[REVIEW]: ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran

whedon commented 4 years ago

Submitting author: @shahmoradi (Amir Shahmoradi) Repository: https://github.com/cdslaborg/paramonte Version: v1.5.1 Editor: @VivianePons Reviewer: @milancurcic, @williamfgc Archive: 10.5281/zenodo.4749957

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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

@milancurcic & @williamfgc, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 @milancurcic

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 (@shahmoradi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 @williamfgc

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 (@shahmoradi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[X] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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.) I don't have enough domain knowledge to conduct a study on the topic

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. Reviewer: There are build instructions, but
[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? There are manual steps, but not automatic CI
[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 Since it's hosted on GitHub it's following the typical workflow, issues, PR

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 commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2304
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02741
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

Congratulations to @shahmoradi (Amir Shahmoradi) and co-author!!

And thanks to @milancurcic and @williamfgc for reviewing, and @VivianePons for editing!

whedon commented 3 years ago

: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.02741/status.svg)](https://doi.org/10.21105/joss.02741)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02741">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02741/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02741/status.svg
   :target: https://doi.org/10.21105/joss.02741

This is how it will look in your documentation:

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danielskatz commented 3 years ago

@arfon and @shahmoradi - I just realized (due to a comment by @kyleniemeyer in another review) that I made a mistake when suggesting edits to this paper, which removed some of the references. Specifically, in https://github.com/cdslaborg/paramonte/pull/14, I put multiple references together with commas, instead of the correct semicolons, which led to all but the first of each set not being included in the pdf.

I'm quite sorry about this.

I'm not sure how to fix this, as I think the paper src has been deleted.

Can we fix this? If so, how?

shahmoradi commented 3 years ago

Thanks for the note. I have revived the manuscript Markdown file in the project's repository. Please let me know if I have to do anything else. Thank you.

danielskatz commented 3 years ago

Thanks @shahmoradi - can you merge https://github.com/cdslaborg/paramonte/pull/15

arfon commented 3 years ago

Can we fix this? If so, how?

I think this should be fixed in https://github.com/openjournals/joss-papers/commit/c529ab42dd63f73bccc42b105115deca72b468c8 (which basically includes all of these changes @danielskatz)

danielskatz commented 3 years ago

The two references at the end of the paragraph that starts with "For each parallel simulation" also should be put together, I think

danielskatz commented 3 years ago

And the same with the two at the end of the paragraph that starts with "To alleviate"

arfon commented 3 years ago

Done and done. The updated paper might take a few hours to show up due to caching but it should be fixed.

danielskatz commented 3 years ago

Thanks! And again, sorry for this mistake on my part.

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