[REVIEW]: Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development #6415

editorialbot · 2024-02-26T18:33:03Z

Submitting author: @jpmorgan98 (J. Piper Morgan)
Repository: https://github.com/CEMeNT-PSAAP/MCDC
Branch with paper.md (empty if default branch):
Version: 0.9.1
Editor: @kellyrowland
Reviewers: @lewisfish, @szabo137
Archive: 10.5281/zenodo.10576604

Status

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Markdown: [![status](https://joss.theoj.org/papers/2974750fe1da49e79bc155f1171263d9/status.svg)](https://joss.theoj.org/papers/2974750fe1da49e79bc155f1171263d9)

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

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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 ✨

Checklists

📝 Checklist for @lewisfish

📝 Checklist for @szabo137

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-02-26T18:33:06Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2024-02-26T18:33:09Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.19 s (751.4 files/s, 113950.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         112           3083           3292          12881
reStructuredText                 6            269            316            343
Markdown                         5            103              0            335
YAML                             9             25             40            222
TeX                              1             15              0            103
Bourne Shell                     3             26             13             56
TOML                             1              4              0             50
DOS Batch                        1              8              1             26
make                             1              4              7              9
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           140           3537           3669          14026
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-26T18:33:10Z

Wordcount for paper.md is 1051

editorialbot · 2024-02-26T18:33:32Z

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

OK DOIs

- 10.1145/2833157.2833162 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1080/00295639.2022.2143704 is OK
- 10.1080/00295639.2022.2091906 is OK
- 10.48550/arXiv.2305.07636 is OK
- 10.1145/3626957 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-26T18:34:09Z

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

kellyrowland · 2024-03-11T18:19:10Z

@lewisfish @szabo137 checking in here on getting reviews started; you can generate your checklist via:

@editorialbot generate my checklist

please let me know if you need to set this down or if you have any other questions/concerns.

lewisfish · 2024-03-21T10:21:58Z

Review checklist for @lewisfish

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/CEMeNT-PSAAP/MCDC?
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 (@jpmorgan98) 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?

lewisfish · 2024-03-22T13:16:29Z

@jpmorgan98 For the section in the paper discussing MCDC vs other codes. How does MCDC compare with open source neutron codes such as openMC or GEANT4? Also what codes are hard to aquire, install etc (guessing MCNP?)? It would be good to cite these packages (or others if the ones I chose are not appropriate).

jpmorgan98 · 2024-03-22T19:55:07Z

OpenMC is the other major open source transport code we usually make comparisons to but we can certainly talk about Geant4 as well. I will add that to the paper.

MCNP and Shift where the two major softwares we had in mind for difficult to access. Both of them are export controlled and only available via RSICC which can come with significant cost and time delays. I will expand on that in the paper and add those citations.

I will also dig into those issues with the team!

Thanks!

jpmorgan98 · 2024-03-27T23:00:43Z

@lewisfish We have edited those sections of the paper to include comments about other software in this space and fixed/explained all the issues you raised in CEMeNT-PSAAP/MCDC#173 and CEMeNT-PSAAP/MCDC#174. The changes have been merged into our main branch. Let me know if there is anything we need from us to complete your review! Thank you again!

szabo137 · 2024-03-28T10:22:50Z

Review checklist for @szabo137

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/CEMeNT-PSAAP/MCDC?
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 (@jpmorgan98) 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?

lewisfish · 2024-03-28T15:06:39Z

@lewisfish We have edited those sections of the paper to include comments about other software in this space and fixed/explained all the issues you raised in CEMeNT-PSAAP/MCDC#173 and CEMeNT-PSAAP/MCDC#174. The changes have been merged into our main branch. Let me know if there is anything we need from us to complete your review! Thank you again!

Looks great! One final issue I've noticed is that with the updated doc strings, it seems the readthedocs website has not been rebuilt with them. If you update the online docs I think that the review done from my side.

@editorialbot generate pdf

jpmorgan98 · 2024-03-28T20:41:01Z

Ugh right, always more buttons to push. Changes are live. lmk if there's anything further. Thanks again

lewisfish · 2024-03-28T22:35:36Z

I feel your pain.
I think that's it from my side. Thanks for responding to all my issues so quickly!

szabo137 · 2024-04-02T19:12:37Z

@jpmorgan98 First of all, I like the package, and the paper, especially the focus on usability is very positive for scalable software, which is supposed to be executed in HPC environments.

Regarding this review, I have no concerns with this one.

Beyond this, you could think of adding a docker file to improve the installation procedure even further.

jpmorgan98 · 2024-04-02T19:22:01Z

A docker container is a great idea and I will add an issue to track that! Is there anything else I need to do on my front or is this review done? Thank you both again!

kellyrowland · 2024-04-08T17:12:27Z

Looks like the reviewers have checked off all of their boxes, so I'll move along with getting this wrapped up.

kellyrowland · 2024-04-08T17:12:57Z

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

Read the text of the paper and offer comments/corrections (as either a list or a pull request)
Check that the archive title, author list, version tag, and the license are correct
Set archive DOI with @editorialbot set <DOI here> as archive
Set version with @editorialbot set <version here> as version
Double check rendering of paper with @editorialbot generate pdf
Specifically check the references with @editorialbot check references and ask author(s) to update as needed
Recommend acceptance with @editorialbot recommend-accept

kellyrowland · 2024-04-08T17:13:13Z

@editorialbot generate pdf

editorialbot · 2024-04-08T17:14:36Z

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

kellyrowland · 2024-04-08T17:14:54Z

@editorialbot check references

kellyrowland · 2024-04-08T17:53:13Z

@editorialbot generate pdf

editorialbot · 2024-04-08T17:54:55Z

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

kellyrowland · 2024-04-08T18:19:52Z

@jpmorgan98 please issue a new tagged release of the software (if changed since the start of the review), and archive it (on Zenodo, figshare, or elsewhere). Then, please then post the version number and archive DOI here in the review issue, and I'll follow some subsequent wrap-up steps from there.

jpmorgan98 · 2024-04-08T18:36:00Z

Version number 0.9.1 tagged
Zenodo Archive: 10.5281/zenodo.10576604

Thanks

kellyrowland · 2024-04-08T18:48:25Z

@editorialbot set 0.9.1 as version

editorialbot · 2024-04-08T18:48:27Z

Done! version is now 0.9.1

kellyrowland · 2024-04-08T18:48:49Z

@editorialbot set 10.5281/zenodo.10576604 as archive

editorialbot · 2024-04-08T18:48:51Z

Done! archive is now 10.5281/zenodo.10576604

kellyrowland · 2024-04-08T18:52:45Z

thanks @jpmorgan98 - can you edit the archive metadata so that:

the licenses match (repo has BSD, archive lists CC)
the authors are listed in the same order between the paper and the archive

jpmorgan98 · 2024-04-08T18:59:47Z

@kellyrowland - fixed

kellyrowland · 2024-04-08T19:01:33Z

@editorialbot recommend-accept

editorialbot · 2024-04-08T19:01:36Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-04-08T19:01:59Z

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

OK DOIs

- 10.1145/2833157.2833162 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1080/00295639.2022.2143704 is OK
- 10.48550/arXiv.2403.06106 is OK
- 10.48550/arXiv.2306.11600 is OK
- 10.13182/physor22-37871 is OK
- 10.48550/arXiv.2305.07646 is OK
- 10.48550/arXiv.2305.07641 is OK
- 10.1080/00295639.2022.2091906 is OK
- 10.1016/j.jqsrt.2024.108958 is OK
- 10.48550/arXiv.2305.07636 is OK
- 10.1145/3626957 is OK
- 10.1016/j.anucene.2019.01.012 is OK
- 10.1016/j.anucene.2014.08.047 is OK
- 10.2172/1909545 is OK
- 10.1016/j.anucene.2014.07.048 is OK
- 10.1016/S0168-9002(03)01368-8 is OK
- 10.48550/arXiv.2403.06362 is OK

MISSING DOIs

- No DOI given, and none found for title: Computational methods of neutron transport

INVALID DOIs

- None

editorialbot · 2024-04-08T19:03:01Z

👋 @openjournals/pe-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#5232, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2024-04-09T06:20:41Z

@editorialbot accept

editorialbot · 2024-04-09T06:20:43Z

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

editorialbot · 2024-04-09T06:27:55Z

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: Morgan
  given-names: Joanna Piper
  orcid: "https://orcid.org/0000-0003-1379-5431"
- family-names: Variansyah
  given-names: Ilham
  orcid: "https://orcid.org/0000-0003-3426-7160"
- family-names: Pasmann
  given-names: Samuel L.
  orcid: "https://orcid.org/0000-0003-1391-1471"
- family-names: Clements
  given-names: Kayla B.
  orcid: "https://orcid.org/0000-0003-3358-5618"
- family-names: Cuneo
  given-names: Braxton
  orcid: "https://orcid.org/0000-0002-6493-0990"
- family-names: Mote
  given-names: Alexander
  orcid: "https://orcid.org/0000-0001-5099-0223"
- family-names: Goodman
  given-names: Charles
- family-names: Shaw
  given-names: Caleb
- family-names: Northrop
  given-names: Jordan
  orcid: "https://orcid.org/0000-0003-0420-9699"
- family-names: Pankaj
  given-names: Rohan
  orcid: "https://orcid.org/0009-0005-0445-9323"
- family-names: Lame
  given-names: Ethan
  orcid: "https://orcid.org/0000-0001-7686-9755"
- family-names: Whewell
  given-names: Benjamin
  orcid: "https://orcid.org/0000-0001-7826-5525"
- family-names: McClarren
  given-names: Ryan G.
  orcid: "https://orcid.org/0000-0002-8342-6132"
- family-names: Palmer
  given-names: Todd S.
  orcid: "https://orcid.org/0000-0003-3310-5258"
- family-names: Chen
  given-names: Lizhong
  orcid: "https://orcid.org/0000-0001-5890-7121"
- family-names: Anistratov
  given-names: Dmitriy Y.
- family-names: Kelley
  given-names: C. T.
- family-names: Palmer
  given-names: Camille J.
  orcid: "https://orcid.org/0000-0002-7573-4215"
- family-names: Niemeyer
  given-names: Kyle E.
  orcid: "https://orcid.org/0000-0003-4425-7097"
contact:
- family-names: Morgan
  given-names: Joanna Piper
  orcid: "https://orcid.org/0000-0003-1379-5431"
- family-names: Variansyah
  given-names: Ilham
  orcid: "https://orcid.org/0000-0003-3426-7160"
doi: 10.5281/zenodo.10576604
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Morgan
    given-names: Joanna Piper
    orcid: "https://orcid.org/0000-0003-1379-5431"
  - family-names: Variansyah
    given-names: Ilham
    orcid: "https://orcid.org/0000-0003-3426-7160"
  - family-names: Pasmann
    given-names: Samuel L.
    orcid: "https://orcid.org/0000-0003-1391-1471"
  - family-names: Clements
    given-names: Kayla B.
    orcid: "https://orcid.org/0000-0003-3358-5618"
  - family-names: Cuneo
    given-names: Braxton
    orcid: "https://orcid.org/0000-0002-6493-0990"
  - family-names: Mote
    given-names: Alexander
    orcid: "https://orcid.org/0000-0001-5099-0223"
  - family-names: Goodman
    given-names: Charles
  - family-names: Shaw
    given-names: Caleb
  - family-names: Northrop
    given-names: Jordan
    orcid: "https://orcid.org/0000-0003-0420-9699"
  - family-names: Pankaj
    given-names: Rohan
    orcid: "https://orcid.org/0009-0005-0445-9323"
  - family-names: Lame
    given-names: Ethan
    orcid: "https://orcid.org/0000-0001-7686-9755"
  - family-names: Whewell
    given-names: Benjamin
    orcid: "https://orcid.org/0000-0001-7826-5525"
  - family-names: McClarren
    given-names: Ryan G.
    orcid: "https://orcid.org/0000-0002-8342-6132"
  - family-names: Palmer
    given-names: Todd S.
    orcid: "https://orcid.org/0000-0003-3310-5258"
  - family-names: Chen
    given-names: Lizhong
    orcid: "https://orcid.org/0000-0001-5890-7121"
  - family-names: Anistratov
    given-names: Dmitriy Y.
  - family-names: Kelley
    given-names: C. T.
  - family-names: Palmer
    given-names: Camille J.
    orcid: "https://orcid.org/0000-0002-7573-4215"
  - family-names: Niemeyer
    given-names: Kyle E.
    orcid: "https://orcid.org/0000-0003-4425-7097"
  date-published: 2024-04-09
  doi: 10.21105/joss.06415
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6415
  title: "Monte Carlo / Dynamic Code (MC/DC): An accelerated Python
    package for fully transient neutron transport and rapid methods
    development"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06415"
  volume: 9
title: "Monte Carlo / Dynamic Code (MC/DC): An accelerated Python
  package for fully transient neutron transport and rapid methods
  development"

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.

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editorialbot · 2024-04-09T06:27:59Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-04-09T06:28:00Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06415 joss-papers#5233
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06415
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2024-04-09T06:28:26Z

@lewisfish, @szabo137 – many thanks for your reviews here and to @kellyrowland for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@jpmorgan98 – your paper is now accepted and published in JOSS ⚡🚀💥

editorialbot · 2024-04-09T06:28:28Z

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

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kyleniemeyer · 2024-04-12T12:53:47Z

@openjournals/dev it looks like @kellyrowland's name in the "Editor:" field has a different link color - and in fact the link there seems broken. Any idea what's going on? The ORCID link works ok. I assume that is supposed to link to a personal webpage?

arfon · 2024-05-13T06:59:28Z

It looks like @kellyrowland's URL on her JOSS editor profile was incomplete. I've fixed it now and will try reaccepting.

arfon · 2024-05-13T06:59:39Z

@editorialbot reaccept

editorialbot · 2024-05-13T06:59:41Z

Rebuilding paper!

editorialbot · 2024-05-13T07:01:47Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5343

editorialbot added Python review Shell Track: 3 (PE) Physics and Engineering labels Feb 26, 2024

editorialbot assigned kellyrowland Feb 26, 2024

editorialbot mentioned this issue Feb 26, 2024

[PRE REVIEW]: Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development #6353

Closed

This was referenced Mar 21, 2024

Installation issue CEMeNT-PSAAP/MCDC#170

Closed

Broken examples CEMeNT-PSAAP/MCDC#173

Closed

Missing/incomplete Documentation CEMeNT-PSAAP/MCDC#174

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 8, 2024

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[REVIEW]: Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development #6415

[REVIEW]: Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development #6415

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editorialbot commented Feb 26, 2024 • edited

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lewisfish commented Mar 21, 2024 • edited

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lewisfish commented Mar 22, 2024

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szabo137 commented Mar 28, 2024 • edited

Review checklist for @szabo137

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lewisfish commented Mar 28, 2024

jpmorgan98 commented Mar 28, 2024 • edited

lewisfish commented Mar 28, 2024

szabo137 commented Apr 2, 2024

jpmorgan98 commented Apr 2, 2024

kellyrowland commented Apr 8, 2024

kellyrowland commented Apr 8, 2024 • edited

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editorialbot commented Feb 26, 2024 •

edited

lewisfish commented Mar 21, 2024 •

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szabo137 commented Mar 28, 2024 •

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jpmorgan98 commented Mar 28, 2024 •

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kellyrowland commented Apr 8, 2024 •

edited