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

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editorialbot opened this issue Jun 25, 2024 · 38 comments
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[PRE REVIEW]: ASIMTools: A lightweight workflow and simulation manager for reproducible atomistic simulations #6929

editorialbot opened this issue Jun 25, 2024 · 38 comments
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@abhishektiwari @HaoZeke @imtambovtcev
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pre-review Python Shell TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Jun 25, 2024 •
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Submitting author: @mkphuthi (Mgcini Keith Phuthi)
Repository: https://github.com/BattModels/asimtools.git
Branch with paper.md (empty if default branch):
Version: v0.0.0
Editor: @HaoZeke
Reviewers: @abhishektiwari, @imtambovtcev
Managing EiC: Daniel S. Katz

Status

status

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HTML: <a href="https://joss.theoj.org/papers/26d152a1bceadb270aedc0cac93478dd"><img src="https://joss.theoj.org/papers/26d152a1bceadb270aedc0cac93478dd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/26d152a1bceadb270aedc0cac93478dd/status.svg)](https://joss.theoj.org/papers/26d152a1bceadb270aedc0cac93478dd)

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Thanks for submitting your paper to JOSS @mkphuthi. Currently, there isn't a JOSS editor assigned to your paper.

@mkphuthi if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Jun 25, 2024
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Hello human, 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

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

OK DOIs

- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1038/s41563-023-01699-7 is OK
- 10.1002/cpe.3505 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.5281/zenodo.8317316 is OK
- 10.1016/j.commatsci.2021.110731 is OK
- 10.1038/s41597-020-00638-4 is OK
- 10.1021/acsomega.3c10014 is OK

MISSING DOIs

- No DOI given, and none found for title: Vibrational Entropy and Free Energy of Solid Lithi...

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (2218.5 files/s, 130276.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53            771           1399           4417
YAML                            73             44             95           1414
Markdown                         3            101              0            440
reStructuredText                19            279            557            430
TeX                              1             13              0            203
Bourne Shell                    29             89            159            100
DOS Batch                        1              8              1             26
make                             1              5              7             12
-------------------------------------------------------------------------------
SUM:                           180           1310           2218           7042
-------------------------------------------------------------------------------

Commit count by author:

   150	mkphuthi
     6	emilannevelink
     3	Keith Phuthi

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Paper file info:

📄 Wordcount for paper.md is 2071

✅ The paper includes a Statement of need section

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License info:

✅ License found: MIT License (Valid open source OSI approved license)

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

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Five most similar historical JOSS papers:

strucscan: A lightweight Python-based framework for high-throughput material simulation
Submitting author: @thohamm
Handling editor: @ppxasjsm (Active)
Reviewers: @mturiansky, @wcwitt
Similarity score: 0.7614

Simmate: a framework for materials science
Submitting author: @jacksund
Handling editor: @rkurchin (Active)
Reviewers: @bocklund, @utf
Similarity score: 0.7469

excitingtools: An exciting Workflow Tool
Submitting author: @AlexBuccheri
Handling editor: @richardjgowers (Active)
Reviewers: @fjmartinmartinez, @hmacdope
Similarity score: 0.7426

FHI-vibes: Ab Initio Vibrational Simulations
Submitting author: @flokno
Handling editor: @jgostick (Active)
Reviewers: @keipertk, @ajjackson
Similarity score: 0.7332

matscipy: materials science at the atomic scale with Python
Submitting author: @pastewka
Handling editor: @diehlpk (Active)
Reviewers: @rashatwi, @mbarzegary, @mastricker
Similarity score: 0.7277

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@danielskatz
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👋 @mkphuthi - thanks for your submission.

Can you please add the countries to the author affiliations?

Also, JOSS papers are requested to be around 1000 words at most, and this is 2000, so you will have to reduce the content somewhat. Sometimes, there are parts of the paper that either duplicate documentation in the repo, or that could move into documentation in the repo (in this case, perhaps one or both of the examples).

Finally, you need to add a references header at the end of the .md file, so that when the references are added to the PDF, they have a header in front of them.

After you make changes in your .md file, you can then use the command @editorialbot generate pdf to make a new PDF and recount the word length. editorialbot commands need to be the first entry in a new comment.

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@editorialbot generate pdf

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

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Five most similar historical JOSS papers:

excitingtools: An exciting Workflow Tool
Submitting author: @AlexBuccheri
Handling editor: @richardjgowers (Active)
Reviewers: @fjmartinmartinez, @hmacdope
Similarity score: 0.8011

Atomic Simulation Interface (ASI): application programming interface for electronic structure codes
Submitting author: @PavelStishenko
Handling editor: @rkurchin (Active)
Reviewers: @xwang862, @junghans, @srmnitc
Similarity score: 0.7607

ShakeNBreak: Navigating the defect configurational landscape
Submitting author: @ireaml
Handling editor: @rkurchin (Active)
Reviewers: @obaica, @mkhorton
Similarity score: 0.7524

Surfaxe: Systematic surface calculations
Submitting author: @brlec
Handling editor: @danielskatz (Active)
Reviewers: @pzarabadip, @eihernan
Similarity score: 0.7474

GIMS: Graphical Interface for Materials Simulations
Submitting author: @kokookster
Handling editor: @jgostick (Active)
Reviewers: @marshallmcdonnell, @jgostick
Similarity score: 0.7443

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@mkphuthi
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Potential reviewers based on my search from the JOSS list are given below. I have no strong preferences.

yw-fang
ericfell
RMeli
ml-evs
jfaraudo

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (2229.5 files/s, 130055.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          53            771           1399           4417
YAML                            73             44             95           1414
reStructuredText                19            279            557            430
Markdown                         3             86              0            385
TeX                              1             13              0            203
Bourne Shell                    29             89            159            100
DOS Batch                        1              8              1             26
make                             1              5              7             12
-------------------------------------------------------------------------------
SUM:                           180           1295           2218           6987
-------------------------------------------------------------------------------

Commit count by author:

   152	mkphuthi
     6	emilannevelink
     3	Keith Phuthi

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Paper file info:

📄 Wordcount for paper.md is 1690

✅ The paper includes a Statement of need section

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License info:

✅ License found: MIT License (Valid open source OSI approved license)

@danielskatz
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thanks @mkphuthi - we're just having a short discussion about which JOSS track this best fits in, then we'll start the process

@editorialbot editorialbot added Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials and removed Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Jun 26, 2024
@danielskatz
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👋 @mkphuthi - we've moved this, as you can see, and you should hear from the new track editor next

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jul 3, 2024
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@editorialbot invite @HaoZeke as editor

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Invitation to edit this submission sent!

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HaoZeke commented Jul 9, 2024

@editorialbot assign @HaoZeke as editor

Thanks for the invite @Kevin-Mattheus-Moerman, I'm happy to accept

@mkphuthi thanks for the suggestions, I will start sending out invitations by the end of this week.

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Assigned! @HaoZeke is now the editor

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HaoZeke commented Jul 9, 2024

hi @utf @Andrew-S-Rosen @janosh 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on atomate and jobflow.

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HaoZeke commented Jul 9, 2024

hi @askhl 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on ASE and ASE workflows...

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HaoZeke commented Jul 9, 2024

hi @PavelStishenko @thohamm 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

If not, could you recommend any potential reviewers? I was hoping to have your insights because of your work on ASI woskflows and strucscan..

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Andrew-S-Rosen commented Jul 9, 2024 •
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@HaoZeke: Thank you for reaching out. Unfortunately, I will have to decline, as I have too much of a conflict of interest due to https://github.com/Quantum-Accelerators/quacc.

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janosh commented Jul 10, 2024

I also have to decline due to CoI.

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thohamm commented Jul 10, 2024

I'm sorry but I have to decline due to time constraints.

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HaoZeke commented Jul 29, 2024

Hi @imtambovtcev 👋 would you be interested in and available to review this JOSS submission? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

@askhl
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askhl commented Aug 6, 2024 via email

@abhishektiwari
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@HaoZeke I will be open to review this submission. Feel free to tag me as additional reviewer.

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HaoZeke commented Aug 7, 2024

@editorialbot add @abhishektiwari as reviewer

@abhishektiwari thanks for volunteering :)

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@abhishektiwari added to the reviewers list!

@imtambovtcev
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@HaoZeke, I just came from vacation and am ready to review

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HaoZeke commented Aug 7, 2024

@editorialbot add @imtambovtcev as reviewer

@imtambovtcev thanks stepping up :)

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@imtambovtcev added to the reviewers list!

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HaoZeke commented Aug 7, 2024

@editorialbot start review

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OK, I've started the review over in #7085.

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pre-review Python Shell TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode.
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