editorialbot commented 2 months ago

Submitting author: !--author-handle-->@rrsettgast@lucydot<!--end-editor-- Reviewers: @MakisH, @timokoch, @berenger-eu Archive: 10.5281/zenodo.7151031

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/5a00d91636edd7cdf6449776a60dffcf/status.svg)](https://joss.theoj.org/papers/5a00d91636edd7cdf6449776a60dffcf)

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

@MakisH & @timokoch & @berenger-eu, 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 @MakisH

📝 Checklist for @timokoch

📝 Checklist for @berenger-eu

lucydot commented 1 week ago

In the meantime, and assuming all is well, I will generate the post-review checklist - please let me know when each author item is done @rrsettgast.

lucydot commented 1 week ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[ ] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[ ] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

lucydot commented 1 week ago

Some small edits for the paper @rrsettgast :

line 46: , Darts ---> and Darts
line 71: (“CHAI,” 2023) The formatting of the title doesn't look correct, remove quotes?
line 73: provide an inline link to the performance portable website if required, rather than link via a reference. As a general rule, we try to only give references when there is a unique and persistent identifier (such as DOI).

timokoch commented 1 week ago

I can see some action in GEOS-DEV/GEOS#3332 - can you confirm you are happy with changes made, and recommend acceptance @timokoch ?

@lucydot Yes everything has been thoroughly addressed and I can recommend acceptance :)

rrsettgast commented 1 week ago

Some small edits for the paper @rrsettgast :

line 46: , Darts ---> and Darts

line 71: (“CHAI,” 2023) The formatting of the title doesn't look correct, remove quotes?

line 73: provide an inline link to the performance portable website if required, rather than link via a reference. As a general rule, we try to only give references when there is a unique and persistent identifier (such as DOI).

@lucydot I have edited the document to address these edits.

rrsettgast commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

rrsettgast commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

rrsettgast commented 4 days ago

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper. (v1.1.0)
[x] Archive the release on Zenodo/figshare/etc and post the DOI here. DOI 10.5281/zenodo.7151031
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper. @lucydot There is a bit of a difference. I added everyone who ever made a commit to the repo on the CITATION.cff file, which I assume translates to the archive. For this JOSS publication, I only include authors who made commits of substance. (i.e. not just a typo fix, or a code that was eventually discarded). Additionally the JOSS paper includes folks who are involved with the project (e.g. Professors and managers) but have never committed to the repository. Do you have guidance on what you would like me to do regarding this difference?
[x] Make sure that the license listed for the archive is the same as the software license.

lucydot commented 1 day ago

@editorialbot set v1.1.0 as version

editorialbot commented 1 day ago

Done! version is now v1.1.0

lucydot commented 1 day ago

@editorialbot set 10.5281/zenodo.7151031 as archive

editorialbot commented 1 day ago

Done! archive is now 10.5281/zenodo.7151031

lucydot commented 1 day ago

Do you have guidance on what you would like me to do regarding this difference?

Reading our editors Slack channel, I can see that there are previous examples where author list on the Zenodo and JOSS paper differ, for the reason you give above. So this is fine 👍

lucydot commented 1 day ago

@rrsettgast I see different licenses listed on the repository (GNU LPGL) and Zenodo (CC-BY). Is this intentional? We usually expect them to be the same.

lucydot commented 1 day ago

@rrsettgast I understand this may take some time given the length of the author list, but please could you include Orcid IDs where they are available.

lucydot commented 1 day ago

@editorialbot check references

editorialbot commented 1 day ago

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@article{Kochetal2020Dumuxtitle={DuMu\textsuperscript{x} 3 - an open-source simulator for solving flow and transport problems in porous media with a focus on model coupling},journal=Computers \& Mathematics with Applications,year=2020,issn=0898-1221,doi=10.1016/j.camwa.2020.02.012,author=Timo Koch and Dennis Gl\aserandKilianWeishauptandSinaAckermannandMartinBeckandBeatrixBeckerandSamuelBurbullaandHolgerClassandEdwardColtmanandSimonEmmertandThomasFetzerandChristophGr\

rrsettgast commented 1 day ago

@rrsettgast I see different licenses listed on the repository (GNU LPGL) and Zenodo (CC-BY). Is this intentional? We usually expect them to be the same.

@lucydot I don't know why that was the case. I thought it would have grabbed the proper license from the repo. I have updated the license to LGPL on Zenodo. I am surprised I missed that. Thanks!

rrsettgast commented 1 day ago

@rrsettgast I understand this may take some time given the length of the author list, but please could you include Orcid IDs where they are available.

Yes. I will get the ones that are available..but I don't think all the authors have an Orcid ID. I assume this is ok?

rrsettgast commented 1 day ago

@editorialbot check references

editorialbot commented 1 day ago

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@article{Kochetal2020Dumuxtitle={DuMu\textsuperscript{x} 3 - an open-source simulator for solving flow and transport problems in porous media with a focus on model coupling},journal=Computers \& Mathematics with Applications,year=2020,issn=0898-1221,doi=10.1016/j.camwa.2020.02.012,author=Timo Koch and Dennis Glaser and Kilian Weishaupt and Sina Ackermann and Martin Beck and Beatrix Becker and Samuel Burbulla and Holger Class and Edward Coltman and Simon Emmert and Thomas Fetzer and Christoph Gr\uningerandKatharinaHeckandJohannesHommelandTheresaKurzandMelanieLippandFaridMohammadiandSamuelScherrerandMartinSchneiderandGabrieleSeitzandLeopoldStadlerandMartinUtzandFelixWeinhardtandBerndFlemisch, keywords = Porousmedia,Multi-phaseflow,,Coupledproblems,Open-sourcesoftware,Researchsoftware, abstract = Wepresentversion3oftheopen-sourcesimulatorforflowandtransportprocessesinporousmediaDuMux.DuMuxisbasedonthemodularC++frameworkDune(

rrsettgast commented 1 day ago

@lucydot The title of this issue is currently: GEOS: A performance portable multi-physics 2 simulation framework for subsurface applications

I think you may have copied the "2" from the line numbers in the pdf?

rrsettgast commented 1 day ago

@editorialbot check references

editorialbot commented 1 day ago

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

✅ OK DOIs

- 10.1002/nag.2557 is OK
- 10.5281/zenodo.11396894 is OK
- 10.1109/P3HPC49587.2019.00012 is OK
- 10.1147/JRD.2019.2954403 is OK
- 10.1007/3-540-47789-6_66 is OK
- 10.1145/1089014.1089021 is OK
- 10.1137/19M1256117 is OK
- 10.1016/j.cma.2021.114111 is OK
- 10.1017/9781009157926 is OK
- 10.2118/218015-PA is OK
- 10.5281/zenodo.11652195 is OK
- 10.1016/j.camwa.2020.02.012 is OK
- 10.21105/joss.06737 is OK
- 10.1145/3581784.3607089 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CHAI
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: GEOS Documentation

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1016/j.camwa.2020.05.014 is INVALID because of 'https://doi.org/' prefix

rrsettgast commented 1 day ago

@editorialbot check references

editorialbot commented 1 day ago

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

✅ OK DOIs

- 10.1002/nag.2557 is OK
- 10.5281/zenodo.11396894 is OK
- 10.1109/P3HPC49587.2019.00012 is OK
- 10.1147/JRD.2019.2954403 is OK
- 10.1007/3-540-47789-6_66 is OK
- 10.1145/1089014.1089021 is OK
- 10.1137/19M1256117 is OK
- 10.1016/j.cma.2021.114111 is OK
- 10.1017/9781009157926 is OK
- 10.2118/218015-PA is OK
- 10.5281/zenodo.11652195 is OK
- 10.1016/j.camwa.2020.02.012 is OK
- 10.1016/j.camwa.2020.05.014 is OK
- 10.21105/joss.06737 is OK
- 10.1145/3581784.3607089 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CHAI
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: GEOS Documentation

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

lucydot commented 1 day ago

but I don't think all the authors have an Orcid ID. I assume this is ok?

@rrsettgast, yes - that's fine

lucydot commented 1 day ago

@editorialbot generate pdf

lucydot commented 1 day ago

I think you may have copied the "2" from the line numbers in the pdf?

eek! Thanks for catching. I've fixed it.

editorialbot commented 1 day ago

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

rrsettgast commented 1 day ago

@editorialbot generate pdf

editorialbot commented 1 day ago

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

rrsettgast commented 6 hours ago

@editorialbot generate pdf

editorialbot commented 6 hours ago

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

rrsettgast commented 6 hours ago

@lucydot I have added orcid id's for the majority of authors

openjournals / joss-reviews

[REVIEW]: GEOS: A performance portable multi-physics simulation framework for subsurface applications #6973

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Additional Author Tasks After Review is Complete