[REVIEW]: The MOOSE geochemistry module

whedon commented 3 years ago

Submitting author: @WilkAndy (Andy Wilkins) Repository: https://github.com/idaholab/moose Version: Snapshop 21-November-14 Editor: @jedbrown Reviewers: @smolins, @volpatto Archive: 10.5281/zenodo.5701422

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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

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

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Review checklist for @smolins

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 (@WilkAndy) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @volpatto

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 (@WilkAndy) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

kyleniemeyer commented 2 years ago

It looks like this submission is in good shape to proceed, so I'm going to step in and get this past the finish line.

@WilkAndy thanks for addressing the reviewer comments. At this stage, could you now archive the software repository (for example, on Zenodo), make sure the title and authors list match the paper, and let us know the DOI here?

Also, I noticed a minor typo in the first paragraph in "Statement of Need": a missing comma after "e.g.".

WilkAndy commented 2 years ago

@kyleniemeyer

i have published on zonodo: https://doi.org/10.5281/zenodo.5701422
i have added the comma that you mentioned, and the change has been merged into the "next" branch. However, it will take 1-2 days to merge into "master".

jedbrown commented 2 years ago

@whedon set 10.5281/zenodo.5701422 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5701422 is the archive.

jedbrown commented 2 years ago

@whedon set Snapshop 21-November-14 as version

whedon commented 2 years ago

OK. Snapshop 21-November-14 is the version.

jedbrown commented 2 years ago

Thanks for your patience, @WilkAndy, and thanks to @kyleniemeyer for backstopping. Please consider the PR (https://github.com/idaholab/moose/pull/19404) with minor copy edits and fixing the duplicate link for the PETSc website (also updated to the new URL). We can proceed as soon as that is in a branch (any branch) of the main repo.

jedbrown commented 2 years ago

@whedon generate pdf

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:

jedbrown commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.1007/s11004-020-09898-7 is OK
- 10.2138/gselements.15.2.117 is OK
- 10.1007/s10596-015-9475-x is OK
- 10.1007/s10596-014-9443-x is OK
- 10.3133/wri954227 is OK
- 10.3133/wri994259 is OK
- 10.3133/tm6A35 is OK
- 10.2172/834237 is OK
- 10.1007/978-3-642-27177-9 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.21105/joss.02176 is OK
- 10.1002/nme.5284 is OK
- 10.1002/nme.6215 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1007/978-1-4612-1986-6_8 is OK
- 10.1016/j.engfracmech.2019.106713 is OK
- 10.1007/s00466-018-1544-2 is OK
- 10.1017/CBO9780511619670 is OK
- 10.2172/138894 is OK
- 10.1016/0016-7037(88)90334-1 is OK
- 10.15121/1638710 is OK
- 10.2172/1524048 is OK
- 10.1002/2012WR013483 is OK

MISSING DOIs

- 10.3133/ofr20041068 may be a valid DOI for title: A compilation of rate parameters of water-mineral interaction kinetics for application to geochemical modeling

INVALID DOIs

- None

jedbrown commented 2 years ago

Returning from the holiday, I'm sorry I missed this the first time around. This fixes the missing DOI. I guess it needs an issue and a PR referencing that issue. https://github.com/jedbrown/moose/commit/836b5f6867dbba0d897ddf403b09de9a1207260c

jedbrown commented 2 years ago

@whedon check references from branch next

whedon commented 2 years ago

Attempting to check references... from custom branch next

whedon commented 2 years ago

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

OK DOIs

- 10.1007/s11004-020-09898-7 is OK
- 10.2138/gselements.15.2.117 is OK
- 10.1007/s10596-015-9475-x is OK
- 10.1007/s10596-014-9443-x is OK
- 10.3133/wri954227 is OK
- 10.3133/wri994259 is OK
- 10.3133/tm6A35 is OK
- 10.2172/834237 is OK
- 10.1007/978-3-642-27177-9 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.21105/joss.02176 is OK
- 10.1002/nme.5284 is OK
- 10.1002/nme.6215 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1007/978-1-4612-1986-6_8 is OK
- 10.1016/j.engfracmech.2019.106713 is OK
- 10.1007/s00466-018-1544-2 is OK
- 10.1017/CBO9780511619670 is OK
- 10.2172/138894 is OK
- 10.3133/ofr20041068 is OK
- 10.1016/0016-7037(88)90334-1 is OK
- 10.15121/1638710 is OK
- 10.2172/1524048 is OK
- 10.1002/2012WR013483 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jedbrown commented 2 years ago

@whedon generate pdf from branch next

whedon commented 2 years ago

Attempting PDF compilation from custom branch next. 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:

jedbrown commented 2 years ago

@whedon recommend-accept from branch next

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

- 10.1007/s11004-020-09898-7 is OK
- 10.2138/gselements.15.2.117 is OK
- 10.1007/s10596-015-9475-x is OK
- 10.1007/s10596-014-9443-x is OK
- 10.3133/wri954227 is OK
- 10.3133/wri994259 is OK
- 10.3133/tm6A35 is OK
- 10.2172/834237 is OK
- 10.1007/978-3-642-27177-9 is OK
- 10.1007/s11242-019-01310-1 is OK
- 10.21105/joss.02176 is OK
- 10.1002/nme.5284 is OK
- 10.1002/nme.6215 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.1007/978-1-4612-1986-6_8 is OK
- 10.1016/j.engfracmech.2019.106713 is OK
- 10.1007/s00466-018-1544-2 is OK
- 10.1017/CBO9780511619670 is OK
- 10.2172/138894 is OK
- 10.3133/ofr20041068 is OK
- 10.1016/0016-7037(88)90334-1 is OK
- 10.15121/1638710 is OK
- 10.2172/1524048 is OK
- 10.1002/2012WR013483 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/2781

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2781, 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 next

WilkAndy commented 2 years ago

Confirming that i cannot find any mistakes in the final proof

kthyng commented 2 years ago

Ok everything looks ready to go!

kthyng commented 2 years ago

@whedon accept deposit=true from branch next

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:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2786
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03314
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 2 years ago

Congrats on your new publication @WilkAndy! Thanks to editor @jedbrown and reviewers @smolins and @volpatto for your time, hard work, and expertise!!

whedon commented 2 years ago

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.03314/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03314/status.svg
   :target: https://doi.org/10.21105/joss.03314

This is how it will look in your documentation:

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