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[PRE REVIEW]: calorine: A Python package for constructing and sampling neuroevolution potential models #6040

Closed editorialbot closed 7 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@elindgren<!--end-author-handle-- (Eric Lindgren) Repository: https://gitlab.com/materials-modeling/calorine Branch with paper.md (empty if default branch): joss-paper Version: v2.0 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @Chronum94, @naik-aakash Managing EiC: Kyle Niemeyer

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Markdown: [![status](https://joss.theoj.org/papers/701ba7ae234081b2a0369668005a8ade/status.svg)](https://joss.theoj.org/papers/701ba7ae234081b2a0369668005a8ade)

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

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editorialbot commented 10 months ago

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
editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.23 s (298.6 files/s, 137565.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                     3             29             26          12680
Python                          32           1135           1363           5117
C++                              2            255            192           3224
TeX                              1            156              0           2397
XML                              1              0              0            564
Jupyter Notebook                 8              0           2795            538
Markdown                         4             57              0            277
YAML                             1             16             18            121
HTML                             3              6              1             65
Dockerfile                       1              6              5             56
reStructuredText                 9             41             55             47
CSS                              1             11              8             38
SVG                              1              0              0             23
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            68           1712           4463          25150
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 678

editorialbot commented 10 months ago

Failed to discover a Statement of need section in paper

editorialbot commented 10 months ago

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

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.softx.2015.06.001 is OK
- 10.1063/1.4745205 is OK
- 10.1063/1.2766943 is OK
- 10.1038/ncomms2969 is OK
- 10.1038/s41467-022-29939-5 is OK
- 10.5772/6741 is OK
- 10.1021/acs.chemrev.0c00868 is OK
- 10.1214/10-BA524 is OK
- 10.1021/acs.jctc.2c01034 is OK
- 10.1021/acs.jctc.8b00446 is OK
- 10.1103/PhysRevB.93.195206 is OK
- 10.1016/j.cplett.2017.03.056 is OK
- 10.1063/1.2408420 is OK
- 10.1016/j.jnucmat.2018.06.005 is OK
- 10.1051/sfn/201112010 is OK
- 10.1089/cmb.2012.0239 is OK
- 10.1103/PhysRevB.106.L161110 is OK
- 10.1021/acs.chemrev.5b00609 is OK
- 10.1002/chem.200600889 is OK
- 10.1038/s41467-018-06169-2 is OK
- 10.1126/sciadv.adf0873 is OK
- 10.1088/2632-2153/abba6f is OK
- 10.1103/PhysRevB.72.094108 is OK
- 10.1063/1.464528 is OK
- 10.1039/B700625J is OK
- 10.1039/C6CP00415F is OK
- 10.1039/C7NR07870F is OK
- 10.1093/nar/gkx312 is OK
- 10.1021/acs.jpcb.7b00272 is OK
- 10.1103/PhysRevB.99.014104 is OK
- 10.1103/PhysRevB.99.014104 is OK
- 10.1002/aenm.201703401 is OK
- 10.1016/j.physb.2018.02.034 is OK
- 10.1002/adts.201800184 is OK
- 10.48550/arXiv.2304.06978 is OK
- 10.1088/1361-648X/ac462b is OK
- 10.1088/1361-648X/ac462b is OK
- 10.1016/j.cpc.2017.05.003 is OK
- 10.1063/5.0106617 is OK
- 10.1103/PhysRevB.104.104309 is OK
- 10.1103/PhysRevB.104.104309 is OK
- 10.1021/acs.jpclett.0c02158 is OK
- 10.1016/0008-6223(94)90119-8 is OK
- 10.48550/arXiv.2307.12100 is OK
- 10.48550/arXiv.2211.08197 is OK
- 10.1038/s42005-023-01297-8 is OK
- 10.1002/adts.202000240 is OK
- 10.48550/arXiv.2301.03497 is OK
- 10.1021/acs.jctc.5b00211 is OK
- 10.1039/C7CC05883G is OK
- 10.1145/1830483.1830557 is OK
- 10.1039/C7CP01368J is OK
- 10.1002/anie.201612047 is OK
- 10.1021/acs.jpca.2c00950 is OK
- 10.1039/B817838K is OK
- 10.1126/sciadv.abi4659 is OK
- 10.1063/5.0036522 is OK
- 10.1021/j100077a003 is OK
- 10.1073/pnas.0408037102 is OK
- 10.1021/ja00214a001 is OK
- 10.1103/PhysRevB.103.174114 is OK
- 10.1073/pnas.2111769119 is OK
- 10.1063/5.0013059 is OK
- 10.1109/NSSMIC.2011.6154732 is OK
- 10.1021/cg1002594 is OK
- 10.1063/1.2145926 is OK
- 10.1016/j.bbapap.2010.10.012 is OK
- 10.1038/srep14822 is OK
- 10.1007/s10822-014-9713-7 is OK
- 10.1063/1.4984764 is OK
- 10.1002/advs.201801650 is OK
- 10.1103/PhysRevB.94.214114 is OK
- 10.1002/adfm.200701496 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1063/1.4932227 is OK
- 10.1063/1.1624057 is OK
- 10.48550/arXiv.1807.03341 is OK
- 10.1103/PhysRevB.108.054312 is OK
- 10.1002/adma.201104447 is OK
- 10.1021/acs.jpcb.1c00147 is OK
- 10.1145/3447548.3467350 is OK
- 10.3390/cryst9060279 is OK
- 10.1021/ct200196m is OK
- 10.1080/00268976.2017.1333644 is OK
- 10.1016/j.bpj.2015.08.015 is OK
- 10.1021/acs.jctc.0c00580 is OK
- 10.1038/s41467-022-35004-y is OK
- 10.1103/PhysRevB.80.024103 is OK
- 10.1080/23746149.2022.2093129 is OK
- 10.1088/0022-3719/13/23/014 is OK
- 10.1063/5.0087042 is OK
- 10.1016/j.matchemphys.2016.06.052 is OK
- 10.1002/adts.202100279 is OK
- 10.1103/PhysRevMaterials.2.083802 is OK
- 10.1007/978-81-322-1038-2_25 is OK
- 10.1021/acs.langmuir.1c01213 is OK
- 10.1063/5.0070488 is OK
- 10.1016/j.commatsci.2017.08.031 is OK
- 10.1016/j.orgel.2018.05.035 is OK
- 10.1021/acs.jpcc.9b02111 is OK
- 10.1063/1.3578472 is OK
- 10.1073/pnas.1711126115 is OK
- 10.1063/1.474493 is OK
- 10.1021/jp7117289 is OK
- 10.1021/acs.jctc.1c00195 is OK
- 10.1063/1.4952970 is OK
- 10.1063/1.5100141 is OK
- 10.1002/pssb.2221540114 is OK
- 10.1021/acsphyschemau.2c00045 is OK
- 10.1007/s11081-021-09608-0 is OK
- 10.1002/smll.202206428 is OK
- 10.1016/j.mtphys.2023.101066 is OK
- 10.48550/arXiv.1811.05868 is OK
- 10.1103/PhysRevLett.110.228701 is OK
- 10.1103/PhysRevB.84.075476 is OK
- 10.1063/1.2894847 is OK
- 10.1021/acs.jpcc.5b07345 is OK
- 10.7566/JPSJ.92.012001 is OK
- 10.1088/1361-648X/acd831 is OK
- 10.1039/D1SM00681A is OK
- 10.1021/acs.chemrev.0c01111 is OK
- 10.1021/acs.jctc.9b00181 is OK
- 10.1016/j.pmatsci.2019.03.006 is OK
- 10.1063/1.5098061 is OK
- 10.1088/2053-1583/ab6f0c is OK
- 10.1063/5.0147039 is OK
- 10.1039/B907366C is OK
- 10.1039/C9CP06561J is OK
- 10.1016/j.ijheatmasstransfer.2022.123681 is OK
- 10.1103/PhysRevLett.127.156002 is OK
- 10.1016/j.aiopen.2021.01.001 is OK

MISSING DOIs

- 10.1063/5.0146905 may be a valid DOI for title: Deep Ensembles vs. Committees for Uncertainty Estimation in Neural-Network Force Fields: Comparison and Application to Active Learning

INVALID DOIs

- None
kyleniemeyer commented 10 months ago

Hi @elindgren, unfortunately we do not have any editors available to handle your submission right now, so I have to put this on our waitlist until someone opens up.

In the meantime, could you edit your paper to include the required Statement of Need section? Also, please take a look at that missing DOI warning. Thanks!

elindgren commented 10 months ago

@editorialbot commands

editorialbot commented 10 months ago

Hello @elindgren, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
elindgren commented 10 months ago

@editorialbot check references

@editorialbot generate pdf

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/23746149.2022.2093129 is OK
- 10.1021/acs.chemrev.0c01111 is OK
- 10.1103/PhysRevB.104.104309 is OK
- 10.1088/1361-648X/ac462b is OK
- 10.1063/5.0106617 is OK
- 10.1103/PhysRevB.108.054312 is OK
- 10.48550/arXiv.2301.03497 is OK
- 10.1038/s42005-023-01297-8 is OK
- 10.1016/j.mtphys.2023.101066 is OK
- 10.1088/1361-648X/aa680e is OK
- 10.1002/adts.201800184 is OK
- 10.7566/JPSJ.92.012001 is OK
- 10.1088/1361-648X/acd831 is OK
- 10.48550/arXiv.2304.06978 is OK

MISSING DOIs

- None

INVALID DOIs

- None
elindgren commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

elindgren commented 10 months ago

Hi @elindgren, unfortunately we do not have any editors available to handle your submission right now, so I have to put this on our waitlist until someone opens up.

In the meantime, could you edit your paper to include the required Statement of Need section? Also, please take a look at that missing DOI warning. Thanks!

Hi Kyle, thanks! I hadn't realized that Statement of Need had to be it's own section, I had incorporated the motivation in the Summary. The paper should be updated now to have Statement of Need as it's own section. The references have been fixed as well.

kyleniemeyer commented 10 months ago

Looks good, thanks @elindgren

elindgren commented 10 months ago

I had a look at the list of reviewers, and there seemed to be quite a few with a background in modeling physical systems that might be a good fit. For example, Marjan Albooyeh, Anshuman Kumar and James Chapman (among others).

kyleniemeyer commented 9 months ago

@editorialbot invite @pdebuyl as editor

Hi @pdebuyl, could you edit this one? Sorry to ask as soon as you wrap up another review 😅

editorialbot commented 9 months ago

Invitation to edit this submission sent!

pdebuyl commented 9 months ago

Hello @kyleniemeyer I just took another assignment, I'd like to pass this one.

lucydot commented 8 months ago

@kyleniemeyer I can edit this if you are looking for someone?

kyleniemeyer commented 8 months ago

@editorialbot add @lucydot as editor

Thanks @lucydot!

editorialbot commented 8 months ago

Assigned! @lucydot is now the editor

lucydot commented 8 months ago

Hi @elindgren 👋 - I'll be editor for this submission. Feel free to ask me any questions about the process in this thread.

lucydot commented 8 months ago

@Materials-Informatics, @vmercel, @Chronum94 - are you available to review this submission to JOSS?

elindgren commented 8 months ago

Hi @elindgren 👋 - I'll be editor for this submission. Feel free to ask me any questions about the process in this thread.

Hi @lucydot, thank you for taking the time! :smile: What is the next step of the process?

Chronum94 commented 8 months ago

@Materials-Informatics, @vmercel, @Chronum94 - are you available to review this submission to JOSS?

I am. Please let me know about next steps and I'd be more than happy to.

lucydot commented 8 months ago

@elindgren - securing reviewers. Once this is done, I'll ask our editorialbot to start a new thread for the review itself. At this point, no action required your end.

lucydot commented 8 months ago

@Chronum94 - great! Once I have secured the other reviewers we'll start the review on a new thread, and instructions will be posted there. FYI we also have JOSS documentation (including review checklist) here: https://joss.readthedocs.io/en/latest/index.html

lucydot commented 8 months ago

@editorialbot add @Chronum94 as reviewer

editorialbot commented 8 months ago

@Chronum94 added to the reviewers list!

lucydot commented 7 months ago

@naik-aakash @RMeli @ZhenchenHong - are you available to review this submission to JOSS?

naik-aakash commented 7 months ago

@naik-aakash @RMeli @ZhenchenHong - are you available to review this submission to JOSS?

Hi @lucydot, Thanks ! Yes, I am available. Kindly let me know the next steps and desired timelines.

RMeli commented 7 months ago

are you available to review this submission to JOSS?

Hi @lucydot. I'm learning the ropes as a new JOSS editor, therefore I prefer to take on more editorial work at this time rather than reviews. Once the dust has settled, I'll be happy to do some reviewing as well.

lucydot commented 7 months ago

Hi @RMeli - apologies I hadn't realised you are also editing - i'm sure that will keep you busy enough ;)

lucydot commented 7 months ago

Hi @naik-aakash - thank you for agreeing to review. I will ask editorialbot to add you to the reviewers list and then give some more instructions...

lucydot commented 7 months ago

@editorialbot add @naik-aakash as reviewer

editorialbot commented 7 months ago

@naik-aakash added to the reviewers list!

lucydot commented 7 months ago

@Chronum94 @naik-aakash - thank you for agreeing to review this submission to JOSS ⭐

If you haven't reviewed for JOSS before, you can find some detailed information about the review process on the documentation pages: reviewing for JOSS, review criteria, review checklist. You don't need to read this all, but it gives some context if wanted.

The key things that are different from standard journals are: i) everything happens in a Github review thread; ii) the review is a conversation back and forth - you do not need to do you review in a single step; iii) the review is structured in that you work your way through a checklist.

We ask that reviews are completed in about 4 weeks. We advise you start the review early, as it is an iterative process between reviewers and authors.

I will now ask editorialbot to generate a new issue thread which is where the review will take place. Instructions for you (to generate your review checklist) will be provided there.

Any questions please just ask - and thanks again for agreeing to review.

lucydot commented 7 months ago

@editorialbot start review

editorialbot commented 7 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6264.