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[REVIEW]: Cacatoo: building, exploring, and sharing spatially structured models of biological systems #3948

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: @bramvandijk88 (Bram van Dijk) Repository: https://github.com/bramvandijk88/cacatoo Version: 1.0.3 Editor: @Bisaloo Reviewer: @emilydolson, @TimKam Archive: 10.5281/zenodo.5918404

:warning: JOSS reduced service mode :warning:

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Status

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Markdown: [![status](https://joss.theoj.org/papers/91fee0cc4c10d0d7696b78819072317a/status.svg)](https://joss.theoj.org/papers/91fee0cc4c10d0d7696b78819072317a)

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

@emilydolson & @TimKam, 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
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Bisaloo 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 @emilydolson

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @TimKam

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

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

:star: Important :star:

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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whedon commented 2 years ago

Wordcount for paper.md is 629

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btt772 is OK
- 10.7554/eLife.61288 is OK
- 10.1101/2021.05.29.446280 is OK
- 10.1016/j.zool.2019.02.007 is OK
- 10.1098/rstb.2019.0248 is OK
- 10.1101/053405 is OK
- 10.3389/fmicb.2015.00728 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (428.6 files/s, 285181.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            67          22318            315          19027
SVG                              9              0              0          16611
JavaScript                      27           1465           3089           9484
JSON                             1              0              0           1794
CSS                              6            199             68           1230
TeX                              1              8              0             75
Markdown                         2             32              0             64
Bourne Shell                     1             17              9             54
-------------------------------------------------------------------------------
SUM:                           114          24039           3481          48339
-------------------------------------------------------------------------------

Statistical information for the repository '41d513f16f9bdba7c5f10c3d' was
gathered on 2021/11/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Bram van Dijk                   24          3508           1172            0.47
bramvandijk88                  153        490986         472663           96.80
jeroenmeijer                     2            26             24            0.01
root                             4         24015           3150            2.73

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
bramvandijk88             16747            3.4          3.4               23.08
jeroenmeijer                  4           15.4          1.6                0.00
whedon commented 2 years ago

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

Bisaloo commented 2 years ago

:wave: :wave: :wave: @bramvandijk88 @emilydolson @TimKam this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3948 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 4-6 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@bisaloo) if you have any questions/concerns.

emilydolson commented 2 years ago

@Bisaloo should I be able to edit this issue to check things off? I don't seem to be able to. I suspect this has to do with me not having accepted the invitation to collaborate on this repository before it expired.

Bisaloo commented 2 years ago

@emilydolson, yes, you should be able to edit the checklist once you have accepted the invitation. I'll re-invite you :relaxed:

Bisaloo commented 2 years ago

@whedon re-invite @emilydolson as reviewer

whedon commented 2 years ago

OK, the reviewer has been re-invited.

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

whedon commented 2 years ago

:wave: @TimKam, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @emilydolson, please update us on how your review is going (this is an automated reminder).

bramvandijk88 commented 2 years ago

Heya,

Just checking in after the holidays, is this review still in progress? I'm not at all in a hurry, but just wanted to make sure it wasn't forgotten.

emilydolson commented 2 years ago

Yes! Apologies for being slow - my university switched teaching modalities and I've been scrambling to adjust my course.

bramvandijk88 commented 2 years ago

Yes! Apologies for being slow - my university switched teaching modalities and I've been scrambling to adjust my course.

No need to apologise, there have been holidays + a new year of teaching, so nobody should expect to stay within standardised deadlines. Thanks for your time! :)

emilydolson commented 2 years ago

Okay, done with my initial review! Really cool project! @bramvandijk88 already added the contributing guidelines, so in my mind the only two issues currently blocking acceptance are:

Bisaloo commented 2 years ago

Thank you for your very insighful comments @emilydolson and thanks @bramvandijk88 for sending a reminder (Sorry for my lack of activity, I'm still on leave without reliable internet access until next week)

emilydolson commented 2 years ago

I'm satisfied that all items on the review checklist are complete!

Bisaloo commented 2 years ago

Thanks @emilydolson!

@TimKam, could you give us an update for your review of this library+paper please? Please let me know if you need anything.

TimKam commented 2 years ago

Sorry, I should be able to complete the review within roughly (but perhaps not exactly) one week.

TimKam commented 2 years ago

I have completed the review and have created an issue in the source code repository that outlines some shortcomings/improvements, with respect to some issues around installation & instructions, automated tests, community guidelines, and the software paper (minor comments). Conceptually/w.r.t. scholarly effort, I assess the paper as reasonable (from an engineering point of view, I do not have any expertise in ecology and evolution).

TimKam commented 2 years ago

@bramvandijk88 responded rather promptly and we have concluded the revisions and discussions regarding my review. I have now completed the review checklist.

bramvandijk88 commented 2 years ago

@TimKam not sure if this is intended, but one of your checkboxes is still unticked.

TimKam commented 2 years ago

Thx, now it's ticked!

Bisaloo commented 2 years ago

Great! Thank you again @emilydolson and @TimKam for your valuable comments!

@bramvandijk88, I'll now do a last review for typos. I encourage you to do the same because there is no proofing after acceptance at JOSS. Once this is done, we can take the final steps to accept this submission.

Bisaloo commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

Bisaloo commented 2 years ago

@whedon check references

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/bioinformatics/btt772 is OK
- 10.7554/eLife.61288 is OK
- 10.1101/2021.05.29.446280 is OK
- 10.1016/j.zool.2019.02.007 is OK
- 10.1098/rstb.2019.0248 is OK
- 10.1101/053405 is OK
- 10.3389/fmicb.2015.00728 is OK

MISSING DOIs

- 10.1098/rstb.2020.0460 may be a valid DOI for title: Introduction: the secret lives of microbial mobile genetic elements

INVALID DOIs

- None
Bisaloo commented 2 years ago

Shouldn't https://github.com/bramvandijk88/cacatoo/blob/65b6e7a2daac8175d65a6052b4f2f6d3652d08b7/paper/paper.bib#L1-L10 be @article instead of @misc anyways?

bramvandijk88 commented 2 years ago

I've added the DOI of "Introduction: the secret lives of Mobile genetic Elements".

Google indexed that citation as @misc, probably because it's not an article in the strict sense, it's just an overview of the content in the special issue.

bramvandijk88 commented 2 years ago

I've checked the proof for typos (caught a few!) Please let me know what happens next.

Bisaloo commented 2 years ago

At this point could you:

I can then move forward with accepting the submission.

bramvandijk88 commented 2 years ago

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.

Done. The archived Zenodo DOI is 10.5281/zenodo.5918404

Bisaloo commented 2 years ago

@whedon set 1.0.1 as version

whedon commented 2 years ago

OK. 1.0.1 is the version.

Bisaloo commented 2 years ago

@bramvandijk88, there is a mismatch in the version listed in Zenodo and the actual tag in GitHub. If you can easily fix it, it would be great. But if it's too difficult, then we can ignore it and proceed.

Additionally, could you please edit the license on Zenodo. It's listed as 'Other' when it should be 'GPL-3'?

bramvandijk88 commented 2 years ago

What mismatch is there? They are both 1.0.1 as far as I can tell.

I've changed the licence to "GPL-3" in the zenodo.json file, but it only updates this upon republishing the package. Zenodo complains when I do that without bumping the version, but I actually don't want to bump the version without having any changes in the code. Is there a way around this?

Bisaloo commented 2 years ago

Here is what I see. And the link to 1.0.3 on GitHub doesn't work because this version doesn't exist.

image

bramvandijk88 commented 2 years ago

Not sure what's going on here. V1.0.3 was the result of me testing the metadata, for which I was forced to publish (or Zenodo wouldn't reindex them).

I'm not sure how to resolve this. There's no way to edit these things after publication as far as I can tell, but the DOI-link on the github page itself should get you to version 1.0.1.

Bisaloo commented 2 years ago

Okay, let's go with this then. It's not super important. The most important thing is that the submission is actually archived.

Bisaloo commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

No archive DOI set. Exiting...

Bisaloo commented 2 years ago

@whedon set 10.5281/zenodo.5918404 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5918404 is the archive.

Bisaloo commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1098/rstb.2020.0460 is OK
- 10.1093/bioinformatics/btt772 is OK
- 10.7554/eLife.61288 is OK
- 10.1101/2021.05.29.446280 is OK
- 10.1016/j.zool.2019.02.007 is OK
- 10.1098/rstb.2019.0248 is OK
- 10.1101/053405 is OK
- 10.3389/fmicb.2015.00728 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 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/2921

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2921, 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 commented 2 years ago

@whedon set 1.0.3 as version