[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

diehlpk commented 1 year ago

Hi @stefanradev93 do you have time to review this paper?

gchure commented 1 year ago

Hi @gchure do you have time to review this paper?

Hi @diehlpk, I can review. This will be my first review with JOSS, so I would appreciate it if you could point me in the direction of some best practices.

shahmoradi commented 1 year ago

Thank you for the revision @dokempf. While I realize the majority of testing gaps are in a specific file, the authors should strive to bring code coverage above 90% across the whole project. @diehlpk, thank you for your reminder. The review of this paper is complete from my perspective.

diehlpk commented 1 year ago

@editorialbot add @gchure as reviewer

editorialbot commented 1 year ago

@gchure added to the reviewers list!

diehlpk commented 1 year ago

@gchure please have a look at the guidelines here

https://joss.readthedocs.io/en/latest/review_criteria.html

I am happy to answer all questions.

gchure commented 1 year ago

Review checklist for @gchure

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/parafields/parafields?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

gchure commented 1 year ago

I'm opening issues on the parafields repository as I go along through my review. My comments on the paper text are listed in #141.

Note that my paper comments are non-blocking and I leave it up to the discretion of @dokempf.

gchure commented 1 year ago

Here is an open issue (#142) outlining a error in reproducing the example for parallel usage of parafields. This is a blocking issue that should resolved before formal publication.

gchure commented 1 year ago

Here is an open issue (#143) which highlights an unsupported option in interactive mode. This is non-blocking and is at @dokempf's discretion.

gchure commented 1 year ago

Here is an open issue (#144) which highlights non-tested code that is advertised as a feature of parafields. I personally think that judging testing over coverage percent is silly (which is why I'm fine with 80% coverage), but the fenicsx integration function seems to be entirely untested. I don't think this should be a blocking issue, but really should be addressed. I leave that up to @diehlpk's discretion.

This is my final review comment. Once these issues are closed, I'm happy to recommend it be formally published in JOSS.

diehlpk commented 1 year ago

Here is an open issue (#144) which highlights non-tested code that is advertised as a feature of parafields. I personally think that judging testing over coverage percent is silly (which is why I'm fine with 80% coverage), but the Fenicsx integration function seems to be entirely untested. I don't think this should be a blocking issue, but really should be addressed. I leave that up to @diehlpk's discretion.

This is my final review comment. Once these issues are closed, I'm happy to recommend it be formally published in JOSS.

@gchure and @dokempf yes, I think it is non-blocking but I would recommend mentioning that the Fenics integration is untested in the documentation.

diehlpk commented 12 months ago

@dokempf can you please have a look at the comment above?

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

@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 We have addressed all review comments and are good to proceed. Thanks to @gchure and @shahmoradi for the work they put into this. Regarding the testing coverage of the FeniCSx integration, we went with documenting its state.

diehlpk commented 11 months ago

@gchure could you please have a final look amd check the two last missing boxes?

gchure commented 11 months ago

All of my issues have been addressed. Happy to close out my review. Congrats to @dokempf and the rest of the parafields contributors.

diehlpk commented 11 months ago

@shahmoradi and @gchure thanks for your helpful comments during the review. I will handle the submission now as editor.

diehlpk commented 11 months ago

@editorialbot check references

diehlpk commented 11 months ago

@editorialbot generate paper

editorialbot commented 11 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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

@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

@dokempf I read the paper and request the following editorial changes:

[Cameletti et al. (2013)](Sain et al., 2011)(Dodwell et al., 2015). -> It is strange to use different parentheses, e.g. () and []
material sciences(Torquato & -> add a space
Bayesian estimation(Scheichl et al. -> add a space
C++ looks not nice, and you could use C\texttt{++} or https://isocpp.org/wiki/faq/misc-environmental-issues#latex-macros

Please fix these and we can proceed with the publication preparation.

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 I addressed your comments. Thanks for having a look.

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

@dokempf Thanks, it looks good now.

Please do the following:

[ ] Generate a new release l, including all the changes made during the review. Please post the new version here.
[ ] Upload that release to Zenodo and post the DOI here. Note the title and authors of the paper need to match with the archive on Zenodo.

dokempf commented 11 months ago

@diehlpk All done, The DOI is 10.5281/zenodo.10391370

diehlpk commented 11 months ago

@diehlpk All done, The DOI is 10.5281/zenodo.10391370

And the version of the release?

diehlpk commented 11 months ago

The title on Zenodo seems to be wrong

parafields/parafields: parafields v1.0.1

There should be the same title as on the paper.

diehlpk commented 11 months ago

@editorialbot set v1.0.1 as version

editorialbot commented 11 months ago

Done! version is now v1.0.1

diehlpk commented 11 months ago

@diehlpk All done, The DOI is 10.5281/zenodo.10391370

And the version of the release?

Nevermind, I found the version in the wrong Zenodo title.

dokempf commented 11 months ago

Oh, actually our paper is lacking a title. Funny how that went completely unnoticed so far.

diehlpk commented 11 months ago

@editorialbot generate pdf

diehlpk commented 11 months ago

Oh, the title should be parafields: A generator for distributed, stationary Gaussian processes or?

Please add that to the paper and archive.

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 Finished, here is the DOI: 10.5281/zenodo.10355636

diehlpk commented 11 months ago

@editorialbot set 10.5281/zenodo.10355636 as archive

editorialbot commented 11 months ago

Done! archive is now 10.5281/zenodo.10355636

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

@dokempf the pdf is missing the title.

openjournals / joss-reviews