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

[whedon]

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

⚠️ 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

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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

• 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 (@bramvandijk88) 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 @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

• 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 (@bramvandijk88) 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. @emilydolson, @TimKam 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 629

[whedon]

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]

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]

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

[Bisaloo]

👋 👋 👋 @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]

@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]

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

[Bisaloo]

@whedon re-invite @emilydolson as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[whedon]

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

[whedon]

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

[bramvandijk88]

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]

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

[bramvandijk88]

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]

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:

• Improved unit tests
• A little more discussion of the state of the field

[Bisaloo]

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)

[whedon]

OK. 1.0.1 is the version.

[Bisaloo]

@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]

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]

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

[bramvandijk88]

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]

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

[Bisaloo]

@whedon recommend-accept

[whedon]

No archive DOI set. Exiting...

[Bisaloo]

@whedon set 10.5281/zenodo.5918404 as archive

[whedon]

OK. 10.5281/zenodo.5918404 is the archive.

[Bisaloo]

@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

- 10.1098/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]

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

Check final proof 👉 openjournals/joss-papers#2921

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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]

@whedon set 1.0.3 as version

[whedon]

OK. 1.0.3 is the version.

[Kevin-Mattheus-Moerman]

@bramvandijk88 @Bisaloo I have read the paper and inspected the archive. I only had to update the version since the archived version was 1.0.3. All seems in order now to proceed to acceptance.

[Kevin-Mattheus-Moerman]

@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.03948 joss-papers#2930
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03948
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...

[Kevin-Mattheus-Moerman]

Congratulations @bramvandijk88 on your publication! 🎉

Thank you @emilydolson and @TimKam for your review efforts!!

Thanks @Bisaloo for editing this.

[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.03948/status.svg)](https://doi.org/10.21105/joss.03948)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03948">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03948/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03948/status.svg
   :target: https://doi.org/10.21105/joss.03948

This is how it will look in your documentation:

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