[REVIEW]: parafields: A generator for distributed, stationary Gaussian processes

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@dokempf@diehlpk<!--end-editor-- Reviewers: @shahmoradi, @gchure Archive: 10.5281/zenodo.10355636

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/74bf5e003d1fe3bab04c107a5d7c1cce"><img src="https://joss.theoj.org/papers/74bf5e003d1fe3bab04c107a5d7c1cce/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/74bf5e003d1fe3bab04c107a5d7c1cce/status.svg)](https://joss.theoj.org/papers/74bf5e003d1fe3bab04c107a5d7c1cce)

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

@max-little & @shahmoradi, 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 @diehlpk 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 @shahmoradi

📝 Checklist for @gchure

dokempf commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

dokempf commented 11 months ago

@diehlpk Fixed now, I had only pushed to main and not to joss-paper that the bot builds from. Sorry about that.

diehlpk commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

diehlpk commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 11 months ago

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

OK DOIs

- 10.1016/j.advwatres.2016.12.006 is OK
- 10.1137/s1064827592240555 is OK
- 10.1137/17m1149730 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.camwa.2020.06.007 is OK
- 10.5281/zenodo.2565368 is OK
- 10.2307/1390903 is OK
- 10.18637/jss.v055.i09 is OK
- 10.21105/joss.05595 is OK
- 10.5194/gmd-15-3161-2022 is OK

MISSING DOIs

- 10.1007/s10182-012-0196-3 may be a valid DOI for title: Spatio-temporal modeling of particulate matter concentration through the SPDE approach
- 10.1214/10-aoas369 may be a valid DOI for title: A spatial analysis of multivariate output from regional climate models
- 10.1137/130915005 may be a valid DOI for title: A hierarchical multilevel Markov chain Monte Carlo algorithm with applications to uncertainty quantification in subsurface flow
- 10.1016/j.neuroimage.2004.08.034 may be a valid DOI for title: Bayesian fMRI time series analysis with spatial priors
- 10.1115/1.1483342 may be a valid DOI for title: Random heterogeneous materials: microstructure and macroscopic properties
- 10.1137/16m1061692 may be a valid DOI for title: Quasi-Monte Carlo and multilevel Monte Carlo methods for computing posterior expectations in elliptic inverse problems

INVALID DOIs

- None

diehlpk commented 11 months ago

@dokempf I recommend your paper for acceptance. The EIC will have a final look and publish the paper.

editorialbot commented 11 months ago

:wave: @openjournals/csism-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/4848, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

diehlpk commented 11 months ago

@dokempf please add the missing DOIs to the paper.

danielskatz commented 11 months ago

@dokempf - As the track editor, I'll proofread this next, later today. Please do add the DOIs as requested by @diehlpk, and let us know when you have done so.

dokempf commented 11 months ago

@danielskatz Missing DOIs are added on the joss-paper branch.

danielskatz commented 11 months ago

@editorialbot check references

editorialbot commented 11 months ago

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

OK DOIs

- 10.1016/j.advwatres.2016.12.006 is OK
- 10.1137/s1064827592240555 is OK
- 10.1137/17m1149730 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.camwa.2020.06.007 is OK
- 10.5281/zenodo.2565368 is OK
- 10.2307/1390903 is OK
- 10.18637/jss.v055.i09 is OK
- 10.21105/joss.05595 is OK
- 10.5194/gmd-15-3161-2022 is OK
- 10.1214/10-AOAS369 is OK
- 10.1137/130915005 is OK
- 10.1016/j.neuroimage.2004.08.034 is OK
- 10.1115/1.1483342 is OK
- 10.1137/16m1061692 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1007/s10182-012-0193-3 is INVALID

danielskatz commented 11 months ago

@dokempf - https://doi.org/10.1007/s10182-012-0193-3 doesn't resolve. Is this correct?

danielskatz commented 11 months ago

I think this should be https://doi.org/10.1007/s10182-012-0196-3 , though I can't see the difference by eye

dokempf commented 11 months ago

@danielskatz Neither could I - so I accepted CoPilots suggestion of a DOI, because it looked exactly like the one I had double-checked. Lesson learned: Never do that. It is fixed now.

danielskatz commented 11 months ago

@editorialbot recommend-accept

editorialbot commented 11 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 11 months ago

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

OK DOIs

- 10.1016/j.advwatres.2016.12.006 is OK
- 10.1137/s1064827592240555 is OK
- 10.1137/17m1149730 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/j.camwa.2020.06.007 is OK
- 10.5281/zenodo.2565368 is OK
- 10.2307/1390903 is OK
- 10.18637/jss.v055.i09 is OK
- 10.21105/joss.05595 is OK
- 10.5194/gmd-15-3161-2022 is OK
- 10.1007/s10182-012-0196-3 is OK
- 10.1214/10-AOAS369 is OK
- 10.1137/130915005 is OK
- 10.1016/j.neuroimage.2004.08.034 is OK
- 10.1115/1.1483342 is OK
- 10.1137/16m1061692 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 11 months ago

:wave: @openjournals/csism-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/4849, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 11 months ago

@dokempf - I've suggested some small changes in https://github.com/parafields/parafields/pull/153. Please merge this, or let me know what you disagree with.

In addition, please add countries to the affiliations in the paper. I'm also confused by the casing for parafields, which is "parafields" in the title, but "Parafields" in the paper in a number of places, such as the start of the first and second paragraphs.

dokempf commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

dokempf commented 11 months ago

@danielskatz Thanks a lot for your suggestions, which I have merged into the paper. Also added the requested geographic information. Regarding capitalization: parafields is only capitalized at the start of the sentence, where I though it is mandatory, but please correct me if I am wrong. As a german, I typically struggle with capitalization in english because we have quite unique capitalization rules...

danielskatz commented 11 months ago

There is no consistent rule for this. There are many style guides, and they are not consistent. One option suggested is to try to move the term away from the start of the sentence. In this case, I'm just going to go ahead and accept it the way it is.

danielskatz commented 11 months ago

@editorialbot accept

editorialbot commented 11 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 11 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Kempf given-names: Dominic orcid: "https://orcid.org/0000-0002-6140-2332" - family-names: Klein given-names: Ole orcid: "https://orcid.org/0000-0002-3295-7347" - family-names: Kutri given-names: Robert orcid: "https://orcid.org/0009-0004-8123-4673" - family-names: Scheichl given-names: Robert orcid: "https://orcid.org/0000-0001-8493-4393" - family-names: Bastian given-names: Peter contact: - family-names: Kempf given-names: Dominic orcid: "https://orcid.org/0000-0002-6140-2332" doi: 10.5281/zenodo.10355636 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Kempf given-names: Dominic orcid: "https://orcid.org/0000-0002-6140-2332" - family-names: Klein given-names: Ole orcid: "https://orcid.org/0000-0002-3295-7347" - family-names: Kutri given-names: Robert orcid: "https://orcid.org/0009-0004-8123-4673" - family-names: Scheichl given-names: Robert orcid: "https://orcid.org/0000-0001-8493-4393" - family-names: Bastian given-names: Peter date-published: 2023-12-18 doi: 10.21105/joss.05735 issn: 2475-9066 issue: 92 journal: Journal of Open Source Software publisher: name: Open Journals start: 5735 title: "parafields: A generator for distributed, stationary Gaussian processes" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05735" volume: 8 title: "parafields: A generator for distributed, stationary Gaussian processes" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 11 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 11 months 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/4854
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05735
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 11 months ago

Congratulations to @dokempf (Dominic Kempf) and co-authors on your publication!!

And thanks to @shahmoradi and @gchure for reviewing, and to @diehlpk for editing! JOSS depends on volunteers, and we couldn't do this without you.

editorialbot commented 11 months 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.05735/status.svg)](https://doi.org/10.21105/joss.05735)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05735">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05735/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05735/status.svg
   :target: https://doi.org/10.21105/joss.05735

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews