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[REVIEW]: SIMsalabim: A time resolved drift-diffusion simulation software #3727

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @ljakoster (Lambert Jan Anton Koster) Repository: https://github.com/kostergroup/SIMsalabim Version: v4.29-JOSS Editor: @rkurchin Reviewer: @UTH-Tuan, @shahmoradi, @roderickmackenzie Archive: 10.5281/zenodo.6010442

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Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/83fbf3b968bd0e69ddfbeca6668469cf"><img src="https://joss.theoj.org/papers/83fbf3b968bd0e69ddfbeca6668469cf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/83fbf3b968bd0e69ddfbeca6668469cf/status.svg)](https://joss.theoj.org/papers/83fbf3b968bd0e69ddfbeca6668469cf)

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

@UTH-Tuan & @shahmoradi & @roderickmackenzie, 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 @rkurchin 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 ✨

Review checklist for @UTH-Tuan

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @shahmoradi

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @roderickmackenzie

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

OK. v4.29-JOSS is the version.

rkurchin commented 2 years ago

@whedon set https://doi.org/10.5281/zenodo.6010442 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.6010442 is the archive.

rkurchin commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

PDF failed to compile for issue #3727 with the following error: 

 Can't find any papers to compile :-(
rkurchin commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 2 years ago

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

rkurchin commented 2 years ago

@whedon check references from branch paper

whedon commented 2 years ago 
Attempting to check references... from custom branch paper
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.xcrp.2021.100346 is OK
- 10.1021/acsenergylett.0c02599 is OK
- 10.1039/D0EE00714E is OK
- 10.1021/acsami.0c16411 is OK
- 10.1103/PhysRevApplied.15.014006 is OK
- 10.1021/acsenergylett.9b02720 is OK
- 10.1021/acsami.8b20493 is OK
- 10.1021/acsaem.9b00856 is OK
- 10.1007/s10825-019-01396-2 is OK
- 10.1016/S0040-6090(99)00825-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
rkurchin commented 2 years ago

Dear @ljakoster and reviewers @UTH-Tuan, @shahmoradi, and @roderickmackenzie,

Whew, this review has been a bit of a saga! Thank you all for your continued thoughtfulness, engagement, courtesy, and good faith throughout the process. I think everyone can agree the submission improved substantially (both in functionality and clarity of messaging), which is really the goal and gold standard of JOSS reviews. I'm so happy to have been able to edit and help shepherd this through, and congratulations! 👏 🚀

Rachel

rkurchin commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago

PDF failed to compile for issue #3727 with the following error: 

 Can't find any papers to compile :-(
rkurchin commented 2 years ago

@whedon recommend-accept from branch paper

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.xcrp.2021.100346 is OK
- 10.1021/acsenergylett.0c02599 is OK
- 10.1039/D0EE00714E is OK
- 10.1021/acsami.0c16411 is OK
- 10.1103/PhysRevApplied.15.014006 is OK
- 10.1021/acsenergylett.9b02720 is OK
- 10.1021/acsami.8b20493 is OK
- 10.1021/acsaem.9b00856 is OK
- 10.1007/s10825-019-01396-2 is OK
- 10.1016/S0040-6090(99)00825-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2933

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2933, 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 paper
ljakoster commented 2 years ago

@rkurchin: we have checked the proof and it looks perfect, thanks!

Prof. Dr. L.J.A. (Jan Anton) Koster Zernike Institute for Advanced Materials University of Groningen open-source simulator for perovskite and organic PV https://github.com/kostergroup/SIMsalabim group website http://www.koster-group.nl

On Tue, Feb 8, 2022 at 7:23 PM whedon @.***> wrote:

👋 @openjournals/joss-eics https://github.com/orgs/openjournals/teams/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2933 https://github.com/openjournals/joss-papers/pull/2933

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2933 https://github.com/openjournals/joss-papers/pull/2933, 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 paper

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3727#issuecomment-1032924766, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJFMMVB2A4CRDGSUFGW4MLTU2FNQZANCNFSM5EAXX2FQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 2 years ago

Hi @ljakoster! A few last items:

  1. zenodo and version look good.
  2. I recommend putting ` aroundSIMsalabim` so it stands out as software.
  3. Is Hu et al missing a title?
  4. MacKenzie et al seems like it is missing information?
  5. Do your references just happen to stop at M? Seems odd.
ljakoster commented 2 years ago

@whedon https://github.com/whedon generate pdf from branch paper

-- Prof. Dr. L.J.A. (Jan Anton) Koster Zernike Institute for Advanced Materials University of Groningen open-source simulator for perovskite and organic PV https://github.com/kostergroup/SIMsalabim group website http://www.koster-group.nl

On Thu, Feb 10, 2022 at 12:37 AM Kristen Thyng @.***> wrote:

Hi @ljakoster https://github.com/ljakoster! A few last items:

  1. zenodo and version look good.
  2. I recommend putting `` around SIMsalabim so it stands out as software.
  3. Is Hu et al missing a title?
  4. MacKenzie et al seems like it is missing information?
  5. Do your references just happen to stop at M? Seems odd.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3727#issuecomment-1034315422, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJFMMVE6EUFWB6V52NO7JZLU2L3BVANCNFSM5EAXX2FQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

whedon commented 2 years ago

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

@whedon commands
kostergroup commented 2 years ago

@whedon generate pdf from branch paper

Prof. Dr. L.J.A. (Jan Anton) Koster Zernike Institute for Advanced Materials University of Groningen open-source simulator for perovskite and organic PV https://github.com/kostergroup/SIMsalabim group website http://www.koster-group.nl

On Thu, Feb 10, 2022 at 10:33 AM Jan Anton Koster @.***> wrote:

@whedon https://github.com/whedon generate pdf from branch paper

-- Prof. Dr. L.J.A. (Jan Anton) Koster Zernike Institute for Advanced Materials University of Groningen open-source simulator for perovskite and organic PV https://github.com/kostergroup/SIMsalabim group website http://www.koster-group.nl

On Thu, Feb 10, 2022 at 12:37 AM Kristen Thyng @.***> wrote:

Hi @ljakoster https://github.com/ljakoster! A few last items:

  1. zenodo and version look good.
  2. I recommend putting `` around SIMsalabim so it stands out as software.
  3. Is Hu et al missing a title?
  4. MacKenzie et al seems like it is missing information?
  5. Do your references just happen to stop at M? Seems odd.

— Reply to this email directly, view it on GitHub < https://github.com/openjournals/joss-reviews/issues/3727#issuecomment-1034315422 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AJFMMVE6EUFWB6V52NO7JZLU2L3BVANCNFSM5EAXX2FQ

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675

or Android < https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub .

You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3727#issuecomment-1034693500, or unsubscribe https://github.com/notifications/unsubscribe-auth/API5RQZR2KF3DKZ5OOV5YXTU2OBAFANCNFSM5EAXX2FQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 2 years ago

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

ljakoster commented 2 years ago

Dear Kristen,

thanks for your email.

2: thanks, done.

3: yes, this was missing; we've added the title, looks like this was a BibTeX issue.

4: This is a reference to an internet site. We've asked this author (= one of the reviewers) how they would like to be cited and they have provided this reference.

5: that is odd, yet correct!

best wishes,

Jan Anton

Prof. Dr. L.J.A. (Jan Anton) Koster Zernike Institute for Advanced Materials University of Groningen open-source simulator for perovskite and organic PV https://github.com/kostergroup/SIMsalabim group website http://www.koster-group.nl

On Thu, Feb 10, 2022 at 10:36 AM whedon @.***> wrote:

👉📄 Download article proof https://raw.githubusercontent.com/openjournals/joss-papers/joss.03727/joss.03727/10.21105.joss.03727.pdf 📄 View article proof on GitHub https://github.com/openjournals/joss-papers/blob/joss.03727/joss.03727/10.21105.joss.03727.pdf 📄 👈

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3727#issuecomment-1034696357, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJFMMVDDKVMWITNLO4JJOILU2OBKNANCNFSM5EAXX2FQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

kthyng commented 2 years ago

@ljakoster ok! One thing — I meant `` around your software name throughout the paper, but it is up to you. Would you like to change that before we accept the final version of the paper?

kostergroup commented 2 years ago

Dear Kristen,

ah, sorry, we misunderstood. We've changed all mentions of SIMsalabim to the `` version.

best wishes, Jan Anton

-- Prof. Dr. L.J.A. (Jan Anton) Koster Zernike Institute for Advanced Materials University of Groningen open-source simulator for perovskite and organic PV https://github.com/kostergroup/SIMsalabim group website http://www.koster-group.nl

On Thu, Feb 10, 2022 at 9:09 PM Kristen Thyng @.***> wrote:

@ljakoster https://github.com/ljakoster ok! One thing — I meant `` around your software name throughout the paper, but it is up to you. Would you like to change that before we accept the final version of the paper?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3727#issuecomment-1035444895, or unsubscribe https://github.com/notifications/unsubscribe-auth/API5RQZ3UIREXHO6MG7DIHTU2QLOVANCNFSM5EAXX2FQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 2 years ago

@whedon generate pdf from branch paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch paper. Reticulating splines etc...
whedon commented 2 years ago

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

kthyng commented 2 years ago

Ok everything looks great!

kthyng commented 2 years ago

@whedon accept deposit=true from branch paper

whedon commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/2950
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03727
  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...

kthyng commented 2 years ago

Congratulations on your new publication @ljakoster! Many thanks to editor @rkurchin and reviewers @UTH-Tuan, @shahmoradi, and @roderickmackenzie for your time, hard work, and expertise!!

whedon commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.03727/status.svg)](https://doi.org/10.21105/joss.03727)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03727">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03727/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03727/status.svg
   :target: https://doi.org/10.21105/joss.03727

This is how it will look in your documentation:

DOI

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