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[REVIEW]: PyVOLCANS: A Python package to flexibly explore similarities and differences between volcanic systems #3649

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @PTierz (Pablo Tierz Lopez) Repository: https://github.com/BritishGeologicalSurvey/pyvolcans Version: v1.3.2 Editor: @elbeejay Reviewer: @jifarquharson, @meghanrjones Archive: 10.5281/zenodo.5809105

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Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5148a124aa6c9aecf5936022dd1a2bf3"><img src="https://joss.theoj.org/papers/5148a124aa6c9aecf5936022dd1a2bf3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5148a124aa6c9aecf5936022dd1a2bf3/status.svg)](https://joss.theoj.org/papers/5148a124aa6c9aecf5936022dd1a2bf3)

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

@jifarquharson & @meghanrjones, 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 @elbeejay 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 @jifarquharson

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @meghanrjones

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch JOSS_paper. 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:

elbeejay commented 2 years ago

@whedon check references from branch JOSS_paper

whedon commented 2 years ago 
Attempting to check references... from custom branch JOSS_paper
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1029/2020gc009219 may be a valid DOI for title: Event trees and epistemic uncertainty in long-term volcanic hazard assessment of rift volcanoes: The example of Aluto (Central Ethiopia)
- 10.1007/s00445-019-1336-3 may be a valid DOI for title: VOLCANS: an objective, structured and reproducible method for identifying sets of analogue volcanoes
- 10.1007/s004450100173 may be a valid DOI for title: Constructing event trees for volcanic crises
- 10.1016/j.jvolgeores.2017.08.003 may be a valid DOI for title: WOVOdat–an online, growing library of worldwide volcanic unrest
- 10.5194/nhess-21-3509-2021 may be a valid DOI for title: A unified probabilistic framework for volcanic hazard and eruption forecasting
- 10.1016/b978-0-12-818082-2.00001-9 may be a valid DOI for title: Some relevant issues in volcanic hazard forecasts and management of volcanic crisis

INVALID DOIs

- None
elbeejay commented 2 years ago

@PTierz and co-authors, I've opened up a small PR to modify a bit of formatting in the .bib file. I also made some suggestions for minor edits to the paper itself. The removal of non-DOI links in particular is something I think is important and will help the paper remain durable in the future. The PR should also help resolve some of the missing DOIs whedon has identified above.

Once you've taken action on the paper and the bibliography, please merge your paper branch into the main branch of the code.

Following that, there are a few items that need to be taken care of:

Thanks, please just reply with the above items once they are complete. Once that is done, I will briefly review the paper once more before referring it to one of the EiCs for publication.

PTierz commented 2 years ago

Hi @elbeejay,

Thank you so very much for all your help and support.

I proceeded with merging your suggested PR into the JOSS_paper branch. I also added a couple of commits to the branch. I will wait for your confirmation that these changes look reasonable before I complete the PR for the branch, OK?

Very many thanks in advance.

Best regards, Pablo

elbeejay commented 2 years ago

@whedon generate pdf from branch JOSS_paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch JOSS_paper. Reticulating splines etc...
elbeejay commented 2 years ago

@whedon check references from branch JOSS_paper

whedon commented 2 years ago 
Attempting to check references... from custom branch JOSS_paper
whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1029/2020GC009219 is OK
- 10.1007/s00445-019-1336-3 is OK
- 10.1017/CBO9781316276273 is OK
- 10.1007/s004450100173 is OK
- 10.1016/j.jvolgeores.2017.08.003 is OK
- 10.3389/feart.2014.00028 is OK
- 10.7488/era/1087 is OK
- 10.5479/si.GVP.VOTW4-2013 is OK
- 10.5194/nhess-21-3509-2021 is OK
- 10.1016/B978-0-12-818082-2.00001-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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:

elbeejay commented 2 years ago

Hi @elbeejay,

Thank you so very much for all your help and support.

I proceeded with merging your suggested PR into the JOSS_paper branch. I also added a couple of commits to the branch. I will wait for your confirmation that these changes look reasonable before I complete the PR for the branch, OK?

Very many thanks in advance.

Best regards, Pablo

@PTierz this looks good to me. At this time I'd say go ahead and merge the paper into the main branch and then proceed to complete the items on that checklist I provided above. If you notice something or want to make minor changes to the paper feel free to go ahead and do so, I'd just ask that you use the whedon commands (like those above) to regenerate the PDF and check the references to ensure nothing has broken in the paper or bibliography files.

Let me know if you have any questions as you are tagging or archiving the code.

Thanks, Jay

PTierz commented 2 years ago

Dear @elbeejay,

Thank you very much once again for all your support and assistance during the entire review process.

I have just merged the JOSS_paper branch into main and released version v1.3.2.

I have also archived this version on Zenodo and obtained the following badge:

DOI

If there was anything else required from me, please do not hesitate to let me know.

Very many thanks for everything.

Best wishes, Pablo

elbeejay commented 2 years ago

@whedon set v1.3.2 as version

whedon commented 2 years ago

OK. v1.3.2 is the version.

elbeejay 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

- 10.1029/2020GC009219 is OK
- 10.1007/s00445-019-1336-3 is OK
- 10.1017/CBO9781316276273 is OK
- 10.1007/s004450100173 is OK
- 10.1016/j.jvolgeores.2017.08.003 is OK
- 10.3389/feart.2014.00028 is OK
- 10.7488/era/1087 is OK
- 10.5479/si.GVP.VOTW4-2013 is OK
- 10.5194/nhess-21-3509-2021 is OK
- 10.1016/B978-0-12-818082-2.00001-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None
elbeejay 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:

elbeejay commented 2 years ago

@whedon set 10.5281/zenodo.5809105 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5809105 is the archive.

elbeejay commented 2 years ago

Cool, everything looks good to me. Big thanks again to @meghanrjones and @jifarquharson for providing constructive and helpful reviews.

@PTierz and co-authors: At this point I will recommend PyVOLCANS for publication in JOSS. Next an Editor-in-Chief will review the submission and review thread here to double-check that we haven't missed anything and will either notify you of any minor changes needed or will publish your article in JOSS. Thanks for your cooperation, I hope you all found the process to be helpful.

elbeejay commented 2 years ago

@whedon recommend-accept

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

- 10.1029/2020GC009219 is OK
- 10.1007/s00445-019-1336-3 is OK
- 10.1017/CBO9781316276273 is OK
- 10.1007/s004450100173 is OK
- 10.1016/j.jvolgeores.2017.08.003 is OK
- 10.3389/feart.2014.00028 is OK
- 10.7488/era/1087 is OK
- 10.5479/si.GVP.VOTW4-2013 is OK
- 10.5194/nhess-21-3509-2021 is OK
- 10.1016/B978-0-12-818082-2.00001-9 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/2855

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2855, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
arfon commented 2 years ago

@whedon accept deposit=true

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:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2856
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03649
  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 2 years ago

@jifarquharson, @meghanrjones – many thanks for your thoughtful and detailed reviews here and to @elbeejay for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@PTierz – your paper is now accepted and published in JOSS :zap::rocket::boom:

whedon commented 2 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.03649/status.svg)](https://doi.org/10.21105/joss.03649)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03649">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03649/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03649/status.svg
   :target: https://doi.org/10.21105/joss.03649

This is how it will look in your documentation:

DOI

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PTierz commented 2 years ago

Hi everyone,

Apologies for my late reply.

Very many thanks @arfon for your message, and once again to @jifarquharson and @meghanrjones for their invaluable reviews and comments, to @elbeejay for his never-ending support throughout the entire process, and to all the co-authors (@mobiuscreek, @volcan01010) for all the amazing collaborative work they did to help make PyVOLCANS happen.

Best wishes to you all! Pablo

elbeejay commented 2 years ago

@openjournals/dev is it possible to add a sentence to the acknowledgements section even though this has been technically published already? The sentence would read:

Published with permission of the Executive Director of British Geological Survey (NERC-UKRI).

@PTierz please feel free to add further details as you deem appropriate.

elbeejay commented 2 years ago

Pinging folks with the requested alteration test from @PTierz, just to make sure this doesn't get lost in the shuffle. Thanks all.

Very many thanks for this, @elbeejay, and apologies for not having replied before.

Dear @openjournals/dev, @openjournals/joss-eics,

The only additions that I would like to make to the Acknowledgements are the following (in bold text):

"The research leading to these results has been mainly supported by the UK National Capability Funding (Innovation Flexible Fund programme) and by the Global Geological Risk Platform of the British Geological Survey NC-ODA grant NE/R000069/1: Geoscience for Sustainable Futures […] Moreover, we would like to sincerely thank a number of colleagues with whom we shared very insightful conversations about analogue volcanoes and/or PyVOLCANS: Chris Newhall, Isla Sim- mons, Adriano Pimentel, Julia Crummy, Gezahegn Yirgu, Charlotte Vye-Brown, Lara Smale, Karen Fontijn, Ben Clarke, Susanna Jenkins, Elly Tennant, Pierre Barbillon, Elaine Spiller, Philippa White, Teresa Ubide, Sebastián García, Victoria Olivera, Jeremy Pesicek, Vanesa Burgos Delgado, Einat Lev, Jonty Rougier, Willy Aspinall, Paolo Papale, Monse Cascante and Thomas Giachetti. Published with permission of the Executive Director of British Geological Survey (NERC-UKRI)."

Would it be possible to add those two sentences to the Acknowledgements without modifying the publishing date?

I apologise in advance for having missed the inclusion of these sentences during the page-proofing stage.

Very many thanks in advance.

Kind regards, Pablo

arfon commented 2 years ago

@openjournals/dev is it possible to add a sentence to the acknowledgements section even though this has been technically published already? The sentence would read:

Yes, it's possible. @PTierz – please make the changes to your paper.md file (in the repo) and let me (@arfon) know when you've done this.

PTierz commented 2 years ago

Dear @arfon,

Thank you very much for your message and your support.

Please accept my apologies for not having replied to this message considerably earlier. I had to be out of the office 22 Jan-1 Feb, and I am catching up with my emails only from this morning.

I have just added the small amending sentences to the Acknowledgements section via commit 1713702.

If there is anything else required from me, please do not hesitate to let me know. I sincerely hope that the publishing date/year (2021) can be kept, as this would be very important for me.

Very many thanks once again for your support.

Best wishes, Pablo

arfon commented 2 years ago

@PTierz – the paper is now updated. The new PDF might take ~24 hours to show as updated on the JOSS site.

PTierz commented 2 years ago

Thank you very much for your support, @arfon, it is extremely appreciated.

I checked the DOI link to the article and it seems that it has been already updated!

Many thanks again. Best wishes, Pablo