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[REVIEW]: planetMagFields: A Python package for analyzing and plotting planetary magnetic field data #6677

Closed editorialbot closed 6 months ago

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@AnkitBarik<!--end-author-handle-- (Ankit Barik) Repository: https://github.com/AnkitBarik/planetMagFields Branch with paper.md (empty if default branch): Version: 1.4.3 Editor: !--editor-->@dfm<!--end-editor-- Reviewers: @athulpg007, @kjg136 Archive: 10.5281/zenodo.4690524

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cba7fd0934d76b39ec197f5cdd12298b"><img src="https://joss.theoj.org/papers/cba7fd0934d76b39ec197f5cdd12298b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cba7fd0934d76b39ec197f5cdd12298b/status.svg)](https://joss.theoj.org/papers/cba7fd0934d76b39ec197f5cdd12298b)

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

@athulpg007 & @kjg136, 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 @dfm 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

πŸ“ Checklist for @kjg136

πŸ“ Checklist for @athulpg007

editorialbot commented 6 months ago

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:

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editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1029/2012JE004159 is OK
- 10.1029/2018JE005835 is OK
- 10.1029/2021JE007055 is OK
- 10.1038/s41586-018-0468-5 is OK
- 10.1002/2018GL077312 is OK
- 10.1029/97JA03726 is OK
- 10.1029/JA092iA13p15329 is OK
- 10.1029/91JA01165 is OK
- 10.1006/icar.2002.6834 is OK
- 10.1186/s40623-020-01288-x is OK
- 10.1126/science.aat5434 is OK
- 10.1016/j.pepi.2011.05.013 is OK
- 10.1093/acrefore/9780190647926.013.31 is OK
- 10.1146/annurev-fluid-122109-160727 is OK
- 10.1201/b12985 is OK
- 10.1002/ggge.20071 is OK
- 10.2151/jmsj.2018-019 is OK
- 10.1007/s11214-023-00961-3 is OK
- 10.5281/zenodo.10602418 is OK
- 10.1186/s40623-020-01252-9 is OK
- 10.5281/zenodo.10598528 is OK
- 10.5281/zenodo.4080294 is OK
- 10.1109/MCSE.2007.53 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- No DOI given, and none found for title: The ParaView Guide: A Parallel Visualization Appli...
- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

INVALID DOIs

- https://doi.org/10.1016/j.pepi.2017.07.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.pss.2009.04.008 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.icarus.2019.113541 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-0-12-415845-0.00006-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-012387582-2/50038-1 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 6 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1217.4 files/s, 143891.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            459            741           1095
TeX                              1             42              2            433
Markdown                         2            104              0            235
reStructuredText                 8            218            276            144
YAML                             3             12             15             66
TOML                             1              6              0             44
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            167             23
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            35            853           1209           2075
-------------------------------------------------------------------------------

Commit count by author:

   103  AnkitBarik
    69  Ankit Barik
     6  Arthus
     1  reguang
dfm commented 6 months ago

@athulpg007, @kjg136 β€” This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

πŸ‘‰ Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6677 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

editorialbot commented 6 months ago

Paper file info:

πŸ“„ Wordcount for paper.md is 1983

βœ… The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

🟑 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 6 months ago

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

kjg136 commented 6 months ago

Review checklist for @kjg136

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

athulpg007 commented 6 months ago

Review checklist for @athulpg007

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

athulpg007 commented 6 months ago

@AnkitBarik please take a look at the comments below. More details are available in the linked issues.

  1. Several example snippets use datDir='planetmagfields/data/' which will not exist if the package was installed using pip. Please see https://github.com/AnkitBarik/planetMagFields/issues/8.
  2. Please add a section for "Contributions/Community Guidelines" to README. See https://github.com/AnkitBarik/planetMagFields/issues/9
  3. Please see the suggested improvements for automated unit tests. https://github.com/AnkitBarik/planetMagFields/issues/10
athulpg007 commented 6 months ago

Thanks for addressing the above issues. Please also see: https://github.com/AnkitBarik/planetMagFields/issues/11

athulpg007 commented 6 months ago

I have completed my initial review of the submission. This is a useful package for researchers working in the area of planetary magnetic fields by providing a fast method of plotting field data for various planets. The package is well written, along with documentation and examples to help new users get started.

My concerns raised earlier have been fixed, thanks. Please see further comments below:

  1. According to the JOSS formatting guidelines, the paper should be between 250-1000 words. Currently, the word count is ~2k. Please consider revising the paper to reduce the length. Some suggestions are given below:

My suggestion is to shorten the paper to ~5 pages or less, including references. It would then be easier for a diverse, non-specialist audienceto quickly get a high-level understanding of the package, and then refer to the documentation for more mathematical details, example Jupyter notebook etc.

  1. I could run the interactive Jupyter Notebook locally. When trying to run the binder online, the page loaded but the interactive notebook kept trying to load, but could not succeed. Please verify if the binder notebooks still work as expected.

Thanks!

AnkitBarik commented 6 months ago

@athulpg007 Thank you very much for the comments. I have made the following changes:

    • Added an additional reference I had missed earlier to the package SHTools.
    • Shortened the "Mathematics" section and removed the figure on there and moved the details to the documentation. I think the remaining description is required for readers to understand what is going on in the package. If you think it's still too much, I can try cutting it down even more with a link to the documentation.
    • Removed input lines [3,4] as suggested from "Description of Software, Software package".
    • Shortened the "Jupyter frontend" section significantly with only a sentence and the link to the binder.
    • Removed screenshot figures 5 and 6. The main text of the paper is now 4 pages long (including figures). However, because of the large number of references, the total length is 7 pages. I believe the references should be there as the libraries and other studies used, need to be cited. If you have any other suggestions for slashing down on content, I would be happy to do so.
  1. I verified on my end that the binder works as intended. I'm not entirely sure why it didn't work.

Thank you!

AnkitBarik commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

kjg136 commented 6 months ago

I have completed my review of the submission, including the changes made in response to the first reviewer's comments. I agree that the package is useful for visualizing and analyzing planetary magnetic fields. To my knowledge, the authors are correct in their statement that no such package for a high-level language is currently established and therefore, the submission represents a valuable contribution. The documentation and examples are clear, making the package easy to understand and use.

I see no major issues and wish to only make two quick comments:

  1. Grammatical error in line 53 of the paper: ...as how that field looks like at...
  2. I can confirm I was able to use the binder.
athulpg007 commented 6 months ago

Thanks for the updates to the paper.

I have completed my review, and recommend to accept this submission.

AnkitBarik commented 6 months ago

@kjg136 @athulpg007 Thank you very much for your reviews. I have fixed the grammatical error.

AnkitBarik commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

AnkitBarik commented 6 months ago

I made one last change to the paper, I updated the citation for PlanetMag to the correct zenodo doi.

AnkitBarik commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

AnkitBarik commented 6 months ago

Sorry for the spam on a Sunday, I added one final bit. I realized I had forgotten an Acknowledgements section. This has not led to any additional pages. :)

Cheers, Ankit

AnkitBarik commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

dfm commented 6 months ago

@athulpg007, @kjg136 β€” Thanks for your thorough and constructive reviews!!

@AnkitBarik β€” I've opened a small PR with some minor edits to the manuscript, please take a look and merge or let me know what you think.

Once you've done that:

  1. Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
  2. Increment the version number of the software and report that version number back here.
  3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.
AnkitBarik commented 6 months ago

@dfm Thank you very much for the minor edits.

  1. The manuscript seems okay to me.
  2. I have bumped up the version number to 1.4.3 everywhere (including PyPI).
  3. A zenodo release has been automatically created through GitHub : 10.5281/zenodo.4690524 .
dfm commented 6 months ago

Thanks! Can you update the metadata on the Zenodo archive so that the title is the same as the paper?

AnkitBarik commented 6 months ago

Done !

dfm commented 6 months ago

@editorialbot set 1.4.3 as version

editorialbot commented 6 months ago

Done! version is now 1.4.3

dfm commented 6 months ago

@editorialbot set 10.5281/zenodo.4690524 as archive

editorialbot commented 6 months ago

Done! archive is now 10.5281/zenodo.4690524

dfm commented 6 months ago

@editorialbot check references

dfm commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1029/2012JE004159 is OK
- 10.1029/2018JE005835 is OK
- 10.1029/2021JE007055 is OK
- 10.1038/s41586-018-0468-5 is OK
- 10.1002/2018GL077312 is OK
- 10.1029/97JA03726 is OK
- 10.1029/JA092iA13p15329 is OK
- 10.1029/91JA01165 is OK
- 10.1006/icar.2002.6834 is OK
- 10.1186/s40623-020-01288-x is OK
- 10.1126/science.aat5434 is OK
- 10.1016/j.pepi.2011.05.013 is OK
- 10.1093/acrefore/9780190647926.013.31 is OK
- 10.1146/annurev-fluid-122109-160727 is OK
- 10.1201/b12985 is OK
- 10.1002/ggge.20071 is OK
- 10.2151/jmsj.2018-019 is OK
- 10.1007/s11214-023-00961-3 is OK
- 10.5281/zenodo.10602418 is OK
- 10.1186/s40623-020-01252-9 is OK
- 10.5281/zenodo.10598528 is OK
- 10.5281/zenodo.4080294 is OK
- 10.1029/2018GC007529 is OK
- 10.5281/zenodo.10864719 is OK
- 10.1109/MCSE.2007.53 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- No DOI given, and none found for title: The ParaView Guide: A Parallel Visualization Appli...
- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

INVALID DOIs

- https://doi.org/10.1016/j.pepi.2017.07.001 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.pss.2009.04.008 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.icarus.2019.113541 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-0-12-415845-0.00006-2 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/B978-012387582-2/50038-1 is INVALID because of 'https://doi.org/' prefix
editorialbot commented 6 months ago

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

dfm commented 6 months ago

@AnkitBarik β€” Can you also fix those invalid DOIs listed above? I think the "missing DOIs" are fine to ignore. Thanks!

AnkitBarik commented 6 months ago

@dfm Thank you for pointing it out. I have fixed the DOI errors.

AnkitBarik commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1029/2012JE004159 is OK
- 10.1016/j.pepi.2017.07.001 is OK
- 10.1029/2018JE005835 is OK
- 10.1029/2021JE007055 is OK
- 10.1038/s41586-018-0468-5 is OK
- 10.1002/2018GL077312 is OK
- 10.1029/97JA03726 is OK
- 10.1029/JA092iA13p15329 is OK
- 10.1029/91JA01165 is OK
- 10.1006/icar.2002.6834 is OK
- 10.1186/s40623-020-01288-x is OK
- 10.1016/j.pss.2009.04.008 is OK
- 10.1126/science.aat5434 is OK
- 10.1016/j.icarus.2019.113541 is OK
- 10.1016/j.pepi.2011.05.013 is OK
- 10.1016/B978-0-12-415845-0.00006-2 is OK
- 10.1093/acrefore/9780190647926.013.31 is OK
- 10.1146/annurev-fluid-122109-160727 is OK
- 10.1016/B978-012387582-2/50038-1 is OK
- 10.1201/b12985 is OK
- 10.1002/ggge.20071 is OK
- 10.2151/jmsj.2018-019 is OK
- 10.1007/s11214-023-00961-3 is OK
- 10.5281/zenodo.10602418 is OK
- 10.1186/s40623-020-01252-9 is OK
- 10.5281/zenodo.10598528 is OK
- 10.5281/zenodo.4080294 is OK
- 10.1029/2018GC007529 is OK
- 10.5281/zenodo.10864719 is OK
- 10.1109/MCSE.2007.53 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- No DOI given, and none found for title: The ParaView Guide: A Parallel Visualization Appli...
- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

INVALID DOIs

- None
AnkitBarik commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

dfm commented 6 months ago

@editorialbot recommend-accept

editorialbot commented 6 months ago
Attempting dry run of processing paper acceptance...
editorialbot commented 6 months ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1029/2012JE004159 is OK
- 10.1016/j.pepi.2017.07.001 is OK
- 10.1029/2018JE005835 is OK
- 10.1029/2021JE007055 is OK
- 10.1038/s41586-018-0468-5 is OK
- 10.1002/2018GL077312 is OK
- 10.1029/97JA03726 is OK
- 10.1029/JA092iA13p15329 is OK
- 10.1029/91JA01165 is OK
- 10.1006/icar.2002.6834 is OK
- 10.1186/s40623-020-01288-x is OK
- 10.1016/j.pss.2009.04.008 is OK
- 10.1126/science.aat5434 is OK
- 10.1016/j.icarus.2019.113541 is OK
- 10.1016/j.pepi.2011.05.013 is OK
- 10.1016/B978-0-12-415845-0.00006-2 is OK
- 10.1093/acrefore/9780190647926.013.31 is OK
- 10.1146/annurev-fluid-122109-160727 is OK
- 10.1016/B978-012387582-2/50038-1 is OK
- 10.1201/b12985 is OK
- 10.1002/ggge.20071 is OK
- 10.2151/jmsj.2018-019 is OK
- 10.1007/s11214-023-00961-3 is OK
- 10.5281/zenodo.10602418 is OK
- 10.1186/s40623-020-01252-9 is OK
- 10.5281/zenodo.10598528 is OK
- 10.5281/zenodo.4080294 is OK
- 10.1029/2018GC007529 is OK
- 10.5281/zenodo.10864719 is OK
- 10.1109/MCSE.2007.53 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- No DOI given, and none found for title: The ParaView Guide: A Parallel Visualization Appli...
- No DOI given, and none found for title: Cartopy: a cartographic python library with a Matp...

INVALID DOIs

- None
editorialbot commented 6 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

No declaration for attribute displaystyle of element mfrac
dfm commented 6 months ago

@AnkitBarik β€” I know that that error message is a little opaque, but my guess is that the issue here is with the use of dfrac in the manuscript. Could you try switching it to frac and we can try this again?

AnkitBarik commented 6 months ago

@dfm I have switched it to \frac and verified that it still looks fine on the pdf.