[REVIEW]: parafields: A generator for distributed, stationary Gaussian processes #5735

editorialbot · 2023-08-04T01:39:18Z

Submitting author: @dokempf (Dominic Kempf)
Repository: https://github.com/parafields/parafields
Branch with paper.md (empty if default branch): joss-paper
Version: v1.0.1
Editor: @diehlpk
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

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-08-04T01:39:19Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot · 2023-08-04T01:39:21Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (806.5 files/s, 135174.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             4              0              0           2680
Python                          13            288            371            917
CMake                            4            142             50            853
YAML                             7             54             26            287
Markdown                         3             45              0            161
C++                              1             18              9            148
TeX                              1              2              0            133
Jupyter Notebook                 4              0            820            126
C/C++ Header                     3             22             30             77
TOML                             1              9             21             65
reStructuredText                 3              5             13              3
-------------------------------------------------------------------------------
SUM:                            44            585           1340           5450
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-08-04T01:39:23Z

Wordcount for paper.md is 816

editorialbot · 2023-08-04T01:39:23Z

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

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-08-04T01:41:01Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

diehlpk · 2023-08-11T20:52:25Z

@editorialbot remind @max-little in 2 weeks

editorialbot · 2023-08-11T20:52:26Z

Reminder set for @max-little in 2 weeks

diehlpk · 2023-08-11T20:52:45Z

@editorialbot remind @shahmoradi in 2 weeks

editorialbot · 2023-08-11T20:52:46Z

Reminder set for @shahmoradi in 2 weeks

editorialbot · 2023-08-25T20:52:27Z

👋 @max-little, please update us on how your review is going (this is an automated reminder).

editorialbot · 2023-08-25T20:52:50Z

👋 @shahmoradi, please update us on how your review is going (this is an automated reminder).

diehlpk · 2023-08-31T13:32:18Z

@editorialbot remind @max-little in 1 weeks

editorialbot · 2023-08-31T13:32:20Z

Reminder set for @max-little in 1 weeks

diehlpk · 2023-08-31T13:32:34Z

@editorialbot remind @shahmoradi in 1 weeks

editorialbot · 2023-08-31T13:32:35Z

Reminder set for @shahmoradi in 1 weeks

shahmoradi · 2023-08-31T16:41:24Z

Review checklist for @shahmoradi

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/parafields/parafields?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@dokempf) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

editorialbot · 2023-09-07T13:32:22Z

👋 @max-little, please update us on how your review is going (this is an automated reminder).

editorialbot · 2023-09-07T13:32:41Z

👋 @shahmoradi, please update us on how your review is going (this is an automated reminder).

diehlpk · 2023-09-19T16:28:29Z

Hi @max-little and @shahmoradi how is your review going?

diehlpk · 2023-09-29T14:47:06Z

Hi @max-little and @shahmoradi how is your review going?

diehlpk · 2023-10-13T15:33:44Z

Hi @max-little are you still available for the review?

diehlpk · 2023-10-13T15:34:04Z

Hi @shahmoradi are you still available for the review?

diehlpk · 2023-11-02T14:45:12Z

Hi @max-little I have not heard from you for a while, I will remove you as a reviewer and will add you again once I hear from you.

diehlpk · 2023-12-18T13:14:45Z

@dokempf please add the missing DOIs to the paper.

danielskatz · 2023-12-18T13:28:09Z

@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 · 2023-12-18T14:07:30Z

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

danielskatz · 2023-12-18T14:08:36Z

@editorialbot check references

editorialbot · 2023-12-18T14:08:47Z

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 · 2023-12-18T14:09:35Z

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

danielskatz · 2023-12-18T14:12:28Z

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

dokempf · 2023-12-18T14:13:28Z

@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 · 2023-12-18T14:14:13Z

@editorialbot recommend-accept

editorialbot · 2023-12-18T14:14:15Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-12-18T14:14:41Z

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 · 2023-12-18T14:15:30Z

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4849, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-12-18T16:06:52Z

@dokempf - I've suggested some small changes in parafields/parafields#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 · 2023-12-18T16:55:39Z

@editorialbot generate pdf

editorialbot · 2023-12-18T16:56:45Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

dokempf · 2023-12-18T17:02:11Z

@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 · 2023-12-18T18:07:20Z

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 · 2023-12-18T18:07:26Z

@editorialbot accept

editorialbot · 2023-12-18T18:07:29Z

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

editorialbot · 2023-12-18T18:08:54Z

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 · 2023-12-18T18:08:58Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-12-18T18:08:58Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05735 joss-papers#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 · 2023-12-18T18:14:44Z

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 · 2023-12-18T18:14:46Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

editorialbot added C++ CMake Python review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Aug 4, 2023

editorialbot assigned diehlpk Aug 4, 2023

editorialbot mentioned this issue Aug 4, 2023

[PRE REVIEW]: parafields: A generator for distributed, stationary Gaussian processes #5615

Closed

editorialbot added accepted published Papers published in JOSS labels Dec 18, 2023

danielskatz closed this as completed Dec 18, 2023

editorialbot mentioned this issue Jul 16, 2024

[PRE REVIEW]: 4DModeller: a spatio-temporal modelling package #6996

Closed

editorialbot mentioned this issue Oct 11, 2024

[PRE REVIEW]: PyLops-MPI - MPI Powered PyLops with mpi4py #7339

Closed

editorialbot mentioned this issue Oct 19, 2024

[PRE REVIEW]: hetGPy: Heteroskedastic Gaussian Process Modeling in Python #7374

Closed

[REVIEW]: parafields: A generator for distributed, stationary Gaussian processes #5735

[REVIEW]: parafields: A generator for distributed, stationary Gaussian processes #5735

Comments

editorialbot commented Aug 4, 2023 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented Aug 4, 2023

editorialbot commented Aug 4, 2023

editorialbot commented Aug 4, 2023

editorialbot commented Aug 4, 2023

editorialbot commented Aug 4, 2023

diehlpk commented Aug 11, 2023

editorialbot commented Aug 11, 2023

diehlpk commented Aug 11, 2023

editorialbot commented Aug 11, 2023

editorialbot commented Aug 25, 2023

editorialbot commented Aug 25, 2023

diehlpk commented Aug 31, 2023

editorialbot commented Aug 31, 2023

diehlpk commented Aug 31, 2023

editorialbot commented Aug 31, 2023

shahmoradi commented Aug 31, 2023 • edited Loading

Review checklist for @shahmoradi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented Sep 7, 2023

editorialbot commented Sep 7, 2023

diehlpk commented Sep 19, 2023

diehlpk commented Sep 29, 2023

diehlpk commented Oct 13, 2023

diehlpk commented Oct 13, 2023

diehlpk commented Nov 2, 2023

diehlpk commented Dec 18, 2023

danielskatz commented Dec 18, 2023

dokempf commented Dec 18, 2023

danielskatz commented Dec 18, 2023

editorialbot commented Dec 18, 2023

danielskatz commented Dec 18, 2023

danielskatz commented Dec 18, 2023

dokempf commented Dec 18, 2023

danielskatz commented Dec 18, 2023

editorialbot commented Dec 18, 2023

editorialbot commented Dec 18, 2023

editorialbot commented Dec 18, 2023

danielskatz commented Dec 18, 2023

dokempf commented Dec 18, 2023

editorialbot commented Dec 18, 2023

dokempf commented Dec 18, 2023

danielskatz commented Dec 18, 2023

danielskatz commented Dec 18, 2023

editorialbot commented Dec 18, 2023

editorialbot commented Dec 18, 2023

editorialbot commented Dec 18, 2023

editorialbot commented Dec 18, 2023

danielskatz commented Dec 18, 2023

editorialbot commented Dec 18, 2023

editorialbot commented Aug 4, 2023 •

edited

Loading

shahmoradi commented Aug 31, 2023 •

edited

Loading