[REVIEW]: Simmate: a framework for materials science #4364

editorialbot · 2022-05-02T18:26:04Z

Submitting author: @jacksund (Jack Sundberg)
Repository: https://github.com/jacksund/simmate
Branch with paper.md (empty if default branch): joss
Version: 0.7.1
Editor: @rkurchin
Reviewers: @bocklund, @utf
Archive: 10.5281/zenodo.6863068

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7a2576bce08dd95c1e7410f8e87b5a17"><img src="https://joss.theoj.org/papers/7a2576bce08dd95c1e7410f8e87b5a17/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7a2576bce08dd95c1e7410f8e87b5a17/status.svg)](https://joss.theoj.org/papers/7a2576bce08dd95c1e7410f8e87b5a17)

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

@bocklund & @utf, 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 @rkurchin 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 @utf

📝 Checklist for @bocklund

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

editorialbot · 2022-05-02T18:26:05Z

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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editorialbot · 2022-05-02T18:26:18Z

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

OK DOIs

- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1063/1.4812323 is OK
- 10.1016/j.commatsci.2012.02.005 is OK
- 10.1107/S0021889809016690 is OK
- 10.1038/s41524-020-00440-1 is OK
- 10.1007/s11837-013-0755-4 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1038/s41597-020-00637-5 is OK
- 10.1088/2515-7639/ab13bb is OK
- 10.1016/j.commatsci.2015.09.013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-05-02T18:26:20Z

Software report:

github.com/AlDanial/cloc v 1.88  T=4.14 s (223.7 files/s, 153082.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             10              0              0         307063
HTML                           468          49569            324         226077
Python                         360           6604          13457          22153
Markdown                        54           1546              0           3820
SVG                             16              0              3           1687
YAML                            13             40            139            223
TeX                              1             27              0            150
JavaScript                       1              3              3             40
TOML                             1              5             13             13
Dockerfile                       1             10             42             11
-------------------------------------------------------------------------------
SUM:                           925          57804          13981         561237
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-05-02T18:26:23Z

Wordcount for paper.md is 687

editorialbot · 2022-05-02T18:26:24Z

Failed to discover a Statement of need section in paper

editorialbot · 2022-05-02T18:27:18Z

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

rkurchin · 2022-05-06T15:01:29Z

@bocklund and @utf, feel free to ask if you have any questions about how to get your reviews started!

utf · 2022-05-06T15:03:40Z

Thanks @rkurchin. This project is quite large (20k lines of Python alone), so it may take some time to explore the functionality fully.

danielskatz · 2022-05-06T15:04:27Z

FYI, @editorialbot commands need to be the first thing in a command

utf · 2022-05-06T15:04:33Z

Review checklist for @utf

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/jacksund/simmate?
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 (@jacksund) 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?

utf · 2022-05-06T15:04:51Z

Thanks @danielskatz.

jacksund · 2022-05-06T15:53:49Z

@rkurchin @bocklund @utf Thank you for volunteering to edit and review our package! We're excited for the feedback.

I just wanted to place two things upfront to help with the review.

First, our test suite is currently at 84% coverage, and here's the report:
htmlcov_2022-05-06.zip

Second, I just wanted to repeat my comment from the pre-review thread:
We modeled our paper after the example one provided in the docs, where the "Statement of Need" and "Summary" sections were combined. If that is no longer allowed, we can change this though!

rkurchin · 2022-05-16T20:44:22Z

Hi @bocklund and @utf, just a reminder to get started on/continue your reviews, and feel free to ask any questions here and/or in issues in the repository (do reference this review issue if you do so, please)

bocklund · 2022-05-23T12:51:58Z

Review checklist for @bocklund

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/jacksund/simmate?
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 (@jacksund) 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?

rkurchin · 2022-05-31T16:38:16Z

Hi @utf and @bocklund, just checking in to see how your reviews are going! Feel free to file issues in the project repo for anything that comes up; please link to this review issue for easy tracking if you do so. Thanks!

rkurchin · 2022-06-13T15:29:17Z

Hi again @utf and @bocklund, just checking in again on this!

bocklund · 2022-06-15T16:33:37Z

@rkurchin Thanks for the pings. I had some travel the last few weeks, but getting back to this now!

bocklund · 2022-06-15T16:46:54Z

@rkurchin is an explicit "Statement of Need" section required for the paper? (question here).

rkurchin · 2022-06-15T19:43:47Z

Thanks for checking. @jacksund, if you could split those up I think that would be preferable. While the rendered version of that paper (from 2017) has them combined, if you look at the updated source in the docs, it has separate headers, so I think that's what's recommended currently.

jacksund · 2022-06-25T14:56:14Z

@editorialbot generate pdf

editorialbot · 2022-06-25T14:57:29Z

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

rkurchin · 2022-07-05T16:32:18Z

Hi @utf, have you had a chance to get started on the main section of your review checklist?

And @bocklund, have you gotten a chance to look at some of the functionality claims for your last checkbox?

rkurchin · 2022-07-18T18:06:44Z

Thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)
Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.
Post a comment here with the version number and DOI.

rkurchin · 2022-07-18T18:10:52Z

Some very minor editorial comments (this is by far the smallest number of these I've ever had, so 👏 from my editor hat 🎩):

line 41: when used as a noun, "best practices" doesn't need to be hyphenated
49: "full-feature" -> "full-featured"
42: "high-level" is a compound adjective and should be hyphenated here
66: needs a comma after "integrations"

jacksund · 2022-07-19T01:14:58Z

@editorialbot generate pdf

editorialbot · 2022-07-19T01:16:05Z

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

jacksund · 2022-07-19T01:55:55Z

@rkurchin awesome, thanks for editing the manuscript! 🥳 I've addressed your comments in the newest version.

Also, I'll make a new release + create a DOI on Zenodo once I get the chance. There was a libwebp release made a few hours ago that prevents any conda-forge updates and causes my CI for MacOS to fail. They already have an issue and PR open, so it should hopefully have a fix soon.

jacksund · 2022-07-19T18:44:46Z

@rkurchin I just made the Zenodo upload here

v0.7.1 --> DOI: 10.5281/zenodo.6863068
all versions --> DOI: 10.5281/zenodo.6863067

rkurchin · 2022-07-19T20:01:35Z

@editorialbot set 0.7.1 as version

editorialbot · 2022-07-19T20:01:37Z

Done! version is now 0.7.1

rkurchin · 2022-07-19T20:02:45Z

@editorialbot set 10.5281/zenodo.6863068 as DOI

editorialbot · 2022-07-19T20:02:45Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

rkurchin · 2022-07-19T20:03:03Z

@editorialbot set 10.5281/zenodo.6863068 as archive

editorialbot · 2022-07-19T20:03:05Z

Done! Archive is now 10.5281/zenodo.6863068

rkurchin · 2022-07-19T20:04:28Z

@editorialbot recommend-accept

editorialbot · 2022-07-19T20:04:29Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-07-19T20:04:39Z

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

OK DOIs

- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648x/aa680e is OK
- 10.1063/1.4812323 is OK
- 10.1016/j.commatsci.2012.02.005 is OK
- 10.1107/S0021889809016690 is OK
- 10.1038/s41524-020-00440-1 is OK
- 10.1007/s11837-013-0755-4 is OK
- 10.1103/PhysRevB.54.11169 is OK
- 10.1038/s41597-020-00637-5 is OK
- 10.1088/2515-7639/ab13bb is OK
- 10.1016/j.commatsci.2015.09.013 is OK
- 10.1016/j.commatsci.2017.07.030 is OK
- 10.1002/cpe.3505 is OK

MISSING DOIs

- Errored finding suggestions for "Dask: Parallel computing with task scheduling", please try later
- Errored finding suggestions for "Django: The Web framework for perfectionists with ...", please try later
- Errored finding suggestions for "MPContrib: Platform for materials scientists to co...", please try later

INVALID DOIs

- None

editorialbot · 2022-07-19T20:06:18Z

👋 @openjournals/joss-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#3385, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2022-07-19T20:59:08Z

@editorialbot accept

editorialbot · 2022-07-19T20:59:09Z

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

editorialbot · 2022-07-19T21:00:52Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-07-19T21:00:53Z

🚨🚨🚨 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.04364 joss-papers#3388
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04364
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2022-07-19T21:04:41Z

@bocklund, @utf – many thanks for your reviews here and to @rkurchin 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 ✨

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

editorialbot · 2022-07-19T21:05:01Z

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

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04364/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04364/status.svg
   :target: https://doi.org/10.21105/joss.04364

This is how it will look in your documentation:

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editorialbot added Dockerfile Python review TeX labels May 2, 2022

editorialbot assigned rkurchin May 2, 2022

editorialbot mentioned this issue May 2, 2022

[PRE REVIEW]: Simmate: a framework for materials science #4309

Closed

bocklund mentioned this issue Jun 15, 2022

JOSS software paper feedback jacksund/simmate#176

Closed

bocklund mentioned this issue Jun 25, 2022

simmate.visualization.structure.blender missing __init__.py jacksund/simmate#180

Closed

jacksund mentioned this issue Jul 19, 2022

update using rkurchin notes jacksund/simmate#194

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 19, 2022

editorialbot added accepted published Papers published in JOSS labels Jul 19, 2022

arfon closed this as completed Jul 19, 2022

editorialbot mentioned this issue Jun 25, 2024

[PRE REVIEW]: ASIMTools: A lightweight workflow and simulation manager for reproducible atomistic simulations #6929

Open

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 Jul 15, 2024

[PRE REVIEW]: A Python Library for Pre- and Post-Processing of DAMASK Simulations #6986

Open

[REVIEW]: Simmate: a framework for materials science #4364

[REVIEW]: Simmate: a framework for materials science #4364

Comments

editorialbot commented May 2, 2022 • edited Loading

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Reviewer instructions & questions

Checklists

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rkurchin commented May 6, 2022

utf commented May 6, 2022 • edited Loading

danielskatz commented May 6, 2022

utf commented May 6, 2022 • edited Loading

Review checklist for @utf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

utf commented May 6, 2022

jacksund commented May 6, 2022

rkurchin commented May 16, 2022

bocklund commented May 23, 2022 • edited Loading

Review checklist for @bocklund

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented May 31, 2022

rkurchin commented Jun 13, 2022

bocklund commented Jun 15, 2022

bocklund commented Jun 15, 2022

rkurchin commented Jun 15, 2022

jacksund commented Jun 25, 2022

editorialbot commented Jun 25, 2022

rkurchin commented Jul 5, 2022

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jacksund commented Jul 19, 2022

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