[REVIEW]: Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices

[whedon]

Submitting author: @MikeHeiber (Michael Heiber)
Repository: https://github.com/MikeHeiber/Excimontec
Version: v1.0.0
Editor: @pdebuyl
Reviewers: @mdavezac, @Luthaf
Archive: 10.5281/zenodo.4008122

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1db972a24b6d9a9c2f7ce8658e8a1778"><img src="https://joss.theoj.org/papers/1db972a24b6d9a9c2f7ce8658e8a1778/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1db972a24b6d9a9c2f7ce8658e8a1778/status.svg)](https://joss.theoj.org/papers/1db972a24b6d9a9c2f7ce8658e8a1778)

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

@mdavezac, @Luthaf, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @pdebuyl know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @mdavezac

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @Luthaf

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mdavezac it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ 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:

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.1002/pssb.201350339 is OK
- 10.1088/1361-6633/80/2/026502 is OK
- 10.21105/joss.01072 is OK
- 10.1016/B978-0-08-102284-9.00010-3 is OK
- 10.21105/joss.01168 is OK
- 10.1002/aelm.201800821 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[pdebuyl]

@whedon add @liangtianumich as reviewer

[whedon]

OK, @liangtianumich is now a reviewer

[pdebuyl]

@mdavezac, @liangtianumich , make sure to accept the invitation to the reviewers group and to have a look at the reviewer guidelines.

The review process will happen in this issue page, so questions to the author or to me can be added as comments here.

[mdavezac]

@pdebuyl, I missed the invitation to the reviewer group and it time out. Could you please send it back?

[pdebuyl]

@arfon is it possible for me to restart an invitation to the reviewer group?

[arfon]

It is, you can do @whedon re-invite @reviewer as reviewer

[pdebuyl]

@whedon re-invite @mdavezac as reviewer

[whedon]

OK, the reviewer has been re-invited.

@mdavezac please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[pdebuyl]

@arfon thanks

[mdavezac]

Compilation

The procedure completed almost without a hitch. The issue is that it requires the users to set up their environment with a CXX variable. This may be a standard for a developer, not so much for user. This requirement is missing from the installation guide.

What's weird though is that the environment variable is not actually used to identify the compiler, since the compiler is hard-coded to mpicxx. It's merely a surprising way to specify a set of CXXFLAGS. However, even though CXX is just a switch, it cannot be set in the expected way for a makefile, e.g. make CXX=xxx. It has to be done via an environment variable. And the environment variable cannot be something like g++-8.0. Hence, the setup will fail in any number of standard situations where CXX points to an actual versioned executable.

Among other environments, this makefile will fail on crays, where mpi compiler wrappers have less standard names.

Installation

There is no installation procedure per se. However, the main product is a relocatable executable.

Recommendation

At the low end, it would be sufficient to explain the non-standard usage of CXX in the user-guide and that the executable can be relocated to another location of the user's choosing. It may be good idea to replace CXX with a suitably named makefile variable with a suitable default.

However, I would strongly recommend ditching hand-rolled makefiles in favor of meson or cmake. The advantages will include: (i) out of tree builds, (ii) large set of compilers, (iii) standard installation procedure to /usr/bin, (v) installation of libKMC.a (or .so), (v) build specification shorter and less error prone than a makefile.
Furthermore, it would give the author the opportunity to replace the git submodules with either meson's dependency wrapper or cmake's external project. Submodules are a source of confusion even for expert git users, especially in a multi-developer environment.

[mdavezac]

Software paper: Travis provide continuous integration. Integration testing is something else still. Indeed some of the unit-tests in the code could be termed integration tests, e.g. ExcitonDiffusionTests.

[pdebuyl]

Thank you @mdavezac for the review!

@MikeHeiber you can already reply to @mdavezac , you don't have to wait for @liangtianumich 's review.

The process at JOSS is to discuss the comments as a dialogue on this github issue page.

PS: sorry , I mistyped @liangtianumich 's handle in my previous comment.

[pdebuyl]

@amandadumi would you review the article "Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices" for the Journal of Open Source Software?

[pdebuyl]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a  dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

[pdebuyl]

@whedon remove @liangtianumich as reviewer

[whedon]

OK, @liangtianumich is no longer a reviewer

[pdebuyl]

@whedon accept from branch joss-proofing

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1002/pssb.201350339 is OK
- 10.1088/1361-6633/80/2/026502 is OK
- 10.21105/joss.01072 is OK
- 10.1016/B978-0-08-102284-9.00010-3 is OK
- 10.21105/joss.01168 is OK
- 10.5281/zenodo.4008122 is OK
- 10.1002/aelm.201800821 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1692

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1692, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-proofing 

[pdebuyl]

@MikeHeiber this is a good time to merge if you wish. Else, the process carries on with the other branch. One of the editors-in-chief will take over the rest of the process.

[pdebuyl]

ping @openjournals/joss-eics

[kthyng]

Hi @pdebuyl I saw this but thought I'd give @MikeHeiber a chance to do the merging before I moved ahead. Should I just go ahead now?

[pdebuyl]

Hi @kthyng thanks for the reply. The merge of the custom branch should be a "fast-forward" merge only and the software release won't change. Please go ahead with the custom branch then, @MikeHeiber is waiting to cite this paper in others, so it is better to proceed.

[MikeHeiber]

@kthyng Please go ahead and publish the paper in it's current form. I'll merge the joss-proofing branch in afterwards and also update the branch to include the reference information.

[kthyng]

Hi @MikeHeiber! I'll help finish up the details for your publication. Please change the metadata for your zenodo archive to exactly match your JOSS paper (title and authors).

[kthyng]

I just read through your paper @MikeHeiber. It looks fine, except for some reason all the references were listed after the period of the sentence they were used in. I changed this in this PR. Please look through and see if you want to merge.

[MikeHeiber]

@kthyng The Zenodo archive is now updated as requested, and your PR is merged into the joss-proofing branch.

[kthyng]

@whedon generate pdf from branch joss-proofing

[whedon]

Attempting PDF compilation from custom branch joss-proofing. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kthyng]

@whedon accept from branch joss-proofing

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1002/pssb.201350339 is OK
- 10.1088/1361-6633/80/2/026502 is OK
- 10.21105/joss.01072 is OK
- 10.1016/B978-0-08-102284-9.00010-3 is OK
- 10.21105/joss.01168 is OK
- 10.5281/zenodo.4008122 is OK
- 10.1002/aelm.201800821 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1707

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1707, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss-proofing 

[kthyng]

@whedon accept deposit=true from branch joss-proofing

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02307 joss-papers#1708
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02307
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats to @MikeHeiber on your new publication! Thanks to editor @pdebuyl and reviewers @mdavezac and @Luthaf. This wouldn't be possible without your time and expertise.

[whedon]

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.02307/status.svg)](https://doi.org/10.21105/joss.02307)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02307">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02307/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02307/status.svg
   :target: https://doi.org/10.21105/joss.02307

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss