[REVIEW]: MetObs - a Python toolkit for using non-traditional meteorological observations #5916

editorialbot · 2023-10-02T08:26:56Z

Submitting author: @vergauwenthomas (Thomas Vergauwen)
Repository: https://github.com/vergauwenthomas/MetObs_toolkit
Branch with paper.md (empty if default branch): paper
Version: v0.2.0
Editor: @hugoledoux
Reviewers: @ashwinvis, @Zeitsperre
Archive: 10.5281/zenodo.10794417

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ffa3a79315bdf4c4793992a1de41193d/status.svg)](https://joss.theoj.org/papers/ffa3a79315bdf4c4793992a1de41193d)

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

@ashwinvis & @Zeitsperre, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @hugoledoux 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 @Zeitsperre

📝 Checklist for @ashwinvis

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

editorialbot · 2023-10-02T08:26:58Z

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editorialbot · 2023-10-02T08:27:11Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.27 s (272.0 files/s, 66745.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           45           3924           4372           7755
YAML                              6             11             15            557
reStructuredText                 11            297            344            291
TeX                               1             17              0            201
Markdown                          2             28              0             93
Bourne Shell                      2             44             15             67
TOML                              1              7              0             28
DOS Batch                         1              8              1             26
JSON                              3              1              0             19
make                              1              4              7              9
Bourne Again Shell                1             13              2              6
--------------------------------------------------------------------------------
SUM:                             74           4354           4756           9052
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-10-02T08:27:11Z

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

OK DOIs

- 10.5194/asr-17-153-2020 is OK
- 10.1016/j.uclim.2019.100565 is OK
- 10.3389/fenvs.2021.720747 is OK
- 10.1016/j.uclim.2017.01.006 is OK
- 10.1002/joc.4210 is OK
- 10.1002/qj.3803 is OK
- 10.5281/zenodo.7254221 is OK
- 10.5281/zenodo.7794821 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5281/zenodo.6364594 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-10-02T08:27:13Z

Wordcount for paper.md is 1071

editorialbot · 2023-10-02T08:28:42Z

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

Zeitsperre · 2023-10-02T15:21:07Z

Review checklist for @Zeitsperre

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/vergauwenthomas/MetObs_toolkit?
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 (@vergauwenthomas) 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?

Zeitsperre · 2023-10-02T15:23:01Z

@hugoledoux @vergauwenthomas

Hi there! Thanks for reaching out to me. I'll have some time in the next few weeks to look at this, ideally by October 15th. All the best!

ashwinvis · 2023-10-02T19:48:57Z

I will take a look over the weekend.

ashwinvis · 2023-10-07T10:35:50Z

Review checklist for @ashwinvis

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/vergauwenthomas/MetObs_toolkit?
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 (@vergauwenthomas) 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?

Zeitsperre · 2023-11-03T21:27:53Z

I'm still working on my review checklist, but I've opened a few issues to help with the goals that I think still need to be met (perhaps @ashwinvis agrees?). Will try to finish everything this coming week.

ashwinvis · 2023-11-05T21:49:33Z

I am stuck with the review, because as mentioned in the issue, I cannot run the software without example data. Thus verifying the functionality and some other checks will have to wait until it is resolved.

ashwinvis · 2023-11-12T17:22:32Z

The fix broke the docs, I believe. Waiting for it again... vergauwenthomas/MetObs_toolkit#394

vergauwenthomas · 2023-11-14T08:39:47Z

The fix broke the docs, I believe. Waiting for it again... vergauwenthomas/MetObs_toolkit#394

The docs are back online.

ashwinvis · 2023-11-26T22:40:40Z

I tried to verify the functionality of the software today and I realize that a key attractive feature of this software which is gap-filling relies on Google Earth Engine to access ERA5 reanalysis dataset, a choice which severely restricts the usability (and to some extent the openness) of the software.

While the use of proprietary software IDEs have been mentioned in the JOSS docs, I ask what is the stance for reliance on proprietary network services, @hugoledoux ?

Also I should ask @vergauwenthomas why did you opt for Google Earth Engine for a dataset easily accessible via Copernicus? Would it be easy to add support for Copernicus's Python API cdsapi?

https://climate.copernicus.eu/climate-reanalysis
https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=form

ashwinvis · 2023-11-26T23:06:42Z

Other comments:

Reproducibility: I believe the results shown in Figure 1 is based on the Examples section in the docs. The author should point out that.
References: Fix Caluwaerts et al. title The urban climate of ghent, belgium... and the citation for Pandas.

vergauwenthomas · 2023-11-27T13:51:41Z

Also I should ask @vergauwenthomas why did you opt for Google Earth Engine for a dataset easily accessible via Copernicus? Would it be easy to add support for Copernicus's Python API cdsapi?

@ashwinvis, this is indeed a relevant topic. At the beginning of this project, I considered using the Copernicus API, but the Google Earth Engine integration seems a better choice to me because of:

The presence of the global LCZ map and the worldcover (10m-res) in the GEE.
The transfer speed of GEE is better than Copernicus API (= colleagues advice @saratop-ugent).
The availability of semi-real-time products at the GEE has potential weather-related features.

Since the use of the GEE is limited to 1) static geospatial datasets and 2) time-series, I have never reached the limit of the free computational-units.

If you feel like including the Copernicus API is a valuable addition, I can open a discussion on this.

vergauwenthomas · 2023-11-27T15:14:47Z

FYI, I have created a new label JOSS publication blocking. You can add this to issues if you found them blocking your approval.

I will make a priority of these issues and try to solve them asap.

hugoledoux · 2024-03-07T13:15:27Z

for the version it's ultimately up to you, but I think it might be an idea to bump to a minor version with all the changes made during the JOSS process. I would suggest v0.2.0, this makes it clearer.

For the authors, you added some categories and that mangles the reference and only lists you an as author, can you remove those categories? Researchers + Supervisor.

I'm glad you enjoyed JOSS! Consider adding your name to the potential list of reviewers also: https://reviewers.joss.theoj.org/

(I didn't know it was possible, so I learned that today).

vergauwenthomas · 2024-03-07T16:22:45Z

I have bumped it to v0.2.0.

I had to create a new DOI (because there were still some references to `v0.1.3-joss', which i could not change). You can find it here: 10.5281/zenodo.10794417

And as @hugoledoux pointed out, i have changed the co-authors and the citations seem oke now:

Vergauwen, T., Vieijra, M., Covaci, A., Jacobs, A., Top, S., Dewettinck, W., Vandelanotte, K., Hellebosch, I., & Caluwaerts, S. (2024). MetObs - a Python toolkit for using non-traditional meteorological observations (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.10794417

hugoledoux · 2024-03-08T07:42:57Z

@editorialbot set 10.5281/zenodo.10794417 as archive

editorialbot · 2024-03-08T07:42:59Z

Done! archive is now 10.5281/zenodo.10794417

hugoledoux · 2024-03-08T07:43:12Z

@editorialbot set v0.2.0 as version

editorialbot · 2024-03-08T07:43:14Z

Done! version is now v0.2.0

hugoledoux · 2024-03-08T07:43:19Z

@editorialbot recommend-accept

editorialbot · 2024-03-08T07:43:21Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-03-08T07:43:45Z

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

OK DOIs

- 10.5194/asr-17-153-2020 is OK
- 10.1016/j.uclim.2019.100565 is OK
- 10.3389/fenvs.2021.720747 is OK
- 10.1016/j.uclim.2017.01.006 is OK
- 10.1002/joc.4210 is OK
- 10.1002/qj.3803 is OK
- 10.5281/zenodo.7254221 is OK
- 10.5281/zenodo.7794821 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5281/zenodo.6364594 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-03-08T07:45:04Z

👋 @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#5102, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2024-03-08T15:50:31Z

Great! My steps are:

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 · 2024-03-08T15:57:23Z

Good to go!

kthyng · 2024-03-08T15:57:28Z

@editorialbot accept

editorialbot · 2024-03-08T15:57:30Z

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

editorialbot · 2024-03-08T16:04:36Z

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: Vergauwen
  given-names: Thomas
  orcid: "https://orcid.org/0000-0003-2899-9218"
- family-names: Vieijra
  given-names: Michiel
  orcid: "https://orcid.org/0000-0003-0817-2846"
- family-names: Covaci
  given-names: Andrei
  orcid: "https://orcid.org/0000-0001-5147-2460"
- family-names: Jacobs
  given-names: Amber
  orcid: "https://orcid.org/0000-0002-4628-3988"
- family-names: Top
  given-names: Sara
  orcid: "https://orcid.org/0000-0003-1281-790X"
- family-names: Dewettinck
  given-names: Wout
  orcid: "https://orcid.org/0000-0002-0728-5331"
- family-names: Vandelanotte
  given-names: Kobe
  orcid: "https://orcid.org/0009-0001-1252-7315"
- family-names: Hellebosch
  given-names: Ian
  orcid: "https://orcid.org/0000-0003-0150-529X"
- family-names: Caluwaerts
  given-names: Steven
  orcid: "https://orcid.org/0000-0001-7456-3891"
doi: 10.5281/zenodo.10794417
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Vergauwen
    given-names: Thomas
    orcid: "https://orcid.org/0000-0003-2899-9218"
  - family-names: Vieijra
    given-names: Michiel
    orcid: "https://orcid.org/0000-0003-0817-2846"
  - family-names: Covaci
    given-names: Andrei
    orcid: "https://orcid.org/0000-0001-5147-2460"
  - family-names: Jacobs
    given-names: Amber
    orcid: "https://orcid.org/0000-0002-4628-3988"
  - family-names: Top
    given-names: Sara
    orcid: "https://orcid.org/0000-0003-1281-790X"
  - family-names: Dewettinck
    given-names: Wout
    orcid: "https://orcid.org/0000-0002-0728-5331"
  - family-names: Vandelanotte
    given-names: Kobe
    orcid: "https://orcid.org/0009-0001-1252-7315"
  - family-names: Hellebosch
    given-names: Ian
    orcid: "https://orcid.org/0000-0003-0150-529X"
  - family-names: Caluwaerts
    given-names: Steven
    orcid: "https://orcid.org/0000-0001-7456-3891"
  date-published: 2024-03-08
  doi: 10.21105/joss.05916
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5916
  title: MetObs - a Python toolkit for using non-traditional
    meteorological observations
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05916"
  volume: 9
title: MetObs - a Python toolkit for using non-traditional
  meteorological observations

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 · 2024-03-08T16:04:40Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-08T16:04:41Z

🚨🚨🚨 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.05916 joss-papers#5106
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05916
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-03-08T16:56:06Z

Congrats on your new publication @vergauwenthomas! Many thanks to editor @hugoledoux and reviewers @ashwinvis and @Zeitsperre for your hard work, time, and expertise!!

editorialbot · 2024-03-08T16:56:08Z

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

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editorialbot added Python review Shell Track: 6 (ESE) Earth Sciences and Ecology labels Oct 2, 2023

editorialbot assigned hugoledoux Oct 2, 2023

editorialbot mentioned this issue Oct 2, 2023

[PRE REVIEW]: MetObs - a Python toolkit for using non-traditional meteorological observations #5783

Closed

ashwinvis mentioned this issue Oct 7, 2023

Copyright holder possibly incorrect vergauwenthomas/MetObs_toolkit#382

Closed

This was referenced Oct 28, 2023

Unclear instructions in Examples page in the documentation vergauwenthomas/MetObs_toolkit#384

Closed

Elaborate contributing guidelines vergauwenthomas/MetObs_toolkit#385

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 8, 2024

editorialbot added accepted published Papers published in JOSS labels Mar 8, 2024

kthyng closed this as completed Mar 8, 2024

This was referenced Jul 27, 2024

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Closed

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[REVIEW]: MetObs - a Python toolkit for using non-traditional meteorological observations #5916

[REVIEW]: MetObs - a Python toolkit for using non-traditional meteorological observations #5916

Comments

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Zeitsperre commented Oct 2, 2023 • edited Loading

Review checklist for @Zeitsperre

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Zeitsperre commented Oct 2, 2023

ashwinvis commented Oct 2, 2023

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Review checklist for @ashwinvis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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