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

Closed editorialbot closed 1 year ago

editorialbot commented 2 years ago

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

Status

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

editorialbot commented 2 years ago

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 2 years ago 
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 commented 2 years ago 
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 commented 2 years ago

Wordcount for paper.md is 687

editorialbot commented 2 years ago

Failed to discover a Statement of need section in paper

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rkurchin commented 2 years ago

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

utf commented 2 years ago

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

danielskatz commented 2 years ago

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

utf commented 2 years ago

Review checklist for @utf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

utf commented 2 years ago

Thanks @danielskatz.

jacksund commented 2 years ago

@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 commented 2 years ago

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 commented 2 years ago

Review checklist for @bocklund

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rkurchin commented 2 years ago

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 commented 2 years ago

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

bocklund commented 2 years ago

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

bocklund commented 2 years ago

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

rkurchin commented 2 years ago

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 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rkurchin commented 1 year ago

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?

bocklund commented 1 year ago

@rkurchin @jacksund Yes, sorry for the delay. My review is complete and I can recommend accepting Simmate into JOSS. Very nice work @jacksund!

jacksund commented 1 year ago

@bocklund thank you so much for looking through! Means a lot 😄

rkurchin commented 1 year ago

Thanks @bocklund!

@utf, have you had a chance to proceed with your review?

utf commented 1 year ago

Apologies for the delay getting back my review.

I've finished reviewing simmate and recommend that it be accepted. There is an incredible amount of functionality in the package, the documentation is very thorough and easy to follow, and I can confirm that all examples work as intended.

jacksund commented 1 year ago

@utf Thank you!!

rkurchin commented 1 year ago

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:

  1. 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!)
  2. 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.
  3. Post a comment here with the version number and DOI.
rkurchin commented 1 year ago

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

jacksund commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jacksund commented 1 year ago

@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 commented 1 year ago

@rkurchin I just made the Zenodo upload here

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

rkurchin commented 1 year ago

@editorialbot set 0.7.1 as version

editorialbot commented 1 year ago

Done! version is now 0.7.1

rkurchin commented 1 year ago

@editorialbot set 10.5281/zenodo.6863068 as DOI

editorialbot commented 1 year ago

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

@editorialbot commands

rkurchin commented 1 year ago

@editorialbot set 10.5281/zenodo.6863068 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.6863068

rkurchin commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago 
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 commented 1 year ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3385, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3388
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04364
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 1 year ago

@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 :zap::rocket::boom:

editorialbot commented 1 year 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.04364/status.svg)](https://doi.org/10.21105/joss.04364)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04364">
  <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:

DOI

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