[REVIEW]: DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python

[whedon]

Submitting author: @artgoldberg (Arthur Goldberg)
Repository: https://github.com/KarrLab/de_sim
Version: 1.0.5
Editor: @danielskatz
Reviewers: @gonsie, @carothersc, @yadudoc
Archive: 10.5281/zenodo.4274852

⚠️ 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

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/e3ca43be9717d153672c48239939e993/status.svg)](https://joss.theoj.org/papers/e3ca43be9717d153672c48239939e993)

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

@gonsie & @carothersc, 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 @danielskatz 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 @gonsie

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 (@artgoldberg) 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: Do the authors clearly state 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 @carothersc

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 (@artgoldberg) 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: Do the authors clearly state 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 @yadudoc

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 (@artgoldberg) 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: Do the authors clearly state 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. @gonsie, @carothersc 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]

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

OK DOIs

- 10.1145/2901378.2901402 is OK
- 10.1177/003754978704900506 is OK
- 10.1109/DATE.2001.915002 is OK
- 10.1109/WSC.2003.1261534 is OK
- 10.1109/PADS.2000.847144 is OK
- 10.1016/j.copbio.2017.12.013 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.mib.2015.06.004 is OK
- 10.1016/j.cell.2012.05.044 is OK
- 10.1109/wodes.2006.382398 is OK
- 10.1109/wsc.2005.1574302 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[danielskatz]

👋 @gonsie, @carothersc - Thanks again for agreeing to review. Please read the comments above before starting.

This is the review thread for the paper. All of our communications will happen here from now on.

All 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 #2685 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 2-4 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 (@danielskatz) if you have any questions/concerns.

[danielskatz]

Thanks for getting started @gonsie
@carothersc, let me know if you need anything on your side

[artgoldberg]

Hi @danielskatz. @gonsie finds that one of DE Sim's unit tests fails because of a problem in the capturer testing library. The test passes on multiple platforms (local, Docker on local, Docker in CircleCI) for me and I have not reproduced the capturer failure thus far. See KarrLab/de_sim#55 for the details.

How would you suggest we proceed?

Thanks
Arthur

[danielskatz]

It seems to me that either there is a problem that should be discussed in the documentation, with a workaround, or something else.

[artgoldberg]

Thanks @danielskatz

OK. I have replaced the failing code in DE Sim's tests with a method from Python's standard library that will hopefully avoid the problem. See KarrLab/de_sim#55 for further details.

Arthur

[artgoldberg]

Hello @danielskatz

I'm available to address any other issues reviewers raise.

Arthur

[danielskatz]

@gonsie & @carothersc - can I get an update on your review status? It would be great to get this moving a bit further along...

[danielskatz]

@whedon re-invite @carothersc as reviewer

[whedon]

The reviewer already has a pending invite.

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

[danielskatz]

@whedon re-invite @carothersc as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[artgoldberg]

Hello @danielskatz

I'm beginning to wonder whether Prof. Carothers (@carothersc) will review this paper. I can expand my list of potential reviewers if you would like.

Arthur

[danielskatz]

I was in email contact with @carothersc last week, and he said he should be able to do it soon

[artgoldberg]

Thanks @danielskatz

[carothersc-zz]

Hi all - given that Elsa has confirmed running the software on her side do I need to do the same ? Also, can someone confirm that "pip" won't do anything bad to local "conda" repos?

Thanks everyone!,
Chris

[danielskatz]

We expect the reviewers to be independent in terms of investigation, though they may work together in documenting problems and suggesting solutions.

[danielskatz]

Re pip, I suggest the safest thing is to create a new conda environment for this review

[artgoldberg]

Thanks!

[artgoldberg]

@danielskatz FYI, it may take a few days for me to provide the final version of the paper and the archive DOI. I want my co-author Prof. Karr to have an opportunity to review them, but he's busy with a new child.

[artgoldberg]

@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

[artgoldberg]

Hi @danielskatz

The paper you compiled with Whedon looks fine. Jonathan and I made a couple of dozen small changes to fix typos, improve wording, and clarify a couple of points.

I've created a tagged release of de-sim, with tag 1.0.4.
This release is archived at Zenodo with DOI 10.5281/zenodo.4274852.

Thanks

Arthur

[danielskatz]

@whedon generate pdf

I'll do most of the rest of the processing tomorrow...

[danielskatz]

@whedon set 1.0.5 as version

[whedon]

OK. 1.0.5 is the version.

[danielskatz]

@whedon set 10.5281/zenodo.4274852 as archive

[whedon]

OK. 10.5281/zenodo.4274852 is the archive.

[whedon]

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

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1145/2901378.2901402 is OK
- 10.1177/003754978704900506 is OK
- 10.1109/DATE.2001.915002 is OK
- 10.1109/WSC.2003.1261534 is OK
- 10.1109/PADS.2000.847144 is OK
- 10.1016/j.copbio.2017.12.013 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1016/j.mib.2015.06.004 is OK
- 10.1016/j.cell.2012.05.044 is OK
- 10.1109/wodes.2006.382398 is OK
- 10.1109/wsc.2005.1574302 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#1917

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1917, 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]

@openjournals/dev - note that in the xml to be submitted to Crossref, the ~ in the Matloff unstructured citation has been turned into a space. There's probably a bug in parsing somewhere... Can we (you) manually fix this in this case? If so, now or after I do the actual accept?

[danielskatz]

@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.02685 joss-papers#1918
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02685
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...

[danielskatz]

Congratulations to @artgoldberg (Arthur Goldberg) and co-author!!

and thanks to @gonsie & @yadudoc for reviewing!

[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.02685/status.svg)](https://doi.org/10.21105/joss.02685)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02685">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02685/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02685/status.svg
   :target: https://doi.org/10.21105/joss.02685

This is how it will look in your documentation:

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[arfon]

@openjournals/dev - note that in the xml to be submitted to Crossref, the ~ in the Matloff unstructured citation has been turned into a space. There's probably a bug in parsing somewhere... Can we (you) manually fix this in this case? If so, now or after I do the actual accept?

@danielskatz - Crossref deposit XML is fixed up now and I've opened an issue (openjournals/whedon-api#122) to track this bug.

[artgoldberg]

@danielskatz Greatly appreciate your patience, effort, persistence and care reviewing our paper. Great catch of the s/~/ / bug in, it appears, the LaTeX converter.

I see that you enjoy sailing. Me too. If you come to New York during warm weather, let me know and I'll gladly take you sailing at the City Island Yacht Club.