[REVIEW]: lattice_mc: A Python Lattice-Gas Monte Carlo Module

[whedon]

Submitting author: @bjmorgan (Benjamin J. Morgan)
Repository: https://github.com/bjmorgan/lattice_mc
Version: 1.0.0
Editor: @labarba
Reviewer: @asmit3
Archive: 10.5281/zenodo.582402

Status

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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) 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 questions

Conflict of interest

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (1.0.0)?
• Authorship: Has the submitting author (@bjmorgan) made major contributions to the software?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: Have any performance claims of the software been confirmed?

Documentation

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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[whedon]

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[asmit3]

I was able to tick off all the boxes except the one on Community Guidelines since the LICENSE file appears incomplete (no year or full name of author). Also I didn't see an email address for correspondence.
The default unittest given in the README file throws 3 errors when I run on my mac with python 3.5 (see attachment)

The ipython notebook was very useful in explaining how the code works.

[bjmorgan]

The errors under python 3.5 were due to test methods that were introduced with version 3.6. I have replaced these with 3.5+ compatible versions:
bjmorgan/lattice_mc@695e679

I have added the year and my name to the LICENSE file:
bjmorgan/lattice_mc@eb706fb

My email is given in setup.py, and I have added it to paper.md:
bjmorgan/lattice_mc@0d3287b

I don't know if you would recommend including my email address elsewhere in the package?

[asmit3]

The changes are satisfactory for me. I don't have any more comments. Thanks

[labarba]

@arfon -- We are ready to accept this paper.

[arfon]

@bjmorgan - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[bjmorgan]

The doi for the "as accepted" version (1.0.1) is 10.5281/zenodo.582402
The doi for the original submitted version (1.0.0) is 10.5281/zenodo.546262

[labarba]

@asmit3 : Thank you for your review, and I hope you enjoyed being part of this new publishing model and you'll consider submitting to JOSS in the future!

[arfon]

@whedon set 10.5281/zenodo.582402 as archive

[whedon]

OK. 10.5281/zenodo.582402 is the archive.

[arfon]

Hi @bjmorgan - could you move the references you currently have in the paper.md file into a paper.bib file and cite them directly please? (You can read how to do that here). They are automatically compiled into the PDF when we process the paper.

[bjmorgan]

@arfon: I have updated the paper.md.

bjmorgan/lattice_mc@3ec3074
bjmorgan/lattice_mc@4fc9d03

[arfon]

@asmit3 many thanks for your review and to @labarba for editing this submission ✨

@bjmorgan - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00247 ⚡️:rocket: :boom: