editorialbot commented 9 months ago

Submitting author: !--author-handle-->@mcgalcode@richardjgowers<!--end-editor-- Reviewers: @riesben, @amkrajewski Archive: 10.5281/zenodo.10815119

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)

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

@riesben & @amkrajewski, 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 @richardjgowers 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 @RiesBen

📝 Checklist for @amkrajewski

editorialbot commented 9 months 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 9 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1730.2 files/s, 128237.6 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 commented 9 months ago

Wordcount for paper.md is 1347

editorialbot commented 9 months ago

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

editorialbot commented 9 months ago

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

richardjgowers commented 9 months ago

@riesben @amkrajewski thanks for agreeing to review this. This issue will be used to track the review. There's instructions above for generating a checklist that should guide your review process. If/when you run into issues as part of your review I'd recommend raising these as issues in the github repo for the project. Let me know if you have any questions.

RiesBen commented 9 months ago

Review checklist for @RiesBen

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/mcgalcode/pylattica?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mcgalcode) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

amkrajewski commented 9 months ago

Review checklist for @amkrajewski

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/mcgalcode/pylattica?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@mcgalcode) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

RiesBen commented 8 months ago

Hi, I added my Review here: Review Repository

richardjgowers commented 8 months ago

@amkrajewski have you had time to start your review yet?

richardjgowers commented 8 months ago

@mcgalcode it looks like you've got some reviewer comments to start on linked above

amkrajewski commented 8 months ago

@richardjgowers The holiday season got me a bit delayed. I should be able to submit my review by this Wednesday.

amkrajewski commented 8 months ago

Hi @richardjgowers and @RiesBen, I finished my review. I opened two separate issues: one for code at https://github.com/mcgalcode/pylattica/issues/13 and one for the manuscript at https://github.com/mcgalcode/pylattica/issues/14, just to keep things organized.

mcgalcode commented 8 months ago

Hi @richardjgowers @RiesBen and @amkrajewski, thanks for your feedback and review here - I really appreciate it. I'm sorry to not have responded to them yet. I have been traveling this month, and will return in another week, and I look forward to responding to your comments then!

amkrajewski commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

mcgalcode commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

mcgalcode commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

mcgalcode commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

mcgalcode commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

amkrajewski commented 7 months ago

Hi @richardjgowers! After reviewing the current version of the article and code, I have no further concerns. I have provided some further minor suggestions for @mcgalcode to consider, but overall, I am happy to recommend accepting it.

mcgalcode commented 7 months ago

Hi @richardjgowers, just wanted to let you know, I've responded to all the current reviewer comments!

RiesBen commented 6 months ago

@richardjgowers I did a second round, and there are no concerns from my side. This looks really cool to me.

richardjgowers commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

richardjgowers commented 6 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

richardjgowers commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago

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

mcgalcode commented 6 months ago

Hi @richardjgowers, I've completed the tasks listed above.

The current version is v0.1.3 (https://github.com/mcgalcode/pylattica/releases/tag/v0.1.3, https://pypi.org/project/pylattica/)

The zenodo DOI is here: 10.5281/zenodo.10815119

mcgalcode commented 5 months ago

Hi @richardjgowers just wanted to check in here - are there any more steps I should do? Thanks!

mcgalcode commented 5 months ago

Hey @richardjgowers, any update? - No worries if you're busy, I'll just keep pinging here every couple weeks to make sure it doesn't get lost :)

richardjgowers commented 5 months ago

@editorialbot generate pdf

richardjgowers commented 5 months ago

@editorialbot set 10.5281/zenodo.10815119 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.10815119

richardjgowers commented 5 months ago

@editorialbot set v0.1.3 as version

editorialbot commented 5 months ago

Done! version is now v0.1.3

richardjgowers commented 5 months ago

@editorialbot check references

editorialbot commented 5 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 5 months ago

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

- No DOI given, and none found for title: cellular_automaton
- No DOI given, and none found for title: CellPyLib
- 10.1007/978-3-031-02118-3_5 may be a valid DOI for title: Mathematical Games

INVALID DOIs

- None

richardjgowers commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 4 months ago

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

- No DOI given, and none found for title: cellular_automaton
- No DOI given, and none found for title: CellPyLib
- 10.1007/978-3-031-02118-3_5 may be a valid DOI for title: Mathematical Games

INVALID DOIs

- None

editorialbot commented 4 months ago

:wave: @openjournals/bcm-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/5304, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 4 months ago

@RiesBen thanks for helping with this review. Two of the boxes for your review are unticked. The license (MIT) and the installation instructions seem in order, so if you could tick those boxes at this point that would be great. Thanks!

Kevin-Mattheus-Moerman commented 4 months ago

@mcgalcode as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

[x] In your affiliations please spell out USA as United States of America.
[x] It is not a requirement but it is common to also add the city and state for affiliations.
[x] Please check the suggested DOI in the reference check :point_up:, it seems like that one may be correct? If so, please add it.

mcgalcode commented 4 months ago

@editorialbot generate pdf

openjournals / joss-reviews

[REVIEW]: pylattica: a package for prototyping lattice models in 2 chemistry and materials science #6170

Status

Reviewer instructions & questions

Checklists

Review checklist for @RiesBen

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @amkrajewski

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance