 is OK
- 10.1016/j.neuroimage.2015.02.020 is OK
- 10.1098/rsif.2015.0734 is OK
- 10.1145/2833157.2833162 is OK
- 10.1103/physreve.83.041804 is OK
- 10.3389/fninf.2017.00005 is OK
- 10.1016/j.neuroimage.2019.02.055 is OK
- 10.1364/opex.13.004420 is OK
- 10.1117/1.3241986 is OK
- 10.1016/j.optcom.2020.126113 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-05-03T08:09:20Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2274

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2274, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman · 2021-05-03T08:44:44Z

@whedon accept deposit=true

whedon · 2021-05-03T08:44:47Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2021-05-03T08:46:13Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-05-03T08:46:14Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03042 joss-papers#2275
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03042
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2021-05-03T09:22:59Z

Congratulations @fmatuschke this work is now published in JOSS.
Thank you @oliviaguest for editing this submission!

Thanks also to @vigji, @glyg, @RealPolitiX for your help reviewing this work!!!

whedon · 2021-05-03T09:26:19Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03042/status.svg)](https://doi.org/10.21105/joss.03042)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03042">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03042/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03042/status.svg
   :target: https://doi.org/10.21105/joss.03042

This is how it will look in your documentation:

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[PRE REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #2923

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[REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #3042

[REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #3042

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[REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #3042

[REVIEW]: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI #3042

Comments

whedon commented Feb 15, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @glyg

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @vigji

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @RealPolitiX

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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