[REVIEW]: kinisi: Bayesian analysis of mass transport from molecular dynamics simulations #5984

editorialbot · 2023-10-25T09:54:13Z

Submitting author: @arm61 (Andrew McCluskey)
Repository: https://github.com/bjmorgan/kinisi/
Branch with paper.md (empty if default branch):
Version: 1.0.0
Editor: @zhubonan
Reviewers: @hmacdope, @dengzeyu
Archive: 10.5281/zenodo.10651128

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1ae102ffb6b3c63b04c002976440815d"><img src="https://joss.theoj.org/papers/1ae102ffb6b3c63b04c002976440815d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1ae102ffb6b3c63b04c002976440815d/status.svg)](https://joss.theoj.org/papers/1ae102ffb6b3c63b04c002976440815d)

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

@denzeyu & @hmacdope, 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 @zhubonan 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 @dengzeyu

📝 Checklist for @hmacdope

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

editorialbot · 2023-10-25T09:54:16Z

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

For a list of things I can do to help you, just type:

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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 · 2023-10-25T09:54:20Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (719.1 files/s, 158912.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              4              4              4           3342
Python                          16            568           1374           2596
Markdown                        11            144              0            400
Jupyter Notebook                 6              0           1590            313
TeX                              1             20              0            210
YAML                             4              7              4             93
TOML                             1              7              0             74
CSS                              1              2              0              9
make                             1              4              6              9
reStructuredText                 4              8             32              8
-------------------------------------------------------------------------------
SUM:                            49            764           3010           7054
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-10-25T09:54:21Z

Wordcount for paper.md is 739

editorialbot · 2023-10-25T09:54:28Z

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

OK DOIs

- 10.1103/PhysRevB.47.558 is OK
- 10.1103/PhysRevB.49.14251 is OK
- 10.21105/joss.01864 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.25080/majora-629e541a-00e is OK
- 10.1002/jcc.21787 is OK
- 10.21105/joss.02214 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1103/physrevlett.112.145901 is OK
- 10.1021/acs.chemmater.0c03738 is OK
- 10.1038/s41563-022-01316-z is OK
- 10.1016/j.sbi.2009.03.004 is OK
- 10.1002/jcc.21939 is OK
- 10.1021/acs.chemmater.9b01824 is OK
- 10.1021/la901314b is OK
- 10.1039/c5cp03414k is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-10-25T09:55:50Z

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

zhubonan · 2023-10-25T10:00:10Z

Hi @dengzeyu & @hmacdope, thanks again for agreeing to review this package.

First of all, please run this command to generate the review checklist:

@editorialbot generate my checklist

and tick the boxes as you go through the submission.

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns, please let me know.

We are aiming to have the review done in two weeks if possible - If you need more time, please let me know here in this issue.

For comments and queries, you can open issues/PRs directly in the package's repository. Please mention this issue in the tickets opened in order to keep tracking.

zhubonan · 2023-10-25T10:01:08Z

@editorialbot add @dengzeyu as reviewer

editorialbot · 2023-10-25T10:01:10Z

@dengzeyu added to the reviewers list!

zhubonan · 2023-10-25T10:01:42Z

@editorialbot remove @denzeyu from reviewers

editorialbot · 2023-10-25T10:01:44Z

@denzeyu removed from the reviewers list!

zhubonan · 2023-10-25T10:03:58Z

Err typo.... Apologies for the spam, my bad 😿

arm61 · 2023-10-26T08:36:11Z

@zhubonan, looks like the old title has been carried over to this issue. Will that cause the editoralbot other problems down the line?

zhubonan · 2023-10-26T08:46:48Z

My guess is that the metadata is stored based on the title upon submission. It should affect the review process. We just to the make sure it is corrected in the system before acceptance.

zhubonan · 2023-10-26T08:48:00Z

I have just updated the title of this issue. It should not give rise to problem as things are tracked by the integer issue ids.

dengzeyu · 2023-11-05T06:42:52Z

Review checklist for @dengzeyu

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/bjmorgan/kinisi/?
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 (@arm61) 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?

arm61 · 2023-11-09T08:06:33Z

@editorialbot generate pdf

arm61 · 2023-11-09T08:07:11Z

There has been an update to the author list. Fixing some affiliations and adding the latest contributor.

editorialbot · 2023-11-09T08:08:03Z

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

zhubonan · 2023-11-22T14:21:58Z

Hi @hmacdope, how is your review going?

zhubonan · 2024-02-13T15:59:33Z

@editorialbot set 10.5281/zenodo.10651128 as archive

editorialbot · 2024-02-13T15:59:36Z

Done! archive is now 10.5281/zenodo.10651128

zhubonan · 2024-02-13T16:02:45Z

@editorialbot check references

editorialbot · 2024-02-13T16:02:58Z

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

OK DOIs

- 10.1103/PhysRevB.47.558 is OK
- 10.1103/PhysRevB.49.14251 is OK
- 10.21105/joss.01864 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.25080/majora-629e541a-00e is OK
- 10.1002/jcc.21787 is OK
- 10.21105/joss.02214 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1103/physrevlett.112.145901 is OK
- 10.1021/acs.chemmater.0c03738 is OK
- 10.1038/s41563-022-01316-z is OK
- 10.1016/j.sbi.2009.03.004 is OK
- 10.1002/jcc.21939 is OK
- 10.1021/acs.chemmater.9b01824 is OK
- 10.1021/la901314b is OK
- 10.1039/c5cp03414k is OK

MISSING DOIs

- None

INVALID DOIs

- None

zhubonan · 2024-02-13T16:06:21Z

Hi @arm61, thanks for making the new release! Could you please update the author affiliation of the Zenodo archive? It should match those stated in the paper. The Zenodo author list can be updated without making a new DOI (since it is metadata).

arm61 · 2024-02-13T16:36:31Z

Annoyingly, the Zenodo archive didn't read the affiliations correctly from the CITATION.cff file. I will ask @bjmorgan to sort the Zenodo deposit as he is the owner.

arm61 · 2024-02-13T20:25:24Z

That's it sorted now @zhubonan!

arm61 · 2024-02-14T07:28:04Z

@editorialbot generate pdf

editorialbot · 2024-02-14T07:29:11Z

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

arm61 · 2024-02-14T07:41:18Z

Sorry just caught another missing affiliation. All matching now.

zhubonan · 2024-02-14T16:05:34Z

@editorialbot recommend-accept

editorialbot · 2024-02-14T16:05:37Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-02-14T16:05:47Z

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

OK DOIs

- 10.1103/PhysRevB.47.558 is OK
- 10.1103/PhysRevB.49.14251 is OK
- 10.21105/joss.01864 is OK
- 10.1016/0927-0256(96)00008-0 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.25080/majora-629e541a-00e is OK
- 10.1002/jcc.21787 is OK
- 10.21105/joss.02214 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.2140/camcos.2010.5.65 is OK
- 10.1103/physrevlett.112.145901 is OK
- 10.1021/acs.chemmater.0c03738 is OK
- 10.1038/s41563-022-01316-z is OK
- 10.1016/j.sbi.2009.03.004 is OK
- 10.1002/jcc.21939 is OK
- 10.1021/acs.chemmater.9b01824 is OK
- 10.1021/la901314b is OK
- 10.1039/c5cp03414k is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-14T16:06:59Z

👋 @openjournals/bcm-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#5014, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-02-19T16:17:11Z

@arm61 as AEiC I will now help to process final steps for acceptance in JOSS. I have checked this review, your repository, the paper, and the archive link. All seems in order so I will now process this for acceptance. I do however have the following recommendation, if you do not already, please consider linking to the CONTRIBUTING.md file from the README and documentation. Currently I can see the file, but from having a quick look I cannot see how folks would end up there other than looking for an CONTRIBUTING.md document. A short section in your README that links to it may be nice.

Kevin-Mattheus-Moerman · 2024-02-19T16:17:16Z

@editorialbot accept

editorialbot · 2024-02-19T16:17:19Z

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

editorialbot · 2024-02-19T16:24:21Z

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: McCluskey
  given-names: Andrew R.
  orcid: "https://orcid.org/0000-0003-3381-5911"
- family-names: Squires
  given-names: Alexander G.
  orcid: "https://orcid.org/0000-0001-6967-3690"
- family-names: Dunn
  given-names: Josh
  orcid: "https://orcid.org/0000-0003-2659-0806"
- family-names: Coles
  given-names: Samuel W.
  orcid: "https://orcid.org/0000-0001-9722-5676"
- family-names: Morgan
  given-names: Benjamin J.
  orcid: "https://orcid.org/0000-0002-3056-8233"
doi: 10.5281/zenodo.10651128
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: McCluskey
    given-names: Andrew R.
    orcid: "https://orcid.org/0000-0003-3381-5911"
  - family-names: Squires
    given-names: Alexander G.
    orcid: "https://orcid.org/0000-0001-6967-3690"
  - family-names: Dunn
    given-names: Josh
    orcid: "https://orcid.org/0000-0003-2659-0806"
  - family-names: Coles
    given-names: Samuel W.
    orcid: "https://orcid.org/0000-0001-9722-5676"
  - family-names: Morgan
    given-names: Benjamin J.
    orcid: "https://orcid.org/0000-0002-3056-8233"
  date-published: 2024-02-19
  doi: 10.21105/joss.05984
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5984
  title: "kinisi: Bayesian analysis of mass transport from molecular
    dynamics simulations"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05984"
  volume: 9
title: "kinisi: Bayesian analysis of mass transport from molecular
  dynamics simulations"

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 · 2024-02-19T16:24:25Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-02-19T16:24:26Z

🚨🚨🚨 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.05984 joss-papers#5023
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05984
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arm61 · 2024-02-19T16:36:32Z

🚀🚀🚀

Thanks all for the help in getting this accepted! Great editing work from @zhubonan, thanks for the constructive reviews @hmacdope and @dengzeyu.

@Kevin-Mattheus-Moerman I have added a comment on the README about the CONTRIBUTING guidance too. Cheers for pointing that out.

Kevin-Mattheus-Moerman · 2024-02-20T12:01:12Z

@arm61 congratulations on this JOSS publication!!!

@zhubonan thanks for editing!

And a special thank you to the reviewers: @hmacdope, @dengzeyu !!

editorialbot · 2024-02-20T12:01:14Z

🎉🎉🎉 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.05984/status.svg)](https://doi.org/10.21105/joss.05984)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05984">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05984/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05984/status.svg
   :target: https://doi.org/10.21105/joss.05984

This is how it will look in your documentation:

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zhubonan · 2024-02-20T13:50:06Z

@arm61 congratulations! 🎉🎉
Thank you, @hmacdope, @dengzeyu for reviewing this submission! 👍👍
and @Kevin-Mattheus-Moerman for running the final checks! 🚀🚀

editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Oct 25, 2023

editorialbot assigned zhubonan Oct 25, 2023

editorialbot mentioned this issue Oct 25, 2023

[PRE REVIEW]: kinisi: Bayesian analysis of mass transport from molecular dynamics simulations #5797

Closed

zhubonan changed the title ~~[REVIEW]: kinisi: Accuracy and uncertainty quantification in diffusion~~ [REVIEW]: kinisi: Bayesian analysis of mass transport from molecular dynamics simulations Oct 26, 2023

zhubonan mentioned this issue Nov 5, 2023

Reproducibility of jupyter notebook example bjmorgan/kinisi#44

Closed

This was referenced Nov 5, 2023

Compatibility with Pymatgen in documentation bjmorgan/kinisi#43

Closed

Put "Methodology" to the main page bjmorgan/kinisi#42

Closed

Add instruction for building the documentation bjmorgan/kinisi#41

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 14, 2024

editorialbot added accepted published Papers published in JOSS labels Feb 19, 2024

Kevin-Mattheus-Moerman closed this as completed Feb 20, 2024

editorialbot mentioned this issue Jul 3, 2024

[PRE REVIEW]: MDCraft: A Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems #6957

Closed

editorialbot mentioned this issue Aug 29, 2024

[PRE REVIEW]: RNMC: kinetic Monte Carlo implementations for complex reaction networks #7159

Closed

[REVIEW]: kinisi: Bayesian analysis of mass transport from molecular dynamics simulations #5984

[REVIEW]: kinisi: Bayesian analysis of mass transport from molecular dynamics simulations #5984

Comments

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arm61 commented Oct 26, 2023

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dengzeyu commented Nov 5, 2023 • edited Loading

Review checklist for @dengzeyu

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

arm61 commented Nov 9, 2023

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zhubonan commented Nov 22, 2023

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