[REVIEW]: neworder: a dynamic microsimulation framework for python

[whedon]

Submitting author: @virgesmith (Andrew Smith)
Repository: https://github.com/virgesmith/neworder
Version: v1.0.0
Editor: @danielskatz
Reviewer: @platipodium, @tresoldi
Archive: 10.5281/zenodo.5090120

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Markdown: [![status](https://joss.theoj.org/papers/4b7cc8402819ff48fc7403c0e9a265e9/status.svg)](https://joss.theoj.org/papers/4b7cc8402819ff48fc7403c0e9a265e9)

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Review checklist for @platipodium

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 (@virgesmith) 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 @tresoldi

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 (@virgesmith) 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. @platipodium, @tresoldi 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.

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.17 s (861.2 files/s, 75894.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          71           1242           1373           3360
C++                             13            451            306           1819
Markdown                        27            978              2           1463
C/C++ Header                    14            262            142            632
YAML                             8             72             96            394
TeX                              1              9              0             86
HTML                             1             16              0             75
Bourne Shell                     7             25             16             45
XML                              2              0              0             40
TOML                             1              2              0             13
Dockerfile                       1              8              3             12
JavaScript                       1              0              0             12
-------------------------------------------------------------------------------
SUM:                           147           3065           1938           7951
-------------------------------------------------------------------------------


Statistical information for the repository 'db6585ba2932647bd07e6866' was
gathered on 2021/06/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andrew Smith                    18          1265            760            3.98
virgesmith                     522         28471          20421           96.02

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
virgesmith                 8567           30.1         13.8               17.99

[whedon]

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

OK DOIs

- 10.1007/978-3-319-44663-9 is OK
- 10.1002/nav.3800260304 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[danielskatz]

👋 @platipodium and @tresoldi - Thanks for agreeing to review this submission.
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.

Please read the first couple of comments in this issue carefully, so that you can accept the invitation from JOSS and be able to check items, and so that you don't get overwhelmed with notifications from other activities in JOSS.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3351 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 either 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.

[virgesmith]

thanks @danielskatz @platipodium @tresoldi! I'll aim to respond to any issues you raise as quickly as possible

[platipodium]

Created virgesmith/neworder#60 regarding functionality and example testing.

[platipodium]

Created virgesmith/neworder#61 for duplicated CPU work

[platipodium]

And another one on warnings in default installation virgesmith/neworder#62. I guess I should learn how to link to the upstream repository....

[danielskatz]

@platipodium - see the answer in #3351 (comment)

[platipodium]

And another one on failed import in n-body example: virgesmith/neworder#63

[platipodium]

@platipodium - see the answer in #3351 (comment)

I guess my attempt to mention failed :=( See virgesmith/neworder#63 (comment)

[whedon]

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

[whedon]

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

[danielskatz]

👋 @tresoldi @platipodium - How are things going with your reviews?

[platipodium]

trying again the mentioning thingy ... here again for reference virgesmith/neworder#65

[platipodium]

I am happy with the software and paper pending the two issues with contributing virgesmith/neworder#65 and copyright update virgesmith/neworder#66

[danielskatz]

If you are ok with them, please merge them, and then

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

I can then move forward with accepting the submission.

[virgesmith]

@danielskatz @platipodium @tresoldi thanks for your efforts, really appreciated esp in current circumstances
I will get on with the v1.0.0 release now...

[virgesmith]

@danielskatz. 1.0.0 now released, DOI: 10.5281/zenodo.5090120, however you now appear as an author in the metadata

[edit]...which is now corrected

[danielskatz]

Maybe you can remove me as an author - the metadata is just what zenodo suggests, but you can change it

[virgesmith]

done, thanks

[danielskatz]

@whedon set 10.5281/zenodo.5090120 as archive

[whedon]

OK. 10.5281/zenodo.5090120 is the archive.

[danielskatz]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[danielskatz]

@virgesmith - can you change the metadata in the zenodo archive to make the title of archive match the title of the paper?

[virgesmith]

@danielskatz done

[danielskatz]

@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

- 10.1007/978-3-319-44663-9 is OK
- 10.1002/nav.3800260304 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#2443

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2443, 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]

@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.03351 joss-papers#2444
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03351
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 @virgesmith (Andrew Smith)!!

And thanks to @platipodium and @tresoldi for reviewing!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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