Joss-reviews: [REVIEW]: CancerSim: A python3 package for stochastic cancer simulation in 2D

[whedon]

Submitting author: @CFGrote (Carsten Fortmann-Grote)
Repository: https://github.com/mpievolbio-scicomp/cancer_sim
Version: 2.0.1
Editor: @pdebuyl
Reviewer: @jenzopr, @blakeaw
Archive: 10.5281/zenodo.4034071

: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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/03998bcb956325e7641c3ead54ad20da/status.svg)](https://joss.theoj.org/papers/03998bcb956325e7641c3ead54ad20da)

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

@jenzopr & @blakeaw, 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 @pdebuyl know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @jenzopr

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@CFGrote) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @blakeaw

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@CFGrote) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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. @jenzopr, @blakeaw 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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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]

Reference check summary:

OK DOIs

- 10.1038/s41576-019-0114-6 is OK
- 10.1038/ng.3489 is OK
- 10.1038/nrc4029 is OK
- 10.1186/s12885-019-5597-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pdebuyl]

@blakeaw , @jenzopr , make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

[blakeaw]

@pdebuyl, can you resend my reviewer group invitation? I just tried to accept but it said it had expired.

[pdebuyl]

@whedon re-invite @blakeaw as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[pdebuyl]

@blakeaw this should work again, let me know if there are issues.

[pdebuyl]

@jenzopr reminder for the review of "CancerSim: A python3 package for stochastic cancer simulation in 2D"

[blakeaw]

Hi @CFGrote, based on your software's commit history it looks like you are the only author that made direct contributions to the code itself. Would you mind briefly stating what contributions the other authors listed in the paper made to the project?

[blakeaw]

Possible step missing in the Installation instructions: Issue https://github.com/mpievolbio-scicomp/cancer_sim/issues/5

[jenzopr]

Problems with reproducing the Example usage from README and the docs: Issue https://github.com/mpievolbio-scicomp/cancer_sim/issues/6

[blakeaw]

Recommendation for additional documentation of simulation outputs: https://github.com/mpievolbio-scicomp/cancer_sim/issues/8

[blakeaw]

Low-level API documentation (autogenerated) appears to be missing and possibly didn't build properly: https://github.com/mpievolbio-scicomp/cancer_sim/issues/9

[CFGrote]

dear reviewers, thanks for all the comments so far. i'm currently on
vacation with very limited internet/email access. i'll pick up
immediately after my return on july 27th.

cfg

On 7/15/20 7:01 PM, Blake A. Wilson wrote:

Low-level API documentation (autogenerated) appears to be missing and
possibly didn't build properly: mpievolbio-scicomp/cancer_sim#9
https://github.com/mpievolbio-scicomp/cancer_sim/issues/9

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[jenzopr]

I reviewed the paper in https://github.com/mpievolbio-scicomp/cancer_sim/issues/11 and will grade the submission in category 3) Major revision.

[CFGrote]

Hi @CFGrote, based on your software's commit history it looks like you are the only author that made direct contributions to the code itself. Would you mind briefly stating what contributions the other authors listed in the paper made to the project?

All the commits are from me because I moved the code (initially developed by my co-authors) from a plain directory into github and then took care of integrating new features.

Contributions by author:

• Luka Opasic: Development of the algorithm, initial version of the code, writing of manuscript
• Jacob Scott : contributed to the concept of the software and supervised its
  development
• Arne Traulsen: supervised the development of the software.
• Carsten Fortmann-Grote: OO porting of the code, writing the manuscript, reference manual, documentation of code and examples, development of the test suite

[blakeaw]

I have reviewed the CancerSim paper in https://github.com/mpievolbio-scicomp/cancer_sim/issues/16 and I grade the overall submission as Category 3) Major Revision.
Please note that this represents my initial evaluation and does not take into account recent efforts by @CFGrote to address some issues logged in the cancer_sim repository Issue tracker.

[pdebuyl]

@jenzopr @blakeaw thank you for the reviews.

@CFGrote the bulk of the review so far concerns the paper and the documentation, can you propose a reply to the reviewers?

Regarding the paper, I will only point out that we request for JOSS to not include configuration files or tutorial-type instructions for running the code in the paper. We ask that this type of documentation remains in the README or the documentation of the code.

[CFGrote]

thanks for the reviews. responses are in preparation.

On 8/3/20 11:17 AM, Pierre de Buyl wrote:

@jenzopr https://github.com/jenzopr @blakeaw
https://github.com/blakeaw thank you for the reviews.

@CFGrote https://github.com/CFGrote the bulk of the review so far
concerns the paper and the documentation, can you propose a reply to the
reviewers?

Regarding the paper, I will only point out that we request for JOSS to
not include configuration files or tutorial-type instructions for
running the code in the paper. We ask that this type of documentation
remains in the README or the documentation of the code.

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[CFGrote]

ok, we addressed all issues, but let me check the pdf before marking as "resubmitted". btw, am i supposed/allowed to mark those checkboxes in the review reports or will the reviewers do that as they see fit?

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pdebuyl]

@CFGrote the review checkboxes are for the reviewers of course.

[CFGrote]

sorry for not being specific:
i meant the checkboxes in the lists of review comments in https://github.com/mpievolbio-scicomp/cancer_sim/issues/16 and https://github.com/mpievolbio-scicomp/cancer_sim/issues/11 .

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[CFGrote]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[CFGrote]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1038/s41576-019-0114-6 is OK
- 10.1038/ng.3489 is OK
- 10.1038/nrc4029 is OK
- 10.1186/s12885-019-5597-1 is OK
- 10.1038/nature14971 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pdebuyl]

@CFGrote even though these are issues in your repository, I think that it makes sense for the reviewers to check them. They will go through their remarks anyway while assessing the changes.

[pdebuyl]

@jenzopr @blakeaw , @CFGrote update his submissions, can you provide an update to the review?

[blakeaw]

@pdebuyl, yes, I will start looking over the submission updates.

[CFGrote]

not done yet
Aug 13, 2020 22:12:42 Pierre de Buyl [e-mail]:

@jenzopr[https://github.com/jenzopr] @blakeaw[https://github.com/blakeaw] , @CFGrote[https://github.com/CFGrote] update his submissions, can you provide an update to the review?

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[pdebuyl]

@CFGrote sorry, I thought it was. You can notify us when the update is ready.

[CFGrote]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[CFGrote]

I have just submitted our responses to the reviews: https://github.com/mpievolbio-scicomp/cancer_sim/issues/11#issuecomment-683706999 and https://github.com/mpievolbio-scicomp/cancer_sim/issues/16#issuecomment-683707010 All relevant changes are pushed to the master branch in https://github.com/mpievolbio-scicomp/cancer_sim.

Thanks again to @blakeaw and @jenzopr for the careful reading and detailed comments.

[jenzopr]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pdebuyl]

Thank you @jenzopr for your review!

[pdebuyl]

@blakeaw the reply to your review is at https://github.com/mpievolbio-scicomp/cancer_sim/issues/16

[pdebuyl]

I am not subscribed to the issues at the repo and did not see @blakeaw 's positive evaluation of the changes at https://github.com/mpievolbio-scicomp/cancer_sim/issues/16 . @CFGrote I will proceed to the coming editorial steps in the coming days.

[blakeaw]

Sorry about that @pdebuyl. I forgot to come back and comment here after I finished reviewing the changes.
I've checked off all the boxes in my Reviewer Checklist except the Functionality:Functionality one. For that, I'm planning to execute a few more test simulations with different parameter sets to make sure the code operates smoothly outside of the provided template/examples. I'll update within the next day or two.
Also, it looks like @jenzopr still had an issue with installation and unit tests of the updated code: recorded in https://github.com/mpievolbio-scicomp/cancer_sim/issues/6.

[pdebuyl]

@blakeaw thanks for the correction. I am not used yet to parts of the review occurring at the software's repository. I'll make sure to check the checklist here and the issues there!

[blakeaw]

Hi @pdebuyl, I've completed my Review Checklist.

[pdebuyl]

Thank you @blakeaw ! I see that "Functionality" is still unchecked, does this checkbox need more work?

[pdebuyl]

@CFGrote there still is a testing issue open at your software's repository. I could run the tests just file (python 3.7 linux amd64 using pip), so I guess that the issue can be resolved by updating completely the software on the user's machine.

[jenzopr]

My checklist is complete now.

[pdebuyl]

Thank you @jenzopr for the review!

[blakeaw]

Hi @pdebuyl, Functionality doesn't require any additional work. You can consider it checked.
(The checkbox is showing up as checked on my end. Maybe refreshing the page will update?)

[pdebuyl]

@whedon generate pdf

[whedon]

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

[pdebuyl]

@whedon generate pdf

[whedon]

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

[pdebuyl]

@CFGrote can you archive a release of the code on zenodo? When it is done, I would need the corresponding doi and the version of the release to include in the paper.

[CFGrote]

I drafted the zenodo deposit, the reserved DOI is 10.5281/zenodo.4034071. I'm waiting my co-authors to give their "Ok" before publishing, will let you know.
BTW I bumped the version of cancer_sim to 2.0.1.

[pdebuyl]

@whedon set 10.5281/zenodo.4034071 as archive

[whedon]

OK. 10.5281/zenodo.4034071 is the archive.

[pdebuyl]

@whedon set 2.0.1 as version

[whedon]

OK. 2.0.1 is the version.

[pdebuyl]

@whedon generate pdf

[whedon]

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

[pdebuyl]

@CFGrote you can consider the latest pdf as a proof. Let me know when I can validate the publication. At that point, an editor in chief of JOSS will take over the publication.

[jenzopr]

Well done, @CFGrote ! The review was not "cheap" and you did a lot of work to enhance the manuscript and software! Congratulations 🎉

[CFGrote]

I drafted the zenodo deposit, the reserved DOI is 10.5281/zenodo.4034071. I'm waiting my co-authors to give their "Ok" before publishing, will let you know.
BTW I bumped the version of cancer_sim to 2.0.1.

v2.0.1 is now published on zenodo: https://dx.doi.org/10.5281/zenodo.4034071

[pdebuyl]

@CFGrote should I take this as confirmation to proceed?

[CFGrote]

@CFGrote should I take this as confirmation to proceed?

please wait, i'm checking the binder link, last item on my to do list for the proofs.

[CFGrote]

@whedon commands

[CFGrote]

@whedon generate pdf

[whedon]

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

[CFGrote]

@pdebuyl , all good, please proceed.

[CFGrote]

@pdebuyl, @jenzopr, @blakeaw , thank you very much for your comments, corrections and guidance through the process. It was a very good experience!

[pdebuyl]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41576-019-0114-6 is OK
- 10.1038/ng.3489 is OK
- 10.1038/nrc4029 is OK
- 10.1186/s12885-019-5597-1 is OK
- 10.1038/nature14971 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

: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/1740

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1740, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[CFGrote]

@blakeaw , there's still one checkbox unchecked here (Review Checklist for blakeaw -> Functionality -> Functionality): https://github.com/openjournals/joss-reviews/issues/2436#issue-650881744 . Could you check, please?

[blakeaw]

@CFGrote Ok, it should be checked. Let me know if it is registering as checked now.
(I unchecked that particular box and then re-checked it, as it was already registering as being checked on my end.)

[CFGrote]

@CFGrote Ok, it should be checked. Let me know if it is registering as checked now.
(I unchecked that particular box and then re-checked it, as it was already registering as being checked on my end.)

@blakeaw, looks good now, thanks!

[kyleniemeyer]

Hi @CFGrote, I'm the EIC on duty this week, and doing some final checks before publishing.

In the paper, I noticed a few issues:

• In your title, I think "python3" should be changed to "Python 3"
• You do not have an explicit Statement of Need, one of our required elements, that illustrates the research purpose of the software (you can probably just reorganize your existing text slightly)
• please put commas after "i.e" or "e.g."
• in the third paragraph, I think you can remove the "(see e.g. Ref", and then the final outer ")", and just have the reference directly. With the nested parentheses it looks a little awkward right now.

[pdebuyl]

@kyleniemeyer the paper was submitted before we required the "statement of need", which is why I didn't check for it (or whedon indeed).

Should the software archive be updated if only the paper is modified or can the author keep the current version 2.0.1 and the corresponding zenodo archive?

[kyleniemeyer]

@pdebuyl no worries!

If only the software is modified, the archive does not need to be updated, since we (JOSS) archive the software.

[CFGrote]

Hi @CFGrote, I'm the EIC on duty this week, and doing some final checks before publishing.

In the paper, I noticed a few issues:

* In your title, I think "python3" should be changed to "Python 3"

* You do not have an explicit Statement of Need, one of our [required elements](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain), that illustrates the research purpose of the software (you can probably just reorganize your existing text slightly)

* please put commas after "i.e" or "e.g."

* in the third paragraph, I think you can remove the "(see e.g. Ref", and then the final outer ")", and just have the reference directly. With the nested parentheses it looks a little awkward right now.

done by https://github.com/mpievolbio-scicomp/cancer_sim/pull/29, thanks for the comments @kyleniemeyer .

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

Looks good to me!

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41576-019-0114-6 is OK
- 10.1038/ng.3489 is OK
- 10.1038/nrc4029 is OK
- 10.1186/s12885-019-5597-1 is OK
- 10.1038/nature14971 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

: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/1747

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1747, 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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1748
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02436
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...

[kyleniemeyer]

I see the paper at https://joss.theoj.org/papers/10.21105/joss.02436, but the DOI does not seem to be resolving. I'll hold off closing this until it does.

[kyleniemeyer]

But, in the meantime, congrats @CFGrote on your article's publication in JOSS!

Many thank to @jenzopr and @blakeaw for reviewing this, and @pdebuyl for editing.

[whedon]

: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.02436/status.svg)](https://doi.org/10.21105/joss.02436)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02436">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02436/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02436/status.svg
   :target: https://doi.org/10.21105/joss.02436

This is how it will look in your documentation:

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