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[REVIEW]: KMC_Lattice v2.0: An Object-Oriented C++ Library for Custom Kinetic Monte Carlo Simulations #1168

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whedon opened this Issue Jan 12, 2019 · 54 comments

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whedon commented Jan 12, 2019

Submitting author: @MikeHeiber (Michael Heiber)
Repository: https://github.com/MikeHeiber/KMC_Lattice
Version: v2.0.1
Editor: @katyhuff
Reviewer: @myousefi2016, @mdoucet
Archive: 10.5281/zenodo.2552685

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/db7676d3ffd001b9a981fbbec513394c"><img src="http://joss.theoj.org/papers/db7676d3ffd001b9a981fbbec513394c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/db7676d3ffd001b9a981fbbec513394c/status.svg)](http://joss.theoj.org/papers/db7676d3ffd001b9a981fbbec513394c)

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 instructions & questions

@myousefi2016 & @mdoucet, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @katyhuff know.

Please try and complete your review in the next two weeks

Review checklist for @myousefi2016

Conflict of interest

Code of Conduct

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: v2.0.1
  • Authorship: Has the submitting author (@MikeHeiber) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

  • 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)?

Review checklist for @mdoucet

Conflict of interest

Code of Conduct

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: v2.0.1
  • Authorship: Has the submitting author (@MikeHeiber) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

  • 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)?
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whedon commented Jan 12, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @myousefi2016, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands
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whedon commented Jan 12, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 12, 2019

PDF failed to compile for issue #1168 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 15 0 15 0 0 180 0 --:--:-- --:--:-- --:--:-- 182
Error reading bibliography ./paper.bib (line 47, column 1):
unexpected "t"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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MikeHeiber commented Jan 12, 2019

For the latest draft of the paper, please see the joss-edits branch.

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MikeHeiber commented Jan 12, 2019

@whedon generate pdf from branch joss-edits

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whedon commented Jan 12, 2019

Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
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whedon commented Jan 12, 2019

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myousefi2016 commented Jan 18, 2019

@katyhuff I'm done with the review and everything looks good!

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MikeHeiber commented Jan 18, 2019

For full transparency, @myousefi2016 identified a bug (Issue #62) in KMC_Lattice through testing out the KMC_Lattice_example example program. The issue is now resolved in the KMC_Lattice joss-edits branch and will be merged into master with all other corrections/improvements once the review phase is completed.

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katyhuff commented Jan 18, 2019

Excellent. Thanks for a thorough review @myousefi2016 . It looks like @mdoucet is making good progress as well. I'll have a chance to look this submission over myself in more detail sometime this weekend.

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mdoucet commented Jan 22, 2019

I'm done with my review. The code is well organized and the examples are pretty good. Installing and running the code was easy. There's enough references to dig deeper and understand the problem. Overall everything looks good!

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katyhuff commented Jan 22, 2019

@whedon generate pdf from branch joss-edits

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whedon commented Jan 22, 2019

Attempting PDF compilation from custom branch joss-edits. Reticulating splines etc...
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whedon commented Jan 22, 2019

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katyhuff commented Jan 22, 2019

Thanks @myousefi2016 and @mdoucet for your reviews !

@MikeHeiber thank you for a strong submission and for engaging actively in the review process! I have looked over the paper, double checked all the DOI links, and have conducted a high level review of the code itself. Everything looks ship-shape to me.
Once you have your code and paper all ready in the release version (I assume v2.0.0?), it'll be good to double check the paper, review any lingering details in your code/readme/etc., and then make an archive of the reviewed software in Zenodo/figshare/other service. When you update this thread with the DOI of the archive, I'll move forward with accepting the submission! Until then, now is your moment for final touchups!

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MikeHeiber commented Jan 23, 2019

@whedon generate PDF

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whedon commented Jan 23, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 23, 2019

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MikeHeiber commented Jan 23, 2019

Thank you @katyhuff @myousefi2016 and @mdoucet for reviewing my software tool and making this a smooth process. I look forward to doing this again soon once my Excimontec KMC software tool is complete.

KMC_Lattice v2.0.0 is now released and the paper looks ready to go. v2.0.0 is archived on Zenodo with the following DOI:
10.5281/zenodo.2547139

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MikeHeiber commented Jan 28, 2019

@katyhuff Is there anything else I can do to help things move forward?

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katyhuff commented Jan 28, 2019

Sorry, I just took a break from this over the weekend. Let's move forward. Thanks for the reminder.

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katyhuff commented Jan 28, 2019

I'm going to double check a bunch of things while in meetings today. Should be able to complete publication later this afternoon.

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katyhuff commented Jan 29, 2019

@whedon set 10.5281/zenodo.2547139 as archive

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whedon commented Jan 29, 2019

OK. 10.5281/zenodo.2547139 is the archive.

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katyhuff commented Jan 29, 2019

@whedon set v2.0.0 as version

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whedon commented Jan 29, 2019

OK. v2.0.0 is the version.

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katyhuff commented Jan 29, 2019

@whedon generate pdf

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whedon commented Jan 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 29, 2019

@katyhuff katyhuff added the accepted label Jan 29, 2019

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katyhuff commented Jan 29, 2019

@MikeHeiber Thank you for again for your strong submission and for prompt responses to review comments. I approve acceptance of this paper!

@mdoucet @myousefi2016 Thank you again for your reviews. We couldn't do it without you!

@arfon this paper is ready to accept -- over to you!

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danielskatz commented Jan 29, 2019

@katyhuff - we've moved to rotating editors-in-chief; it's me this week.
Thanks for editing, and to @mdoucet & @myousefi2016 for your reviews

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danielskatz commented Jan 29, 2019

@whedon accept

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whedon commented Jan 29, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 29, 2019

Check final proof 👉 openjournals/joss-papers#457

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#457, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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whedon commented Jan 29, 2019


OK DOIs

- http://doi.org/10.1016/0021-9991(75)90060-1 is OK
- http://doi.org/10.1088/1751-8121/aa95c7 is OK
- http://doi.org/10.1016/0021-9991(76)90041-3 is OK
- http://doi.org/10.1146/annurev.physchem.58.032806.104637 is OK
- http://doi.org/10.1016/j.cpc.2014.04.003 is OK
- http://doi.org/10.1016/j.cpc.2014.04.017 is OK
- http://doi.org/10.1016/j.pmatsci.2017.09.003 is OK
- http://doi.org/10.1088/0953-8984/27/1/013001 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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danielskatz commented Jan 29, 2019

I'm checking on something before I finalize this...

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MikeHeiber commented Jan 29, 2019

@danielskatz Looking over the final proof, I found a small typo error in the manuscript. In one sentence, the word "the" appears twice in a row. How should I go about correcting this?

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danielskatz commented Jan 29, 2019

Just fix it in the .md file, and let me know

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MikeHeiber commented Jan 29, 2019

@whedon generate pdf

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whedon commented Jan 29, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jan 29, 2019

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MikeHeiber commented Jan 29, 2019

@katyhuff @danielskatz The paper is now corrected, and a new release has been issued. Please change the release to v2.0.1 with the DOI: 10.5281/zenodo.2552685

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danielskatz commented Jan 29, 2019

@whedon set v2.0.1 as version

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whedon commented Jan 29, 2019

OK. v2.0.1 is the version.

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danielskatz commented Jan 29, 2019

@whedon set 10.5281/zenodo.2552685 as archive

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whedon commented Jan 29, 2019

OK. 10.5281/zenodo.2552685 is the archive.

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danielskatz commented Jan 29, 2019

@whedon accept

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whedon commented Jan 29, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Jan 29, 2019

Check final proof 👉 openjournals/joss-papers#458

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#458, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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whedon commented Jan 29, 2019


OK DOIs

- http://doi.org/10.1016/0021-9991(75)90060-1 is OK
- http://doi.org/10.1088/1751-8121/aa95c7 is OK
- http://doi.org/10.1016/0021-9991(76)90041-3 is OK
- http://doi.org/10.1146/annurev.physchem.58.032806.104637 is OK
- http://doi.org/10.1016/j.cpc.2014.04.003 is OK
- http://doi.org/10.1016/j.cpc.2014.04.017 is OK
- http://doi.org/10.1016/j.pmatsci.2017.09.003 is OK
- http://doi.org/10.1088/0953-8984/27/1/013001 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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danielskatz commented Jan 29, 2019

@whedon accept deposit=true

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whedon commented Jan 29, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Jan 29, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#459
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01168
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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whedon commented Jan 29, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01168/status.svg)](https://doi.org/10.21105/joss.01168)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01168">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01168/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01168/status.svg
   :target: https://doi.org/10.21105/joss.01168

This is how it will look in your documentation:

DOI

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