[REVIEW]: polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories

whedon commented 3 years ago

Submitting author: @symmy596 (Adam Symington) Repository: https://github.com/symmy596/Polypy Version: 0.8 Editor: @richardjgowers Reviewer: @hmacdope, @lscalfi Archive: 10.5281/zenodo.4568493

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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) 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

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

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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 ✨

Review checklist for @hmacdope

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@symmy596) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @lscalfi

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@symmy596) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

symmy596 commented 3 years ago

@richardjgowers Thanks. I have fixed the doi for MDAnalysis. I have made a tagged release. Tag 1.0.0 Zenodo record has been created, doi - 10.5281/zenodo.4568493

Thanks Adam

richardjgowers commented 3 years ago

@whedon set 10.5281/zenodo.4568493 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4568493 is the archive.

richardjgowers commented 3 years ago

@whedon generate pdf

richardjgowers commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

whedon commented 3 years ago

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

OK DOIs

- 10.1088/2515-7655/ab28b5 is OK
- 10.1098/rsta.2019.0026 is OK
- 10.1039/D0TA05343K is OK
- 10.1002/bbpc.198400007 is OK
- 10.1016/0022-3697(85)90172-6 is OK
- 10.1016/S0167-2738(02)00229-1 is OK
- 10.1063/1.117366 is OK
- 10.1149/1.1507597 is OK
- 10.1103/PhysRevB.58.13901 is OK
- 10.1016/S0263-7855(96)00043-4 is OK
- 10.1080/08927022.2013.839871 is OK
- 10.5281/zenodo.3653157 is OK
- 10.1002/jcc.21787 is OK
- 10.3390/molecules23010036 is OK
- 10.1039/D0TA11539H is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/2130

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2130, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

symmy596 commented 3 years ago

What happens now? Do you need anything further from me?

richardjgowers commented 3 years ago

@symmy596 nope I think you're all done. It's gone up to the editors above me and they'll double check it and do a final accept then it's published.

symmy596 commented 3 years ago

@richardjgowers In that case thanks for all your help! Cheers

danielskatz commented 3 years ago

I've found some minor changes to be merged into the paper: https://github.com/symmy596/Polypy/pull/5

danielskatz commented 3 years ago

Also, please carefully check the references, specifically the titles, to make sure they appear correctly. I think "Monte Carlo" should be capitalized, for example, and some of the chemical names might also need changes.

danielskatz commented 3 years ago

Use @whedon generate pdf as a new comment to regenerate, then let me know when you think that the references are all correct and the PR has been merged.

symmy596 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

symmy596 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

danielskatz commented 3 years ago

@symmy596 - I hope you are still working on the changes in the article titles...

symmy596 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #2824 with the following error:

Error reading bibliography file paper.bib: (line 3, column 115): unexpected "g" expecting space, ",", white space or "}" Looks like we failed to compile the PDF

symmy596 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

symmy596 commented 3 years ago

@danielskatz - Should be ready to go now. Cheers

danielskatz commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2132
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02824
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

Congratulations to @symmy596 (Adam Symington)!!

And thanks to @hmacdope and @lscalfi for reviewing and @richardjgowers for editing!

whedon commented 3 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.02824/status.svg)](https://doi.org/10.21105/joss.02824)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02824">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02824/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02824/status.svg
   :target: https://doi.org/10.21105/joss.02824

This is how it will look in your documentation:

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