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[REVIEW]: caracas: Computer algebra in R #3438

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @mikldk (Mikkel Meyer Andersen) Repository: https://github.com/r-cas/caracas Version: v1.1.1 Editor: @Nikoleta-v3 Reviewer: @EduPH, @MikeLydeamore Archive: 10.5281/zenodo.5070324

:warning: JOSS reduced service mode :warning:

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HTML: <a href="https://joss.theoj.org/papers/fc8a642838e52d656317ce8386e2d974"><img src="https://joss.theoj.org/papers/fc8a642838e52d656317ce8386e2d974/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fc8a642838e52d656317ce8386e2d974/status.svg)](https://joss.theoj.org/papers/fc8a642838e52d656317ce8386e2d974)

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

@EduPH & @MikeLydeamore, 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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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Nikoleta-v3 know.

✨ 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 @EduPH

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @MikeLydeamore

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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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whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.12 s (1235.1 files/s, 246900.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            91           4519           1155          16491
R                               37            933           1679           2372
Markdown                         5            178              0            630
Rmd                              8            322            563            620
CSS                              4             99             48            431
JavaScript                       3             64             32            256
YAML                             3             23              8            192
TeX                              1              7              0             69
Python                           1             22              7             52
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           154           6167           3493          21124
-------------------------------------------------------------------------------

Statistical information for the repository '03af5f61901eeeae44db9dd8' was
gathered on 2021/07/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Mikkel Meyer Anderse             6           456             23          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
Mikkel Meyer Anderse        433           95.0          3.5                9.01
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01763 is OK
- 10.1007/3-540-45470-5_29 is OK
- 10.7717/peerj-cs.103 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

MikeLydeamore commented 3 years ago

@Nikoleta-v3 I have completed my review and have no comments on the work. The software runs as expected and the paper meets the recommended guidelines.

EduPH commented 3 years ago

I agree with @MikeLydeamore . @Nikoleta-v3, the software was revised and all the review tasks were satisfied.

mikldk commented 3 years ago

Thanks both. I will start preparing a release at Zenodo etc.

Nikoleta-v3 commented 3 years ago

Thank you both for your reviews 🙌🏻 @mikldk please hold fire. I would like to have a final read through the paper 😄 👍🏻

Nikoleta-v3 commented 3 years ago

@mikldk I opened some minor issues https://github.com/r-cas/caracas/issues/49 & https://github.com/r-cas/caracas/issues/50 (this is mostly nitpicking and spelling)

mikldk commented 3 years ago

@Nikoleta-v3 : Thanks for catching these. I fixed #49 in 379fb1 and #50 in ac6f07.

Nikoleta-v3 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Nikoleta-v3 commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01763 is OK
- 10.1007/3-540-45470-5_29 is OK
- 10.7717/peerj-cs.103 is OK

MISSING DOIs

- 10.1007/978-3-211-73265-6_1 may be a valid DOI for title: Maple

INVALID DOIs

- None
Nikoleta-v3 commented 3 years ago

Thank you @mikldk 👍🏻 Everything looks good to me.

whedon is suggesting the doi of this book (which discusses both Maple and Mathematica) for the Maple reference. But your current citations for both Maple and Mathematica are inline with the softwares' guidelines 👍🏻

At this point could you:

I can then move forward with accepting the submission.

mikldk commented 3 years ago
mikldk commented 3 years ago

@Nikoleta-v3 Thanks, including agreeing on the references. I now made a release and made it available on Zenodo, cf. above.

Nikoleta-v3 commented 3 years ago

@whedon set 10.5281/zenodo.5070324 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5070324 is the archive.

Nikoleta-v3 commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01763 is OK
- 10.1007/3-540-45470-5_29 is OK
- 10.7717/peerj-cs.103 is OK

MISSING DOIs

- 10.1007/978-3-211-73265-6_1 may be a valid DOI for title: Maple

INVALID DOIs

- None
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2434

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2434, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
Nikoleta-v3 commented 3 years ago

joss-eics team 👋🏻

Regarding the missing doi:

Thank you @mikldk 👍🏻 Everything looks good to me.

whedon is suggesting the doi of this book (which discusses both Maple and Mathematica) for the Maple reference. But your current citations for both Maple and Mathematica are inline with the softwares' guidelines 👍🏻

At this point could you:

  • [x] Make a tagged release of your software, and list the version tag of the archived version here.
  • [x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
  • [x] 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.
  • [x] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

mikldk commented 3 years ago

@Nikoleta-v3 Thanks. I'm not sure if the waitlist label should be removed?

Nikoleta-v3 commented 3 years ago

I have removed the label just to be sure 😄 Nevertheless, @openjournals/joss-eics have been pinned by whedon. I am assuming it's only a matter of days until the paper is published

kthyng commented 3 years ago

Hi @mikldk! A few comments on your paper before we wrap up:

kthyng commented 3 years ago

(otherwise we are ready to go)

mikldk commented 3 years ago

@kthyng Thanks. I'll make the changes and ping you once they're good to go.

mikldk commented 3 years ago

@kthyng Thanks. I have now fixed these in https://github.com/r-cas/caracas/commit/53ff25db23928a3de035b817c1b1f94b1f99a4a8 . As this is only in the paper I am not sure if I should make a new Zenodo release or just keep the "old" one (with reviewed software, but out-of-sync paper source)?

danielskatz commented 3 years ago

You can choose - we don't require the paper source be in the repo at all, so either way is ok.

mikldk commented 3 years ago

@danielskatz Then we'll just use the current archive/release 👍.

mikldk commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

danielskatz commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2463

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2463, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
danielskatz commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2464
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03438
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.01763 is OK
- 10.1007/3-540-45470-5_29 is OK
- 10.7717/peerj-cs.103 is OK

MISSING DOIs

- 10.1007/978-3-211-73265-6_1 may be a valid DOI for title: Maple

INVALID DOIs

- None
danielskatz commented 3 years ago

Congratulations to @mikldk (Mikkel Meyer Andersen) and co-author!

And thanks to @Nikoleta-v3 for editing, and @EduPH and @MikeLydeamore for reviewing!

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.03438/status.svg)](https://doi.org/10.21105/joss.03438)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03438">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03438/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03438/status.svg
   :target: https://doi.org/10.21105/joss.03438

This is how it will look in your documentation:

DOI

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mikldk commented 3 years ago

Thanks to you all, @Nikoleta-v3, @EduPH, @MikeLydeamore, @danielskatz, @kthyng 🥇.