[PRE REVIEW]: pylattica: a package for prototyping lattice models in chemistry and materials science

[editorialbot]

Submitting author: @mcgalcode (Max C. Gallant)
Repository: https://github.com/mcgalcode/pylattica
Branch with paper.md (empty if default branch): paper
Version: v0.1.2
Editor: @richardjgowers
Reviewers: @RiesBen, @amkrajewski
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/265d902b2934e84005a8bd8fd89aaecb"><img src="https://joss.theoj.org/papers/265d902b2934e84005a8bd8fd89aaecb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/265d902b2934e84005a8bd8fd89aaecb/status.svg)](https://joss.theoj.org/papers/265d902b2934e84005a8bd8fd89aaecb)

Author instructions

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

@mcgalcode 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:

@editorialbot commands

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (1947.9 files/s, 144376.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          82           1144            980           3155
Jupyter Notebook                 9              0           3221            518
YAML                             5             34             14            257
TeX                              1             15              0            234
Markdown                        35             86              0            230
TOML                             1             13              0            100
JSON                             2              0              0              5
-------------------------------------------------------------------------------
SUM:                           135           1292           4215           4499
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1347

[editorialbot]

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

OK DOIs

- 10.1016/j.commatsci.2012.08.047 is OK
- 10.5281/ZENODO.3893141 is OK
- 10.1016/j.cpc.2014.04.017 is OK
- 10.1103/PhysRevB.74.045217 is OK
- 10.1007/978-1-84996-217-9_1 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1007/BF01010423 is OK
- 10.1007/978-3-642-40867-0_2 is OK
- 10.1016/S0167-739X(99)00045-X is OK
- 10.1146/annurev.matsci.32.090601.152855 is OK

MISSING DOIs

- 10.21105/joss.00247 may be a valid DOI for title: lattice_mc: A Python Lattice-Gas Monte Carlo Module
- 10.3389/fchem.2019.00202 may be a valid DOI for title: A Practical Guide to Surface Kinetic Monte Carlo Simulations
- 10.1007/978-3-031-02118-3_5 may be a valid DOI for title: Mathematical Games

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

pyscal: A python module for structural analysis of atomic environments
Submitting author: @srmnitc
Handling editor: @melissawm (Retired)
Reviewers: @lucydot, @bocklund
Similarity score: 0.8284

lattice_mc: A Python Lattice-Gas Monte Carlo Module
Submitting author: @bjmorgan
Handling editor: @labarba (Retired)
Reviewers: @asmit3
Similarity score: 0.8228

PyLithics: A Python package for stone tool analysis
Submitting author: @JasonGellis
Handling editor: @Nikoleta-v3 (Active)
Reviewers: @MichaelHoltonPrice, @steko
Similarity score: 0.8149

polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories
Submitting author: @symmy596
Handling editor: @richardjgowers (Active)
Reviewers: @hmacdope, @lscalfi
Similarity score: 0.8078

Kanapy: A Python package for generating complex synthetic polycrystalline microstructures
Submitting author: @mrgprasad
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @heprom, @KedoKudo, @chennachaos
Similarity score: 0.8076

⚠️ 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.

[Kevin-Mattheus-Moerman]

@editorialbot invite @richardjgowers as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@mcgalcode Thanks for this submission. I am the AEiC for this track, and here to help process initial steps. I have started to look for a handling editor. Note that many are handling other submissions so it may take some time before we are able to assign one.

For the moment, could you please try to address the above potentially missing/invalid DOIs? ☝️

You can call @editorialbot generate pdf to update the paper, and you can call @editorialbot check references to check those DOIs again. Thanks.

[mcgalcode]

Hi @Kevin-Mattheus-Moerman, I appreciate your help with the review of my paper! This all sounds good to me.

I fixed the first of the two DOIs, but the third suggestion refers to something unrelated. That bibliography entry is for an article in Scientific American on jstor, which doesn't seem to have a DOI associated with it (https://www.jstor.org/stable/24927642).

@editorialbot generate pdf
@editorialbot check references

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.commatsci.2012.08.047 is OK
- 10.21105/joss.00247 is OK
- 10.5281/ZENODO.3893141 is OK
- 10.1016/j.cpc.2014.04.017 is OK
- 10.1103/PhysRevB.74.045217 is OK
- 10.1007/978-1-84996-217-9_1 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1007/BF01010423 is OK
- 10.1007/978-3-642-40867-0_2 is OK
- 10.1016/S0167-739X(99)00045-X is OK
- 10.3389/fchem.2019.00202 is OK
- 10.1146/annurev.matsci.32.090601.152855 is OK

MISSING DOIs

- 10.1007/978-3-031-02118-3_5 may be a valid DOI for title: Mathematical Games

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@mcgalcode these "calls" (e.g. @editorialbot check references) to the bot need to be the first thing (and perhaps on their own) in a comment.
Also, the DOI checker isn't always right, as you discovered. Thanks for checking though.

[mcgalcode]

Aha, thanks @Kevin-Mattheus-Moerman. I suspected that might be the case. I'll regenerate the paper.

[mcgalcode]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

pyscal: A python module for structural analysis of atomic environments
Submitting author: @srmnitc
Handling editor: @melissawm (Retired)
Reviewers: @lucydot, @bocklund
Similarity score: 0.8283

lattice_mc: A Python Lattice-Gas Monte Carlo Module
Submitting author: @bjmorgan
Handling editor: @labarba (Retired)
Reviewers: @asmit3
Similarity score: 0.8227

PyLithics: A Python package for stone tool analysis
Submitting author: @JasonGellis
Handling editor: @Nikoleta-v3 (Active)
Reviewers: @MichaelHoltonPrice, @steko
Similarity score: 0.8149

polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories
Submitting author: @symmy596
Handling editor: @richardjgowers (Active)
Reviewers: @hmacdope, @lscalfi
Similarity score: 0.8077

Kanapy: A Python package for generating complex synthetic polycrystalline microstructures
Submitting author: @mrgprasad
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @heprom, @KedoKudo, @chennachaos
Similarity score: 0.8076

⚠️ 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.

[Kevin-Mattheus-Moerman]

@editorialbot invite @richardjgowers as editor

[editorialbot]

Invitation to edit this submission sent!

[richardjgowers]

@editorialbot assign @richardjgowers as editor

[editorialbot]

Assigned! @richardjgowers is now the editor

[richardjgowers]

@editorialbot assign @RiesBen as reviewer

[editorialbot]

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

@editorialbot commands

[richardjgowers]

@editorialbot add @RiesBen as reviewer

[editorialbot]

@RiesBen added to the reviewers list!

[richardjgowers]

@amkrajewski would you be interested in reviewing this submission?

[amkrajewski]

@richardjgowers It looks very interesting. I am happy to review it.

[richardjgowers]

@editorialbot add @amkrajewski as reviewer

[editorialbot]

@amkrajewski added to the reviewers list!

[richardjgowers]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6170.