[REVIEW]: Visualization of Multi-Dimensional Data - The data-slicer Package

[whedon]

Submitting author: @kuadrat (Kevin Kramer)
Repository: https://github.com/kuadrat/data_slicer
Version: 0.0.9
Editor: @timtroendle
Reviewer: @sabinomaggi, @Chilipp
Archive: 10.5281/zenodo.4692467

⚠️ 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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a587595d1ce52fd3ff6f8ff7a688cc44"><img src="https://joss.theoj.org/papers/a587595d1ce52fd3ff6f8ff7a688cc44/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a587595d1ce52fd3ff6f8ff7a688cc44/status.svg)](https://joss.theoj.org/papers/a587595d1ce52fd3ff6f8ff7a688cc44)

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

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

1. Make sure you're logged in to your GitHub account
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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 @sabinomaggi

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 (@kuadrat) 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: 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 @Chilipp

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 (@kuadrat) 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: 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?

[whedon]

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

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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]

PDF failed to compile for issue #2969 with the following error:

/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:147:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError) from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:89:in initialize'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in set_paper'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in prepare' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in

'

[whedon]

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

OK DOIs

- 10.1038/nphys3172 is OK
- 10.1088/1361-648x/ab757a is OK
- 10.1107/S2052252519012612 is OK
- 10.1107/S2059798316012304 is OK
- 10.1088/0957-0233/25/5/055604 is OK
- 10.1016/j.mri.2012.05.001 is OK
- 10.1016/j.softx.2020.100472 is OK
- 10.1016/j.softx.2020.100600 is OK
- 10.1063/1.4943208 is OK
- 10.1103/RevModPhys.79.353 is OK
- 10.1103/PhysRev.126.941 is OK
- 10.1103/PhysRevLett.110.087004 is OK
- 10.1103/PhysRevB.46.11830 is OK
- 10.1103/PhysRev.119.980 is OK
- 10.1038/s41586-019-1319-8 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ultramic.2019.112815 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/xrs.3141 is INVALID because of 'https://doi.org/' prefix

[timtroendle]

@whedon re-invite @sabinomaggi as reviewer

[whedon]

OK, the reviewer has been re-invited.

@sabinomaggi please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[timtroendle]

@whedon re-invite @Chilipp as reviewer

[whedon]

OK, the reviewer has been re-invited.

@Chilipp please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[timtroendle]

@sabinomaggi, @Chilipp I've just re-invited you to this review to make sure you have full access.

[sabinomaggi]

Review accepted. It seems I cannot compile the paper due to a missing date in the paper yaml header. May I edit the
data_slicer/paper/paper.md file myself or only the author is supposed to do these changes? Or maybe this is part of the review itself?

[kuadrat]

Hi, and thanks in advance for taking the time to review my submission.
I just took the liberty of putting today's date in the header (I assume the date should be adjusted at a later time?).
Does it compile for you now?
Sorry about the inconvenience. The paper did compile when I tested it with the github action before submission.

[sabinomaggi]

@whedon generate pdf

[whedon]

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

[sabinomaggi]

@kuadrat Hi, yes as you can see the paper compiles fine now. In the meantime I was able to get a decent version of the paper with all references by using pandoc and xelatex, but this automatic compilation is way better than a manual approach.
I am really eager to read the paper and test the package in full.

[timtroendle]

@Chilipp @sabinomaggi This is a gentle reminder that half of the review time has elapsed by now. I will set a reminder for you to notify you one week before the review time will elapse entirely.

[timtroendle]

@whedon remind @Chilipp in 2 weeks

[whedon]

Reminder set for @Chilipp in 2 weeks

[timtroendle]

@whedon remind @sabinomaggi in 2 weeks

[whedon]

Reminder set for @sabinomaggi in 2 weeks

[sabinomaggi]

This is my first review for JOSS and I don't know if solving bugs is part of the review or if it is better to contact the author through the package's GitHub page to solve these issues. In the latter case, please forgive me and I will promptly delete this post. In the meantime, this is a short installation summary of data_slicer on macOS 10.13.6 (aka High Sierra).

Hi Kevin, I have followed the installation instructions in https://data-slicer.readthedocs.io/en/latest/installation.html and everything seems OK.

(base) $ conda create --name dataslicer python==3.7.5
(base) $ conda activate dataslicer
(dataslicer) $ pip install --upgrade pip
[...]
Successfully installed pip-21.0.1

(dataslicer) $ pip install data_slicer
Collecting data_slicer
[...]
Installing collected packages: ipython-genutils, wcwidth, traitlets, six, [...]
Successfully installed [...] data-slicer-0.0.9 [...]

However, when I try to test the installation by running pit I get this error message

(dataslicer) $ pit 
===== 2021.02.08 14:02:05 =====
Traceback (most recent call last):
  File "/Users/maggi/anaconda3/envs/dataslicer/bin/pit", line 5, in <module>
    from data_slicer.pit import start_main_window
  File "/Users/maggi/anaconda3/envs/dataslicer/lib/python3.7/site-packages/data_slicer/pit.py", line 75, in <module>
    cmaps = pickle.load(f)
AttributeError: Can't get attribute 'ds_cmap' on <module '__main__' from '/Users/maggi/anaconda3/envs/dataslicer/bin/pit'>

I have also repeated this precedure using the latest available version of Python and the error is exactly the same.

I have not been able to find any info about package compatibility in the documentation (and also in the paper under review), and therefore it is possible that data-dlicer runs only under Linux. However, if this is true, I think you should explicitly state this fact in the documentation, as well as in the paper (but this last point is clearly part of the review).
If, on the other hand, data-dlicer is supposed to run also under macOS, could you please help to solve this issue?

[kuadrat]

Hi @sabinomaggi,

thanks for the detailed, calm and polite feedback!
If I understand it correctly, problems like these during JOSS review should be opened as Github issues directly in the repo under review (I may be wrong, @timtroendle may want to correct me).
I have taken the liberty of opening the problem you mention as an issue and will reply more specifically there.

Best regards,
-Kevin

[sabinomaggi]

Hi @kuadrat , ok we will solve the issue in the repo. Now I ask @timtroendle if I should delete my report here.

[timtroendle]

@sabinomaggi, no need to delete the report in this issue. As mentioned by @kuadrat , it is standard practice to open issues on the project page. If you do so, please link to this issue so we can keep track. Thanks both!

[sabinomaggi]

@timtroendle Ok. This is the link to the issue, and as far as I can say it will be solved very soon it has already been solved.

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2233

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2233, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/nphys3172 is OK
- 10.1088/1361-648x/ab757a is OK
- 10.1107/S2052252519012612 is OK
- 10.1107/S2059798316012304 is OK
- 10.1088/0957-0233/25/5/055604 is OK
- 10.1016/j.mri.2012.05.001 is OK
- 10.1016/j.softx.2020.100472 is OK
- 10.1016/j.softx.2020.100600 is OK
- 10.1063/1.4943208 is OK
- 10.1103/RevModPhys.79.353 is OK
- 10.1103/PhysRev.126.941 is OK
- 10.1103/PhysRevLett.110.087004 is OK
- 10.1103/PhysRevB.46.11830 is OK
- 10.1103/PhysRev.119.980 is OK
- 10.1038/s41586-019-1319-8 is OK

MISSING DOIs

- 10.1016/b978-012387582-2/50038-1 may be a valid DOI for title: ParaView: An End-User Tool for Large Data Visualization

INVALID DOIs

- https://doi.org/10.1016/j.ultramic.2019.112815 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/xrs.3141 is INVALID because of 'https://doi.org/' prefix

[kyleniemeyer]

Hi @kuadrat, our bot found some possible DOI issues in the references. It does look like that you can add that DOI for the ParaView reference; the other two may be false positives, due to references in your .bib file that aren't actually cited in the paper. Can you review these?

[kuadrat]

@kyleniemeyer indeed, the invalid DOIs appear in the .bib file but are not actually used (and are not needed) in the paper.
Can I just remove them and add the ParaView DOI?

Also, I'll get back to you regarding the proof in about an hour at the latest.

[kyleniemeyer]

@kuadrat no need to do anything about the invalid DOIs, it will not affect the final paper (just adds a bit of noise to that message). But yes, please do add the ParaView DOI

[kuadrat]

@kyleniemeyer Alright, thanks for clarifying. I have added the ParaView DOI and the preview did compile correctly. The proof looks fine to us as well.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2242

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2242, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1038/nphys3172 is OK
- 10.1088/1361-648x/ab757a is OK
- 10.1107/S2052252519012612 is OK
- 10.1107/S2059798316012304 is OK
- 10.1088/0957-0233/25/5/055604 is OK
- 10.1016/j.mri.2012.05.001 is OK
- 10.1016/j.softx.2020.100472 is OK
- 10.1016/j.softx.2020.100600 is OK
- 10.1063/1.4943208 is OK
- 10.1103/RevModPhys.79.353 is OK
- 10.1103/PhysRev.126.941 is OK
- 10.1103/PhysRevLett.110.087004 is OK
- 10.1103/PhysRevB.46.11830 is OK
- 10.1103/PhysRev.119.980 is OK
- 10.1038/s41586-019-1319-8 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ultramic.2019.112815 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/xrs.3141 is INVALID because of 'https://doi.org/' prefix

[kyleniemeyer]

@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.02969 joss-papers#2243
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02969
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...

[kyleniemeyer]

Congrats @kuadrat on your article's publication in JOSS!

Many thanks to @sabinomaggi and @Chilipp for reviewing this submission, and @timtroendle for editing.

[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.02969/status.svg)](https://doi.org/10.21105/joss.02969)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02969">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02969/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02969/status.svg
   :target: https://doi.org/10.21105/joss.02969

This is how it will look in your documentation:

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[kuadrat]

@kyleniemeyer Thank you for finishing up the publication process and thanks to @timtroendle for ediiting!

And many thanks again to @sabinomaggi and @Chilipp for their work, patience and useful inputs on improving the paper & code!
I must say that this has to be the most constructive review process I have witnessed so far.