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[REVIEW]: PorousFlow: a multiphysics simulation code for coupled problems in porous media #2176

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @WilkAndy (Andy Wilkins) Repository: https://github.com/idaholab/moose Version: snapshot-20-10-27 Editor: @jedbrown Reviewer: @jbrezmorf, @rpodgorney Archive: 10.5281/zenodo.4071026

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0778dd9013e04c0ccde9fc6d2469e550"><img src="https://joss.theoj.org/papers/0778dd9013e04c0ccde9fc6d2469e550/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0778dd9013e04c0ccde9fc6d2469e550/status.svg)](https://joss.theoj.org/papers/0778dd9013e04c0ccde9fc6d2469e550)

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

@jbrezmorf & @rpodgorney, 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 @jedbrown know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @jbrezmorf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rpodgorney

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

WilkAndy commented 3 years ago

I think i've addressed all comments and this can be published

WilkAndy commented 3 years ago

Just wondering if i have to do anything else?

WilkAndy commented 3 years ago

Hi @kthyng . I'm pinging you about this JOSS paper. I'm pretty sure it's ready to publish, but @jedbrown isn't responding. I think he might have accidentally unsubscribed to this issue. Perhaps you can take it from here?

jedbrown commented 3 years ago

Sorry about the delay, I just got swamped.

jedbrown commented 3 years ago

@whedon set snapshot-20-10-27 as version

whedon commented 3 years ago

OK. snapshot-20-10-27 is the version.

jedbrown commented 3 years ago

@whedon generate pdf

jedbrown commented 3 years ago

@whedon set 10.5281/zenodo.4071026 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4071026 is the archive.

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:

jedbrown commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
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/1941

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1941, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s12665-012-1546-x is OK
- 10.1016/j.camwa.2020.05.014 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.21203/rs.2.17644/v1 is OK
- 10.1080/22020586.2019.12073198 is OK

MISSING DOIs

- 10.2139/ssrn.3365603 may be a valid DOI for title: Community Code for Simulating CO_2 Storage: Modelling Multiphase Flow with Coupled Geomechanics and Geochemistry Using the Open-Source Multiphysics Framework MOOSE

INVALID DOIs

- None
jedbrown commented 3 years ago

@WilkAndy It looks like the bib entry for that should be update. (It looks like the 21--26 is actually a date, so maybe you can check the rest of the formatting when you add the DOI.)

While you're at it, could you add the URL https://documentation.pflotran.org/ for PFLOTRAN (as recommended in the bibtex on their website)?

You can just put those small changes in your branch and we'll rebuild the PDF.

WilkAndy commented 3 years ago

Hi @jedbrown. Thanks for all your work on this. I've made the changes your requested above and the result can be found at

https://github.com/WilkAndy/moose branch: joss_bib_16312

You may generate the PDF from there (I have checked it works) or you may wait for my PR (https://github.com/idaholab/moose/pull/16313) to make its way through the MOOSE process, which will 1day - 1week.

jedbrown commented 3 years ago

@whedon generate pdf from branch joss_bib_16312

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss_bib_16312. Reticulating splines etc...
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:

WilkAndy commented 3 years ago

I think the above compilation didn't use my repo . I went to https://whedon.theoj.org/ and entered https://github.com/WilkAndy/moose/ and joss_bib_16312 , and the result is different (it contains the bib changes)

jedbrown commented 3 years ago

Hmm, I see this branch is in a different repository (https://github.com/WilkAndy/moose/tree/joss_bib_16312) and I don't know how to ask Whedon to build from that. But this paper should be ready for acceptance with either a manual build or once it lands in a branch of the main repository.

arfon commented 3 years ago

@whedon accept from branch joss_bib_16312

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
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/1942

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1942, 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 joss_bib_16312
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s12665-012-1546-x is OK
- 10.1016/j.camwa.2020.05.014 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.21203/rs.2.17644/v1 is OK
- 10.1080/22020586.2019.12073198 is OK

MISSING DOIs

- 10.2139/ssrn.3365603 may be a valid DOI for title: Community Code for Simulating CO_2 Storage: Modelling Multiphase Flow with Coupled Geomechanics and Geochemistry Using the Open-Source Multiphysics Framework MOOSE

INVALID DOIs

- None
arfon commented 3 years ago

@jedbrown - is this (☝️) what you were wanting to do with the custom branch?

@WilkAndy - has the DOI suggested by Whedon above (10.2139/ssrn.3365603) been determined to be correct (or incorrect). If it looks correct for the reference item, please add it to your BibTeX file.

WilkAndy commented 3 years ago

Yep, @arfon, the DOI is correct, and i have added to paper.bib. We are now waiting for the updates (https://github.com/idaholab/moose/pull/16313) to pass through the MOOSE review process and then we should be ready for publication. Thank you everyone who contributed to this....

arfon commented 3 years ago

@whedon accept from branch joss_bib_16312

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
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/1943

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1943, 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 joss_bib_16312
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s12665-012-1546-x is OK
- 10.1016/j.camwa.2020.05.014 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.21203/rs.2.17644/v1 is OK
- 10.1080/22020586.2019.12073198 is OK

MISSING DOIs

- 10.2139/ssrn.3365603 may be a valid DOI for title: Community Code for Simulating CO_2 Storage: Modelling Multiphase Flow with Coupled Geomechanics and Geochemistry Using the Open-Source Multiphysics Framework MOOSE

INVALID DOIs

- None
WilkAndy commented 3 years ago

No, the above is still the old version. It is not from https://github.com/WilkAndy/moose/tree/joss_bib_16312 . I'm happy to wait till the bib changes make their way through the review process at https://github.com/idaholab/moose/pull/16313

arfon commented 3 years ago

No, the above is still the old version. It is not from https://github.com/WilkAndy/moose/tree/joss_bib_16312 . I'm happy to wait till the bib changes make their way through the review process at idaholab/moose#16313

Ah, OK. Sorry for being slow here - @whedon doesn't know how to build from a fork branch so yes, we'll need to wait for these changes (https://github.com/idaholab/moose/pull/16313) to land in https://github.com/idaholab/moose.

But then I think you already knew that 😸

jedbrown 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:

arfon commented 3 years ago

@whedon accept from branch next

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s12665-012-1546-x is OK
- 10.1016/j.camwa.2020.05.014 is OK
- 10.1016/j.softx.2020.100430 is OK
- 10.1007/s00366-006-0049-3 is OK
- 10.2139/ssrn.3365603 is OK
- 10.21203/rs.2.17644/v1 is OK
- 10.1080/22020586.2019.12073198 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/1944

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1944, 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
arfon commented 3 years ago

@jedbrown - this looks in good shape to publish now, would you agree?

jedbrown commented 3 years ago

Looks good to me. Thanks, @arfon.

WilkAndy commented 3 years ago

I concur - the paper looks as it should. Thank you everyone who was involved in the review process

WilkAndy commented 3 years ago

@whedon accept deposit=true from branch next

whedon commented 3 years ago

I'm sorry @WilkAndy, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

arfon commented 3 years ago

@whedon accept deposit=true from branch next

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:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1945
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02176
  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...

arfon commented 3 years ago

@jbrezmorf, @rpodgorney - many thanks for your reviews here and to @jedbrown for editing ✨

@WilkAndy - your paper is now accepted into JOSS :zap::rocket::boom:

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.02176/status.svg)](https://doi.org/10.21105/joss.02176)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02176">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02176/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02176/status.svg
   :target: https://doi.org/10.21105/joss.02176

This is how it will look in your documentation:

DOI

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