[REVIEW]: xeofs: Comprehensive EOF analysis in Python with xarray #6060

editorialbot · 2023-11-15T11:37:57Z

Submitting author: @nicrie (Niclas Rieger)
Repository: https://github.com/nicrie/xeofs
Branch with paper.md (empty if default branch): joss-submission
Version: v2.2.4
Editor: @samhforbes
Reviewers: @DamienIrving, @malmans2
Archive: 10.5281/zenodo.10428233

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4f50349ee1777b8a61761183047b1180"><img src="https://joss.theoj.org/papers/4f50349ee1777b8a61761183047b1180/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4f50349ee1777b8a61761183047b1180/status.svg)](https://joss.theoj.org/papers/4f50349ee1777b8a61761183047b1180)

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

@DamienIrving & @malmans2, 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 @samhforbes 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 @DamienIrving

📝 Checklist for @malmans2

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

editorialbot · 2023-11-15T11:37:59Z

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

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

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editorialbot · 2023-11-15T11:38:01Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.24 s (743.3 files/s, 164147.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          92           2861           4129          10126
HTML                             1           1244              2           6337
Markdown                         6            571              0            738
reStructuredText                52           2817           5787            641
TeX                              1             40              0            398
YAML                             8             36             29            162
Jupyter Notebook                15              0           3347            109
TOML                             1              7              0             55
CSS                              1              6              1             29
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           179           7594          13303          18630
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-15T11:38:03Z

Wordcount for paper.md is 805

editorialbot · 2023-11-15T11:38:23Z

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

OK DOIs

- 10.5334/jors.122 is OK
- 10.5334/jors.148 is OK
- 10.1007/978-3-642-86940-2_10 is OK
- 10.1002/joc.1499 is OK
- 10.1175/JCLI-D-20-0266.1 is OK
- 10.1109/TGRS.2020.2969813 is OK
- 10.1007/978-3-030-67073-3 is OK
- 10.2307/2333955 is OK
- 10.1016/0304-4076(76)90010-5 is OK
- 10.1175/1520-0442(1992)005<0541:AIOMFF>2.0.CO;2 is OK
- 10.1175/1520-0442(1995)008<2631:OROSPD>2.0.CO;2 is OK
- 10.1175/JCLI-D-16-0664.1 is OK
- 10.1175/JCLI-D-21-0244.1 is OK
- 10.1080/13658816.2011.554838 is OK
- 10.1016/0167-2789(86)90031-X is OK
- 10.1175/1520-0493(1982)110<0481:EOEEOF>2.0.CO;2 is OK
- 10.1175/1520-0450(1984)023<1660:CPCATA>2.0.CO;2 is OK
- 10.1175/1520-0493(1981)109<0587:BVISTO>2.0.CO;2 is OK
- 10.1175/1520-0493(1983)111<0756:IOTMAP>2.0.CO;2 is OK
- 10.1175/JCLI3879.1 is OK
- 10.1175/1520-0469(2001)058<1341:OPPITV>2.0.CO;2 is OK
- 10.1007/BF02289233 is OK
- 10.1111/j.2044-8317.1964.tb00244.x is OK
- 10.1137/090771806 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-15T11:39:30Z

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

samhforbes · 2023-11-15T11:41:36Z

@DamienIrving, @malmans2 this is our review thread - we track main issues and your checklist in here, following the instructions above. Any issues you encounter or changes to make during your review you can raise as issues in the software repository directly, and feel free to link back here.

DamienIrving · 2023-11-17T21:36:21Z

Review checklist for @DamienIrving

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/nicrie/xeofs?
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 (@nicrie) 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?

kthyng · 2023-12-13T22:45:00Z

Hi @DamienIrving, @malmans2! How are your reviews coming along?

DamienIrving · 2023-12-13T23:48:42Z

I'm all done - sorry for the delay!

The authors have done a really excellent job with the package and associated documentation.

The only very minor issue I found was a broken link to the contributing guide, for which I've submitted a pull request to fix: xarray-contrib/xeofs#129

samhforbes · 2023-12-13T23:49:56Z

That's great, thanks @DamienIrving

malmans2 · 2023-12-14T09:19:53Z

Review checklist for @malmans2

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/nicrie/xeofs?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@nicrie) 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?

malmans2 · 2023-12-14T09:24:36Z

Hi all, sorry about the delay!

I glanced through the repository and xeofs looks in great shape.
I'll go through all the formal steps by the end of the week and will let you know when I'm done.

malmans2 · 2023-12-15T10:24:20Z

Hi everyone! I'm done with my review.

Great package, and it's 100% in line with JOSS standards.
If I'll need to perform EOFs, I will definitely use it.

I opened 2 minor issues:

Add dependencies section in the documentation xarray-contrib/xeofs#132: Although the authors clearly mention the core dependencies, I think it's worth listing somewhere in the documentation all mandatory and optional dependencies.
Keep the documentation in sync with the code xarray-contrib/xeofs#130: This shouldn't be a blocker, so it's up to the authors to decide whether implement my suggestions.

I suggest to open a PR in xarray and add xeofs here: https://docs.xarray.dev/en/stable/ecosystem.html

Suggestion to include [xeofs](https://github.com/nicrie/xeofs) in the xarray ecosystem documentation. xeofs enables fully multidimensional PCA / EOF analysis and related techniques with large datasets, thanks to the integration of xarray and dask. References: - [Github repository](https://github.com/nicrie/xeofs) - [Documentation](https://xeofs.readthedocs.io/en/latest/) - [JOSS review](openjournals/joss-reviews#6060)

nicrie · 2023-12-19T10:28:04Z

Hi, many thanks @DamienIrving and @malmans2 for the reviews and the suggestions for improvement. We have incorporated the feedback and opened a PR for the xarray documentation here.

Suggestion to include [xeofs](https://github.com/nicrie/xeofs) in the xarray ecosystem documentation. xeofs enables fully multidimensional PCA / EOF analysis and related techniques with large datasets, thanks to the integration of xarray and dask. References: - [Github repository](https://github.com/nicrie/xeofs) - [Documentation](https://xeofs.readthedocs.io/en/latest/) - [JOSS review](openjournals/joss-reviews#6060)

samhforbes · 2023-12-20T14:18:22Z

Hi @DamienIrving and @malmans2 I can see you've ticked everything off. Can you confirm you are happy with the changes made and there are no outstanding concerns please?
Thanks for answering the issues so comprehensively @nicrie - I've also tried this out and it works nicely!

nicrie · 2024-01-02T14:21:34Z

Done @samhforbes, thank you !

samhforbes · 2024-01-02T14:41:44Z

@editorialbot set 10.5281/zenodo.10428233 as archive

editorialbot · 2024-01-02T14:41:46Z

Done! archive is now 10.5281/zenodo.10428233

samhforbes · 2024-01-02T14:42:06Z

@editorialbot check references

editorialbot · 2024-01-02T14:42:30Z

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

OK DOIs

- 10.5334/jors.122 is OK
- 10.5334/jors.148 is OK
- 10.1007/978-3-642-86940-2_10 is OK
- 10.1002/joc.1499 is OK
- 10.1175/JCLI-D-20-0266.1 is OK
- 10.1109/TGRS.2020.2969813 is OK
- 10.1007/978-3-030-67073-3 is OK
- 10.2307/2333955 is OK
- 10.1016/0304-4076(76)90010-5 is OK
- 10.1175/1520-0442(1992)005<0541:AIOMFF>2.0.CO;2 is OK
- 10.1175/1520-0442(1995)008<2631:OROSPD>2.0.CO;2 is OK
- 10.1175/JCLI-D-16-0664.1 is OK
- 10.1175/JCLI-D-21-0244.1 is OK
- 10.1080/13658816.2011.554838 is OK
- 10.1016/0167-2789(86)90031-X is OK
- 10.1175/1520-0493(1982)110<0481:EOEEOF>2.0.CO;2 is OK
- 10.1175/1520-0450(1984)023<1660:CPCATA>2.0.CO;2 is OK
- 10.1175/1520-0493(1981)109<0587:BVISTO>2.0.CO;2 is OK
- 10.1175/1520-0493(1983)111<0756:IOTMAP>2.0.CO;2 is OK
- 10.1175/JCLI3879.1 is OK
- 10.1175/1520-0469(2001)058<1341:OPPITV>2.0.CO;2 is OK
- 10.1007/BF02289233 is OK
- 10.1111/j.2044-8317.1964.tb00244.x is OK
- 10.1137/090771806 is OK

MISSING DOIs

- None

INVALID DOIs

- None

samhforbes · 2024-01-02T14:42:46Z

@editorialbot generate pdf

editorialbot · 2024-01-02T14:43:56Z

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

samhforbes · 2024-01-02T14:56:44Z

Great! @nicrie thanks for the great work you have done on this package - I am happy to recommend acceptance and pass it over to the EiCs.
Thanks @DamienIrving, @malmans2 for your great reviews.

samhforbes · 2024-01-02T14:56:58Z

@editorialbot recommend-accept

editorialbot · 2024-01-02T14:57:00Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-01-02T14:57:09Z

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

OK DOIs

- 10.5334/jors.122 is OK
- 10.5334/jors.148 is OK
- 10.1007/978-3-642-86940-2_10 is OK
- 10.1002/joc.1499 is OK
- 10.1175/JCLI-D-20-0266.1 is OK
- 10.1109/TGRS.2020.2969813 is OK
- 10.1007/978-3-030-67073-3 is OK
- 10.2307/2333955 is OK
- 10.1016/0304-4076(76)90010-5 is OK
- 10.1175/1520-0442(1992)005<0541:AIOMFF>2.0.CO;2 is OK
- 10.1175/1520-0442(1995)008<2631:OROSPD>2.0.CO;2 is OK
- 10.1175/JCLI-D-16-0664.1 is OK
- 10.1175/JCLI-D-21-0244.1 is OK
- 10.1080/13658816.2011.554838 is OK
- 10.1016/0167-2789(86)90031-X is OK
- 10.1175/1520-0493(1982)110<0481:EOEEOF>2.0.CO;2 is OK
- 10.1175/1520-0450(1984)023<1660:CPCATA>2.0.CO;2 is OK
- 10.1175/1520-0493(1981)109<0587:BVISTO>2.0.CO;2 is OK
- 10.1175/1520-0493(1983)111<0756:IOTMAP>2.0.CO;2 is OK
- 10.1175/JCLI3879.1 is OK
- 10.1175/1520-0469(2001)058<1341:OPPITV>2.0.CO;2 is OK
- 10.1007/BF02289233 is OK
- 10.1111/j.2044-8317.1964.tb00244.x is OK
- 10.1137/090771806 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-02T14:58:18Z

👋 @openjournals/ese-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#4868, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2024-01-02T16:56:41Z

My steps:

Check that version was updated
Check that software archive exists, has been input to JOSS, and title and author list look good
Check paper

kthyng · 2024-01-02T16:59:51Z

Paper comments:

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.
Seems like the references in the table shouldn't have parentheses around them — you can remove the brackets in the paper to fix this (check the sample paper in the docs: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

nicrie · 2024-01-02T17:49:05Z

Thank you for the comments @kthyng, both points should be addressed now by the recent commits.

kthyng · 2024-01-02T18:08:34Z

@editorialbot generate pdf

editorialbot · 2024-01-02T18:10:04Z

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

kthyng · 2024-01-02T18:21:56Z

Ok ready to go!

kthyng · 2024-01-02T18:22:00Z

@editorialbot accept

editorialbot · 2024-01-02T18:22:03Z

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

editorialbot · 2024-01-02T18:24:50Z

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: Rieger
  given-names: Niclas
  orcid: "https://orcid.org/0000-0003-3357-1742"
- family-names: Levang
  given-names: Samuel J.
doi: 10.5281/zenodo.10428233
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Rieger
    given-names: Niclas
    orcid: "https://orcid.org/0000-0003-3357-1742"
  - family-names: Levang
    given-names: Samuel J.
  date-published: 2024-01-02
  doi: 10.21105/joss.06060
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6060
  title: "xeofs: Comprehensive EOF analysis in Python with xarray"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06060"
  volume: 9
title: "xeofs: Comprehensive EOF analysis in Python with xarray"

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 · 2024-01-02T18:24:54Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-01-02T18:24:55Z

🚨🚨🚨 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.06060 joss-papers#4869
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06060
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-01-02T18:34:53Z

Congrats on your new publication to @nicrie! Many thanks to editor @samhforbes and reviewers @DamienIrving, and @malmans2 for your time, hard work, and expertise!!

editorialbot · 2024-01-02T18:34:55Z

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

If you would like to include a link to your paper from your README use the following code snippets:

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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06060/status.svg
   :target: https://doi.org/10.21105/joss.06060

This is how it will look in your documentation:

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nicrie · 2024-01-02T19:10:39Z

Wonderful! Also from our side many thanks for reviewing and editing the publication! :)

editorialbot added Python review TeX Track: 6 (ESE) Earth Sciences and Ecology labels Nov 15, 2023

editorialbot assigned samhforbes Nov 15, 2023

editorialbot mentioned this issue Nov 15, 2023

[PRE REVIEW]: xeofs: Comprehensive EOF analysis in Python with xarray #6009

Closed

DamienIrving mentioned this issue Dec 13, 2023

docs: Update link to contributing guide xarray-contrib/xeofs#129

Merged

nicrie mentioned this issue Dec 19, 2023

Add xeofs to ecosystem.rst pydata/xarray#8561

Merged

nicrie mentioned this issue Dec 19, 2023

xeofs xarray-contrib/xarray-contrib#13

Closed

7 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 2, 2024

editorialbot added accepted published Papers published in JOSS labels Jan 2, 2024

kthyng closed this as completed Jan 2, 2024

[REVIEW]: xeofs: Comprehensive EOF analysis in Python with xarray #6060

[REVIEW]: xeofs: Comprehensive EOF analysis in Python with xarray #6060

Comments

editorialbot commented Nov 15, 2023 • edited

Status

Reviewer instructions & questions

Checklists

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samhforbes commented Nov 15, 2023

DamienIrving commented Nov 17, 2023 • edited

Review checklist for @DamienIrving

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kthyng commented Dec 13, 2023

DamienIrving commented Dec 13, 2023

samhforbes commented Dec 13, 2023

malmans2 commented Dec 14, 2023 • edited

Review checklist for @malmans2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

malmans2 commented Dec 14, 2023

malmans2 commented Dec 15, 2023 • edited

nicrie commented Dec 19, 2023

samhforbes commented Dec 20, 2023

nicrie commented Jan 2, 2024

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kthyng commented Jan 2, 2024 • edited

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editorialbot commented Nov 15, 2023 •

edited

DamienIrving commented Nov 17, 2023 •

edited

malmans2 commented Dec 14, 2023 •

edited

malmans2 commented Dec 15, 2023 •

edited

kthyng commented Jan 2, 2024 •

edited