[REVIEW]: Simulation Decomposition in Python

[editorialbot]

Submitting author: @tupui (Pamphile ROY)
Repository: https://github.com/Simulation-Decomposition/simdec-python
Branch with paper.md (empty if default branch): joss
Version: 1.2.0
Editor: @crvernon
Reviewers: @JoshuaOsborneDATA, @matt-graham
Archive: 10.5281/zenodo.11535796

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/4099ffcb203538a89427e108392a4423/status.svg)](https://joss.theoj.org/papers/4099ffcb203538a89427e108392a4423)

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

@JoshuaOsborneDATA & @matt-graham, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @matt-graham

📝 Checklist for @JoshuaOsborneDATA

[editorialbot]

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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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[editorialbot]

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1016/j.envsoft.2023.105898 is OK
- 10.21105/joss.05309 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (823.0 files/s, 372517.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              3              0              0          14003
Python                          10            329            207           1107
HTML                             3              6             13            458
YAML                             9             30             26            250
Markdown                         4             95              0            234
make                             2             28             14            117
TOML                             1             11              0             80
Dockerfile                       1             13              8             57
TeX                              1              3              0             44
reStructuredText                 3             14              8             29
JSON                             1              0              0             17
-------------------------------------------------------------------------------
SUM:                            38            529            276          16396
-------------------------------------------------------------------------------

Commit count by author:

   204	Pamphile Roy
     1	gnopik

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 416

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

[editorialbot]

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

[matt-graham]

Review checklist for @matt-graham

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 https://github.com/Simulation-Decomposition/simdec-python?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tupui) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[crvernon]

👋 @tupui, @JoshuaOsborneDATA, and @matt-graham - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) 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 #6713 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[JoshuaOsborneDATA]

Review checklist for @JoshuaOsborneDATA

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 https://github.com/Simulation-Decomposition/simdec-python?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@tupui) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[tupui]

Thank you all for agreeing to review our work. Let us know if there is anything we can do 😃

[crvernon]

👋 @tupi, @JoshuaOsborneDATA, and @matt-graham

I'm just checking in to see how the review is coming along. Could you please provide a short update in this thread. Thanks!

[matt-graham]

I'm just checking in to see how the review is coming along. Could you please provide a short update in this thread. Thanks!

@crvernon I've started on review and raised some issues with regards to some points I've come across so far while working through checklist.

@tupui - a quick general question with regards to list of authors. Is gnopik the GitHub user for author 'Mariia Kozlova'? I'm checking as the reviewer checklist asks us to check that 'the full list of paper authors seem appropriate and complete' with some guidelines on what constitutes authorship given in the JOSS documentation. I can see that gnopik has opened several issues and reviewed pull requests, which I believe would qualify for authorship under the JOSS guidelines, but as they do not have a name listed on their profile I wanted to check if this indeed the same person as included in the author list.

[tupui]

Hi @matt-graham, yes gnopik is Mariia Kozlova. I have written some text in the first JOSS issue regarding authorship, see this #6661 (comment)

Thank you for raising the other issues, I will reply there.

[matt-graham]

Hi @tupui, thanks for the clarification and link to the comment in the pre-review issue, I'd missed that!

[tupui]

Hi all, I took into account all the comments now. Could you please take another look?

[tupui]

@editorialbot generate pdf

[tupui]

Hi everyone, just checking the status here. We addressed all the comments, thank you again 🙇

[editorialbot]

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

[tupui]

I connected with my GitHub auth but filled everything manually. I did not know there was a special thing for software. Shall I start over?

[crvernon]

Yeah, something is off I believe. Usually I do the following workflow:

• Log in to Zenodo using your GitHub account
• In the top right hand corner of the screen where your login name is, click the dropdown and navigate to the "GitHub" tab
• If you don't see any repos, click "Connect". You should then see all GitHub repos you are admin on.
• Navigate to the one you are interested in and click the on/off toggle to on.
• Go to the target repo on GitHub and create the release. This should automatically trigger an archive to start being formed on Zenodo.
• Navigate back to Zenodo and click on your repo of interest, the one you just toggled to "on"
• Once the archive says "Published" with a green check, click the DOI link to navigate to that record.

If you give me the link from that last step, I can run the rest from my side. Thanks!

[tupui]

Hi @crvernon, I deleted the draft on Zenodo and followed your instructions now to create a new version.

Was indeed immediate like that. (Probably a good idea to tell people to do this in the template.)

https://zenodo.org/records/11535796

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1016/j.envsoft.2023.105898 is OK
- 10.21105/joss.05309 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1002/9780470725184 is OK
- 10.5281/zenodo.11261266 is OK

MISSING DOIs

- No DOI given, and none found for title: Sensitivity analysis for non-linear mathematical m...
- No DOI given, and none found for title: Better Regulation Toolbox

INVALID DOIs

- None

[crvernon]

@editorialbot set 10.5281/zenodo.11535796 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11535796

[crvernon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1016/j.envsoft.2023.105898 is OK
- 10.21105/joss.05309 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1002/9780470725184 is OK
- 10.5281/zenodo.11261266 is OK

MISSING DOIs

- No DOI given, and none found for title: Sensitivity analysis for non-linear mathematical m...
- No DOI given, and none found for title: Better Regulation Toolbox

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5471, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

🔍 checking out the following:

• reviewer checklists are completed or addressed
• version set
• archive set
• archive names (including order) and title in archive matches those specified in the paper
• archive uses the same license as the repo and is OSI approved as open source
• archive DOI and version match or redirect to those set by editor in review thread
• paper is error free - grammar and typos
• paper is error free - test links in the paper and bib
• paper is error free - refs preserve capitalization where necessary
• paper is error free - no invalid refs without justification

[crvernon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Roy
  given-names: Pamphile T.
  orcid: "https://orcid.org/0000-0001-9816-1416"
- family-names: Kozlova
  given-names: Mariia
  orcid: "https://orcid.org/0000-0002-6952-7682"
contact:
- family-names: Roy
  given-names: Pamphile T.
  orcid: "https://orcid.org/0000-0001-9816-1416"
doi: 10.5281/zenodo.11535796
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Roy
    given-names: Pamphile T.
    orcid: "https://orcid.org/0000-0001-9816-1416"
  - family-names: Kozlova
    given-names: Mariia
    orcid: "https://orcid.org/0000-0002-6952-7682"
  date-published: 2024-06-10
  doi: 10.21105/joss.06713
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6713
  title: Simulation Decomposition in Python
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06713"
  volume: 9
title: Simulation Decomposition in Python

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06713 joss-papers#5472
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06713
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...

[crvernon]

🥳 Congratulations on your new publication @tupui! Many thanks to @JoshuaOsborneDATA and @matt-graham for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

[editorialbot]

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

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HTML:
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reStructuredText:
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[tupui]

Yay thanks a lot 🥳 And yes I will fill out the form! [done]