[REVIEW]: TidyTensor: Utilities for multidimensional arrays as named hierarchical structures

[whedon]

Submitting author: @oneilsh (Shawn T. O'Neil)
Repository: https://github.com/oneilsh/tidytensor
Version: v1.0.0
Editor: @taless474
Reviewer: @nhejazi, @omid-s
Archive: 10.5281/zenodo.5555276

⚠️ JOSS reduced service mode ⚠️

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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

@nhejazi & @omid-s, 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 @nhejazi

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 (@oneilsh) 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 @omid-s

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 (@oneilsh) 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. @nhejazi, @omid-s 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:

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

2. 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]

Wordcount for paper.md is 448

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.58 s (154.4 files/s, 68276.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            28            684             93          22340
JavaScript                       8           2155           1972           7201
R                               32            353           1415           1209
CSS                              5            107             52            471
SVG                              2              0              1            299
Markdown                         4             78              0            173
Rmd                              1            123            168            173
YAML                             6             16              6            116
XML                              1              0              0             87
TeX                              1              9              0             60
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            89           3525           3707          32130
-------------------------------------------------------------------------------


Statistical information for the repository 'd279adb08f7d1814ce53a323' was
gathered on 2021/07/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Shawn O'Neil                     3         22695              0          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
Shawn O'Neil              11367           50.1          0.0               17.40

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.5334/jors.148 may be a valid DOI for title: xarray: ND labeled arrays and datasets in Python

INVALID DOIs

- None

[whedon]

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

[taless474]

@oneilsh Would you please add the missing DOI?
(There is a Reference check error two cells above)

[oneilsh]

@taless474 done :) (I think)

[taless474]

@whedon check references

[whedon]

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

OK DOIs

- 10.5334/jors.148 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[taless474]

@nhejazi , @omid-s how is the review going?

[oneilsh]

Hi @taless474, quick question: I just noticed a couple of minor typos in the documentation. Should I fix them right away or not make any adjustments to the codebase while the review is ongoing?

[taless474]

Hi @oneilsh. Please go ahead and make a pull request, so the reviewers realize what the recent changes are if they were reviewing those parts.

[whedon]

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

[whedon]

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

[taless474]

@nhejazi, @omid-s How is the review going?

[omid-s]

Execute my belated reply, just saw the messages here :/. I will be done soon :)

[omid-s]

Hi @oneilsh, there are two license files, repo's license link goes to a file with two lines that sets copy right to you, though I can see another "license.md" that has a brief MIT Licence description, I was wondering which one are you planning to keep?

[oneilsh]

Hi @omid-s, I believe that's an artifact of R's restrictions on the LICENSE file not containing the actual text of the license, whereas LICENSE.md is used more commonly as an optional extra. This gitlab issue describes some frustrations developers have had there with the duplicate.

LICENSE + LICENSE.md is how usethis::use_mit_license() set it up. If you think I should remove the extra LICENSE.md I can do so, just let me know. Thanks!

[omid-s]

Hi @taless474, I'm done with my review, everything looks good to me, I particularly loved the guides and the documentation! Very through and I enjoyed following them.
There is just a tiny .bib reference issue for which I left oneilsh/tidytensor#2 for @oneilsh to fix. I'll update my check mark once it's resolved.

[oneilsh]

Hi @omid-s, thank you for the thorough review! I've made a branch with the fixes, here's a quick link to the compiled paper: https://github.com/oneilsh/tidytensor/suites/3607702673/artifacts/87088522 If it looks good I will merge it in and close the issue.

[nhejazi]

Sorry to have missed the comments above, I've been somewhat delayed in completing my review due to outstanding work commitments; however, I can have my review completed by the end of next week.

[taless474]

@oneilsh, I apologize for my belated response. I am reviewing reviews and will comment as soon as possible.

[oneilsh]

Hi @taless474, just checking in to see how the review is going.

[kyleniemeyer]

Hi @oneilsh @taless474, I'm the Associate Editor-in-Chief on duty this week, and since it looks like this submission is essentially ready to be accepted, I'm going to step in and help get it past the finish line!

[kyleniemeyer]

@taless474 I am curious about continuing improvements to the package post-publication; is there any best practice I should follow when making updates? Is the JOSS publication tied to a particular version of the package perhaps, such that creating a new version for changes post-review would make it obvious that those updates weren't part of the review? (I'm thinking especially around continuing documentation improvements e.g. updates to README.md, which I wouldn't normally mint a new version number for, but could.)

Yes, the JOSS publication is "tied" to the version that was reviewed, but we do usually expect that changes made in response to the review are reflected in that version—so if you have bumped it we can update the version here.

Regarding changes made after JOSS publication, you may want to begin archiving future versions yourself, so that others can cite a version they use for reproducibility purposes. If things change substantially in the future, you could even submit to JOSS again for a new review.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

OK, everything looks fine to me. @oneilsh, can you please do the following?

• confirm the final reviewed version number here
• archive your repository on Zenodo or Figshare and provide the DOI here

[oneilsh]

Hi @kyleniemeyer, thanks!

The version that got reviewed is v0.9.1, which has Zenodo DOI 10.5281/zenodo.5098818. The "all versions" Zenodo DOI is 10.5281/zenodo.4968727.

I was contemplating minting a v1.0.0 identical to v0.9.1 for purposes of labeling as the JOSS-reviewed version (and I have some documentation fixups I'd like to add after with subsequent minor version updates), but I'll defer to your wisdom on that. Supposing someone comes across the published PDF, how does it link to the reviewed version? Does the Zenodo version DOI and version number get listed in the PDF somewhere?

[kyleniemeyer]

It's fine if you have some additional documentation improvements that you want to include in a v1.0.0, as long as the software itself is not changing from what was reviewed. If you want to do that, I will hold this open until you report the associated DOI (the one specifically pointing to that version).

The published PDF does link to the specific DOI associated with the software archive (see https://joss.theoj.org/papers/10.21105/joss.03523 for an example).

[oneilsh]

Ok, v1.0.0 created with minor doc improvements and DOI 10.5281/zenodo.5555276. Thank you again!

[kyleniemeyer]

@whedon set 10.5281/zenodo.5555276 as archive

[whedon]

OK. 10.5281/zenodo.5555276 is the archive.

[kyleniemeyer]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[kyleniemeyer]

@whedon accept

[whedon]

To recommend a paper to be accepted use @whedon recommend-accept

[kyleniemeyer]

@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

- 10.5334/jors.148 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#2655

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2655, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[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.03543 joss-papers#2656
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03543
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]

Congratulations @oneilsh on your article's publication in JOSS!

Many thanks to @nhejazi and @omid-s for reviewing this submission, and @taless474 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.03543/status.svg)](https://doi.org/10.21105/joss.03543)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03543/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03543/status.svg
   :target: https://doi.org/10.21105/joss.03543

This is how it will look in your documentation:

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