[REVIEW]: NiTransforms: A Python tool to read, represent, manipulate, and apply n-dimensional spatial transforms

[whedon]

Submitting author: @mgxd (Mathias Goncalves)
Repository: https://github.com/poldracklab/nitransforms
Version: 21.0.0
Editor: @osorensen
Reviewer: @robbisg, @PeerHerholz
Archive: 10.5281/zenodo.5499694

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/10870dbd43c36af2f836e7d3b98d2336/status.svg)](https://joss.theoj.org/papers/10870dbd43c36af2f836e7d3b98d2336)

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

@robbisg & @PeerHerholz, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @robbisg

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 (@mgxd) 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: Do the authors clearly state 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: 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?
• 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 @PeerHerholz

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 (@mgxd) 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: Do the authors clearly state 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: 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?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @robbisg, @PeerHerholz 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:

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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]

Failed to discover a Statement of need section in paper

[whedon]

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

OK DOIs

- 10.5281/zenodo.591597 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1016/j.media.2007.06.004 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1002/(SICI)1099-1492(199706/08)10:4/5	extless171::AID-NBM453	extgreater3.0.CO;2-L is INVALID

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (285.5 files/s, 85904.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          25            772            911           2479
SVG                              4              1              1           1368
YAML                             5             31              7            389
Jupyter Notebook                 3              0           7278            238
make                             1             30              6            148
Dockerfile                       1             18             15            125
Markdown                         2             17              0            100
reStructuredText                 4             16             28             77
TeX                              1              5              0             70
TOML                             1              1              0              9
-------------------------------------------------------------------------------
SUM:                            47            891           8246           5003
-------------------------------------------------------------------------------


Statistical information for the repository '3744697bb45cd68c5f464001' was
gathered on 2021/07/08.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chris Markiewicz                 2             6              2            0.08
Mathias Goncalves                1             1              1            0.02
Oscar Esteban                   16           337             90            4.29
Stefano Moia                     1             1              0            0.01
mathiasg                        43          1873            181           20.66
oesteban                        66          4791           2591           74.24
smoia                            4            42             27            0.69

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
Chris Markiewicz              4           66.7         15.4                0.00
Oscar Esteban              3486         1034.4         16.2               12.65
mathiasg                    657           35.1         10.7               11.42
smoia                        15           35.7         19.5                6.67

[whedon]

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

[PeerHerholz]

To the authors,

I sincerely hope you and your loved ones are still doing ok during these ongoing difficult times.

At first, I would like to thank all authors for their very interesting submission and hard, dedicated work they put into it. The topic and aim of this resource are both fascinating and important. Within the following I would like to provide additional information regarding my review decision, which will be divided into the following respective issues (also linked above) opened within the tool's repository:

• current state & integration to NiBabel
• software paper sections

In case some of my comments are misleading, difficult to understand or simply wrong based on an insufficient understanding on my side, I would like to apologize and kindly ask the authors to address such concerns. The same holds true for the nature of my comments: I aim to only provide helpful and constructive comments and criticism. If my wording appears too harsh or not helpful, please let me know and I will try my best to address this.

The presented tool, NiTransforms, allows researchers to work with an extensive amount and variety of transform formats. This includes both basic file handling (read/write/load/save), conversion between transform formats and application of transforms to images. Given the current state-of-the-art and increasing amount of workflows/pipelines that combine multiple software packages, the presented tool fills a prominent gap in the python neuroimaging ecosystem and will tremendously help to boost the reproducibility of neuroimaging results, while at the same time presenting the foundation for various other applications that could build upon it. Thus, it's clear "accept" from my side after the above outlined points were addressed/discussed.

Thanks again for this great contribution and please let me know if there are questions!

Cheers, Peer

[robbisg]

The proposed tool, nitransforms, is used to convert transformation files and manage them very easily.

I think that this tool is very useful and make it available will extremely help the python neuroimaging community. I agree with @PeerHerholz that this tool is very useful to ease building complex and automated pipelines and help the reproducibility of neuroimaging studies.

I opened an issue in the package repository (nipy/nitransforms#123) with my suggestions.
My suggestions are related to the documentation part, I encouraged the authors to add examples or tutorials, since from my perspective, this is the entry point of new users and a way to understand the usefulness of the software.
Moreover a brief overview of other tools used for this purposes should be included in the paper, if no other tools are available, a clear statement that this is the only tool with these goals can help to add importance to it.

Once that these suggestions will be addressed, I will be happy to accept the publication to JOSS.

If you have any other questions, let me know. I would like to apologize if some of my comments are misleading.

Cheers,
Roberto

[osorensen]

Thanks for the reviews, @robbisg and @PeerHerholz, and for opening issues in the source repository. @mgxd please take your time to resolve the issue, and feel free to reach out to me if there is anything I can help with.

[whedon]

👋 @robbisg, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @PeerHerholz, please update us on how your review is going (this is an automated reminder).

[osorensen]

@mgxd, could you please update us on how it's going with the issues opened by the reviewers in the source repository?

[mgxd]

Hi all,

Thank you @PeerHerholz and @robbisg for the reviews! We have spent the past few weeks addressing concerns, and feel that we're at a good place - when you can, please give nitransforms another look.

Cheers,
Mathias

[PeerHerholz]

@whedon generate pdf

[whedon]

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

[PeerHerholz]

Ahoi hoi folks,

thx so much for all the work on this @mgxd & @oesteban, I think the changes look great!

Two small things: as the contribution guidelines were added, I was wondering about the CoC and regarding the examples, I wanted to ask if a few sentences/explanations could be added to the Preparing Images and AFNI Deoblique notebooks, as well as functionality to download the examples either as .ipynb or .py?

Thanks again, cheers, Peer

[osorensen]

Thanks for all your work with this review @PeerHerholz! If you think that some of the issues on the review checklist have been fixed, please remember to check off the boxes.

[oesteban]

@whedon generate pdf

[whedon]

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

[osorensen]

@oesteban before we proceed, could you please do the following?

• Make a tagged release of the software.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

[oesteban]

Sure thing, I just realized a self-citation was missed (fMRIPrep was the only piece of software mentioned without a due reference). I'll check on the Zenodo record - I believe we set it up, but I might be wrong. Anyways that was on the todo list down the line, so happy to get it right before finishing with the review stage.

[osorensen]

Good! I see there is a Zenodo archive for the paper (https://osf.io/8aq7b/), but please create one for the final version of the software too, so that we can get a doi link for the version that gets published.

[oesteban]

DOI of the archived version: 10.5281/zenodo.5499694

[osorensen]

@whedon generate pdf

[whedon]

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

[osorensen]

@whedon check references

[whedon]

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

OK DOIs

- 10.1002/(SICI)1099-1492(199706/08)10:4/5<171::AID-NBM453>3.0.CO;2-L is OK
- 10.5281/zenodo.591597 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1016/j.media.2007.06.004 is OK
- 10.1038/s41592-018-0235-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[osorensen]

@whedon set 10.5281/zenodo.5499694 as archive

[whedon]

OK. 10.5281/zenodo.5499694 is the archive.

[osorensen]

@whedon set 21.0.0 as version

[whedon]

OK. 21.0.0 is the version.

[osorensen]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1002/(SICI)1099-1492(199706/08)10:4/5<171::AID-NBM453>3.0.CO;2-L is OK
- 10.5281/zenodo.591597 is OK
- 10.1016/j.neuroimage.2012.01.021 is OK
- 10.1016/j.neuroimage.2011.09.015 is OK
- 10.1016/j.media.2007.06.004 is OK
- 10.1038/s41592-018-0235-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2582

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2582, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03459 joss-papers#2583
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03459
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@robbisg, @PeerHerholz – many thanks for your reviews here and to @osorensen for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@mgxd – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 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.03459/status.svg)](https://doi.org/10.21105/joss.03459)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03459">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03459/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03459/status.svg
   :target: https://doi.org/10.21105/joss.03459

This is how it will look in your documentation:

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