[PRE REVIEW]: GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data

[whedon]

Submitting author: @NoraLoose (Nora Loose)
Repository: https://github.com/ocean-eddy-cpt/gcm-filters
Version: v0.1.3
Editor: @elbeejay
Reviewers: @callumrollo, @AleksiNummelin, @isgiddy
Managing EiC: Daniel S. Katz

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Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

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Author instructions

Thanks for submitting your paper to JOSS @NoraLoose. Currently, there isn't an JOSS editor assigned to your paper.

@NoraLoose if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1131

[whedon]

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

OK DOIs

- 10.1029/2021MS002552 is OK
- 10.5334/jors.148 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 1721.1/117188 is OK
- 10.5281/zenodo.4968496 is OK

MISSING DOIs

- 10.25080/majora-7b98e3ed-013 may be a valid DOI for title:  Dask: Parallel Computation with Blocked algorithms and Task Scheduling 

INVALID DOIs

- https://doi.org/10.1029/2019MS001726 is INVALID because of 'https://doi.org/' prefix

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (230.3 files/s, 176058.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            428            366           1502
Jupyter Notebook                 8              0          23079            879
reStructuredText                 6            219            182            259
TeX                              1             18              0            191
YAML                             7             12             15            184
Markdown                         2             35              0            114
TOML                             1              2              0             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            36            718          23649           3149
-------------------------------------------------------------------------------


Statistical information for the repository 'a7710009ba542e7c996313ed' was
gathered on 2021/11/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andrew Ross                      8            89             20            1.10
Arthur                          24           483            420            9.10
Elizabeth A Yankovsk             6           132             41            1.74
Gustavo Marques                 10           632            198            8.37
Ian Grooms                      30           456            305            7.67
Julius Busecke                   6           104            209            3.16
NoraLoose                      116          3111           1557           47.06
Ryan Abernathey                 28          1461            686           21.64
Scott Bachman                    2             8              8            0.16

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Andrew Ross                  70           78.7          0.9               14.29
Arthur                        5            1.0          7.9                0.00
Elizabeth A Yankovsk         25           18.9          1.0               16.00
Gustavo Marques             249           39.4          5.6               10.84
Ian Grooms                  201           44.1          5.7                5.97
Julius Busecke               83           79.8          9.2               39.76
NoraLoose                   936           30.1          4.6               10.36
Ryan Abernathey             727           49.8          5.9                8.12

[whedon]

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

[danielskatz]

@NoraLoose - while we find an editor, can you work on the possibly missing DOI and the incorrect DOI that whedon suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @whedon check references to check again, and the command @whedon generate pdf when the references are right to make a new PDF. Whedon commands need to be the first entry in a new comment.

[danielskatz]

👋 @elbeejay - do you think you could edit this submission for JOSS?

[danielskatz]

@whedon invite @elbeejay as editor

[whedon]

@elbeejay has been invited to edit this submission.

[danielskatz]

@kthyng - just pinging you as well, since this falls into your area, but you currently don't have editing slots open

[NoraLoose]

Thanks @danielskatz for handling our submission and looking for an editor!

while we find an editor, can you work on the possibly missing DOI and the incorrect DOI that whedon suggests

Yes, working on it!

[NoraLoose]

@whedon check references

[whedon]

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

OK DOIs

- 10.1029/2021MS002552 is OK
- 10.5334/jors.148 is OK
- 10.25080/Majora-7b98e3ed-013 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1029/2019MS001726 is OK
- 1721.1/117188 is OK
- 10.5281/zenodo.4968496 is OK

MISSING DOIs

- 10.25080/majora-7b98e3ed-013 may be a valid DOI for title:  Dask: Parallel Computation with Blocked algorithms and Task Scheduling 

INVALID DOIs

- None

[NoraLoose]

@whedon check references

[whedon]

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

OK DOIs

- 10.1029/2021MS002552 is OK
- 10.5334/jors.148 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1029/2019MS001726 is OK
- 1721.1/117188 is OK
- 10.5281/zenodo.4968496 is OK

MISSING DOIs

- 10.25080/majora-7b98e3ed-013 may be a valid DOI for title:  Dask: Parallel Computation with Blocked algorithms and Task Scheduling 

INVALID DOIs

- None

[NoraLoose]

I followed the dask documentation in how to cite dask:

@Manual{,
  title = {Dask: Library for dynamic task scheduling},
  author = {{Dask Development Team}},
  year = {2016},
  url = {https://dask.org},
}

Unfortunately, there is no DOI for this citation, and the DOI that @whedon suggests is not correct. (Instead, it is the DOI for a paper by M. Rocklin.)

[NoraLoose]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3894 with the following error:

[NoraLoose]

@whedon generate pdf

[elbeejay]

@whedon assign me as editor

[whedon]

OK, the editor is @elbeejay

[elbeejay]

@NoraLoose can you try switching the bib entry-type for dask to @misc instead of @Manual? That is the recommended format for citing a software repository per the JOSS docs (link), and so it might play nicer with whedon.

[NoraLoose]

@whedon generate pdf

[whedon]

OK, @callumrollo is now a reviewer

[edoddridge]

Hi @elbeejay. I'm only working part time at the moment and wouldn't be able to do this in any sort of reasonable time frame, so I will need to decline this time. Sorry.

[elbeejay]

Hi @elbeejay. I'm only working part time at the moment and wouldn't be able to do this in any sort of reasonable time frame, so I will need to decline this time. Sorry.

No problem, thanks for letting us know!

[elbeejay]

👋 @AleksiNummelin, would you be willing to review this submission to JOSS? I think your experience working on ocean and climate dynamics using Python would allow you to provide an insightful review. At JOSS we do checklist-driven reviews, the JOSS review criteria can be found here.

The submission is "GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data". This is a pre-review issue which is used to find reviewers. Once 2 or 3 reviewers have been found I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed. If you are not able to review but can recommend someone else, please mention them here (in this case please mention their GitHub handle without the "@" symbol).

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Thank you, feel free to reach out if you have any questions about the JOSS review process. Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time.

[AleksiNummelin]

Hi @elbeejay, I'd be happy to review, I have tested the tool already so this is a good chance to look through the code properly. I will be busy for the next 2 weeks so expect little progress, but after that I'd expect to submit the review relatively quickly.

To be completely open (in accordance with the JOSS spirit), I want to declare that I know the first author well as we worked in the same university before, but we don't have shared publications nor do I have any trouble in providing an impartial assessment (there is no formal conflict of interest).

[elbeejay]

Awesome @AleksiNummelin, sounds like you'll be able to provide perspectives as both a real user and fellow developer. Thank you for being clear about your relationship with the lead-author, I agree that it does not sound like a true COI.

[elbeejay]

@whedon add @AleksiNummelin as reviewer

[whedon]

OK, @AleksiNummelin is now a reviewer

[elbeejay]

👋 @isgiddy, would you be willing to review this submission to JOSS? I think your experience as an ocean scientist would allow you to provide the authors with a constructive review. At JOSS we do checklist-driven reviews, the JOSS review criteria can be found here.

The submission is "GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data". This is a pre-review issue which is used to find reviewers. Once 2 or 3 reviewers have been found I'll start the review on a dedicated GitHub issue. At present we are asking reviewers to complete reviews in 6 weeks, although this can be extended if needed.

If you are interested, please take a look at the journal's conflict of interest policy to ensure you do not have a conflict before agreeing to review this submission.

Thank you, feel free to reach out if you have any questions about the JOSS review process. Please do not feel any pressure to accept this review request if you do not have the time or do not feel comfortable reviewing this software package, we appreciate and respect our peer-reviewers' time.

[NoraLoose]

Hey @elbeejay! Just another thought: in case we are still short on reviewers, here are two more suggestions:

• raphaeldussin
• JiaweiZhuang

[elbeejay]

Hey @elbeejay! Just another thought: in case we are still short on reviewers, here are two more suggestions:

• raphaeldussin
• JiaweiZhuang

Thank you, yes I am hoping to find one more reviewer before we move from "pre-review" to the "review" itself.

[isgiddy]

Hi @elbeejay. This looks interesting and I'd be happy to learn more about this filtering technique and wider applications via the review process.

[elbeejay]

Hi @elbeejay. This looks interesting and I'd be happy to learn more about this filtering technique and wider applications via the review process.

Awesome, thanks!

[elbeejay]

@whedon add @isgiddy as reviewer

[whedon]

OK, @isgiddy is now a reviewer

[elbeejay]

@whedon start review

[whedon]

OK, I've started the review over in #3947.