[REVIEW]: pyEQL: A Python interface for water chemistry

[editorialbot]

Submitting author: !--author-handle-->@rkingsbury<!--end-author-handle-- (Ryan Kingsbury) Repository: https://github.com/rkingsbury/pyEQL Branch with paper.md (empty if default branch): joss Version: v1.0.0 Editor: !--editor-->@lucydot<!--end-editor-- Reviewers: @orionarcher, @JacksonBurns, @yuxuanzhuang Archive: 10.5281/zenodo.8332915

Status

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Markdown: [![status](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6/status.svg)](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6)

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

@orionarcher & @JacksonBurns & @yuxuanzhuang, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lucydot 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 ✨

Checklists

📝 Checklist for @JacksonBurns

📝 Checklist for @yuxuanzhuang

📝 Checklist for @orionarcher

[editorialbot]

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

[rkingsbury]

@editorialbot generate pdf

[editorialbot]

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

[rkingsbury]

@lucydot final .pdf is ready for your review once you're back!

I plan to issue a v1.0.0 in coming days, which we can set as the version of record. I will post here when that release is up.

[rkingsbury]

@editorialbot generate pdf

(Updating the figure with a slightly modernized logo, in honor of v1.0)

[editorialbot]

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

[rkingsbury]

@editorialbot set v1.0.0 as version

[editorialbot]

I'm sorry @rkingsbury, I'm afraid I can't do that. That's something only editors are allowed to do.

[rkingsbury]

@lucydot v1.0.0 is out and the .pdf is finalized. Please set that as the version of record, and let me know if anything else is needed. Thank you again to you and the reviewers for your feedback!

[lucydot]

Hi @rkingsbury - apologies, I managed to miss your comment above re: the conference talk. I'll work through this today to see if we can get it done before your talk..

[lucydot]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[lucydot]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[lucydot]

Ok, paper looks great to me!

[lucydot]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/s10953-019-00871-5 is OK
- 10.1016/j.desal.2013.03.015 is OK
- 10.1039/C7NJ03597G is OK
- 10.1016/j.cageo.2011.02.005 is OK
- 10.1016/s0378-3812(02)00178-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1063/1.4812323 is OK
- 10.1021/je2009329 is OK
- 10.1016/S0016-7037(97)81133-7 is OK

MISSING DOIs

- No DOI given, and none found for title: Description of Input and Examples for PHREEQC Vers...
- No DOI given, and none found for title: Ionic Conductivity and Diffusion at Infinite Dilut...
- No DOI given, and none found for title: PyEquIon: A Python Package For Automatic Speciatio...
- No DOI given, and none found for title: Phreeqpython
- No DOI given, and none found for title: Pint: makes units easy
- No DOI given, and none found for title: Maggma: A files-to-API data pipeline for scientifi...
- No DOI given, and none found for title: The Geochemist’s Workbench, Release 17

INVALID DOIs

- None

[lucydot]

Noting here that three of those missing DOIs are associated with bib entries no longer cited in the paper.

[lucydot]

@rkingsbury one small change - can you add a doi field to the PyEqulon entry? It should then create a url at doi.org rather than pointing to the arxiv.org.

[rkingsbury]

@editorialbot generate pdf

[editorialbot]

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

[rkingsbury]

@lucydot done! Welcome back and thank you 👍🏻

[lucydot]

Excellent - I'll recommend acceptance now. Thanks for submitting your work to JOSS, and hope you have a great conference!

[lucydot]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1007/s10953-019-00871-5 is OK
- 10.1016/j.desal.2013.03.015 is OK
- 10.1039/C7NJ03597G is OK
- 10.1016/j.cageo.2011.02.005 is OK
- 10.48550/arXiv.2101.07246 is OK
- 10.1016/s0378-3812(02)00178-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1063/1.4812323 is OK
- 10.1021/je2009329 is OK
- 10.1016/S0016-7037(97)81133-7 is OK

MISSING DOIs

- No DOI given, and none found for title: Description of Input and Examples for PHREEQC Vers...
- No DOI given, and none found for title: Ionic Conductivity and Diffusion at Infinite Dilut...
- No DOI given, and none found for title: The Geochemist’s Workbench, Release 17

INVALID DOIs

- None

[editorialbot]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

\mathsemicolon
              ^
unexpected control sequence \mathsemicolon
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

[lucydot]

@rkingsbury - the problem is with the charlton2011 entry in the bib file. I think it should be easy enough to fix by using \& for the ampersand.

[rkingsbury]

@rkingsbury - the problem is with the charlton2011 entry in the bib file. I think it should be easy enough to fix by using \& for the ampersand.

Fixed.

@editorialbot generate pdf

[rkingsbury]

Excellent - I'll recommend acceptance now. Thanks for submitting your work to JOSS, and hope you have a great conference!

Thank you @lucydot !

[rkingsbury]

@lucydot I noticed that this paper does not appear on the JOSS website under any status. Is that expected?

https://joss.theoj.org/papers/

[rkingsbury]

@editorialbot generate pdf

[editorialbot]

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

[lucydot]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

[editorialbot]

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

OK DOIs

- 10.1007/s10953-019-00871-5 is OK
- 10.1016/j.desal.2013.03.015 is OK
- 10.1039/C7NJ03597G is OK
- 10.1016/j.cageo.2011.02.005 is OK
- 10.48550/arXiv.2101.07246 is OK
- 10.1016/s0378-3812(02)00178-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1063/1.4812323 is OK
- 10.1021/je2009329 is OK
- 10.1016/S0016-7037(97)81133-7 is OK

MISSING DOIs

- No DOI given, and none found for title: Description of Input and Examples for PHREEQC Vers...
- No DOI given, and none found for title: Ionic Conductivity and Diffusion at Infinite Dilut...
- No DOI given, and none found for title: The Geochemist’s Workbench, Release 17

INVALID DOIs

- None

[lucydot]

@rkingsbury - I'm not quite sure why your paper doesn't appear under Active. It may be because we have recommended accept (it might remove it off active paper database at that point - though I'm not sure of mechanisms under the hood).

It seems that one of the ISBN's is too short; 9 rather than length 10. Looking at .bib file, I think the issue is with Parkhurst2013 entry; could you double check the ISBN/entry?

[rkingsbury]

It seems that one of the ISBN's is too short; 9 rather than length 10. Looking at .bib file, I think the issue is with Parkhurst2013 entry; could you double check the ISBN/entry?

OK, I updated this .bib entry to use a different style that includes a DOI instead of an ISBN. Why do you think this didn't show up in the previous try of recommend-accept? It would be nice to see all these errors at once instead of solving them one at a time.

[rkingsbury]

@editorialbot generate pdf

[editorialbot]

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

[lucydot]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.3133/tm6a43 is OK
- 10.1007/s10953-019-00871-5 is OK
- 10.1016/j.desal.2013.03.015 is OK
- 10.1039/C7NJ03597G is OK
- 10.1016/j.cageo.2011.02.005 is OK
- 10.48550/arXiv.2101.07246 is OK
- 10.1016/s0378-3812(02)00178-4 is OK
- 10.1016/j.commatsci.2012.10.028 is OK
- 10.1063/1.4812323 is OK
- 10.1021/je2009329 is OK
- 10.1016/S0016-7037(97)81133-7 is OK

MISSING DOIs

- No DOI given, and none found for title: Ionic Conductivity and Diffusion at Infinite Dilut...
- No DOI given, and none found for title: The Geochemist’s Workbench, Release 17

INVALID DOIs

- None

[editorialbot]

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5159, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kthyng]

Hi! Here are the steps I have to wrap up this submission:

• [x] Check that version was updated
• [x] Check that software archive exists, has been input to JOSS, and title and author list look good
• [x] Check paper

[kthyng]

Paper:

• type first paragraph 3rd page: "to maintain tranpra..."
• Architecture > The Solution class > "constituitive" is that a word?

[rkingsbury]

* type first paragraph 3rd page: "to maintain tranpra..."

Fixed

* Architecture > The Solution class > "constituitive" is that a word?

Yes, this is a word. See https://en.wikipedia.org/wiki/Constitutive_equation

[rkingsbury]

@editorialbot generate pdf