[REVIEW]: MWRpy: A Python package for processing microwave radiometer data

[editorialbot]

Submitting author: @tobiasmarke (Tobias Marke)
Repository: https://github.com/actris-cloudnet/mwrpy
Branch with paper.md (empty if default branch): paper
Version: v1.0.0
Editor: @mengqi-z
Reviewers: @Subho07, @kvenkman
Archive: 10.5281/zenodo.11614185

Status

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Markdown: [![status](https://joss.theoj.org/papers/5fab8b696409397b3627aaf61da9406d/status.svg)](https://joss.theoj.org/papers/5fab8b696409397b3627aaf61da9406d)

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

@Subho07 & @kvenkman, 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 @mengqi-z 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 @kvenkman

📝 Checklist for @Subho07

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.5281/zenodo.7973552 is OK
- 10.1175/BAMS-88-6-883 is OK
- 10.1175/BAMS-D-23-0064.1 is OK
- 10.21105/joss.02123 is OK
- 10.23919/URSIRSB.2004.7909438 is OK
- 10.1007/s42865-021-00033-w is OK
- 10.1109/TGRS.2006.888434 is OK
- 10.1029/2002RS002634 is OK
- 10.5194/amt-5-1121-2012 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (823.2 files/s, 141212.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          31            854            566           6645
YAML                             9            159            174            351
Markdown                         4            108              0            261
reStructuredText                 5             73             70            106
TeX                              1              8              0            103
TOML                             1             10              0             55
DOS Batch                        1              8              1             26
make                             1              4              7              9
HTML                             2              0              0              5
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            56           1224            818           7564
-------------------------------------------------------------------------------

Commit count by author:

   126	Simo Tukiainen
    70	tobiasmarke
    31	Tuomas Siipola

[editorialbot]

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

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 951

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[mengqi-z]

👋 @tobiasmarke, @Subho07, and @kvenkman, Welcome to the review thread for the paper. All communication regarding this submission will take place here.

Please start by reading the "Reviewer instructions & questions" in the first comment above.

Reviewers, please create your checklists outlining JOSS requirements. As you assess the submission, mark any items you believe have been satisfied. Additionally, refer to the JOSS reviewer guidelines linked at the top of this thread.

Our aim is to collaborate with authors to help them meet our criteria. Reviewers are encouraged to submit issues and pull requests directly on the software repository. When doing so, please tag #6733 in the issue to create a link to this thread, enabling easy tracking. Please feel free to post comments, questions, and suggestions as they arise, rather than waiting until the entire package is reviewed.

We target completing reviews within 4-6 weeks, but please initiate your review well in advance. JOSS reviews are iterative, and your early feedback will help us stay on schedule.

[tobiasmarke]

@editorialbot set v0.9.0 as version

[editorialbot]

I'm sorry @tobiasmarke, I'm afraid I can't do that. That's something only editors are allowed to do.

[kvenkman]

Review checklist for @kvenkman

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/actris-cloudnet/mwrpy?
• 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 (@tobiasmarke) 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?

[mengqi-z]

👋 @Subho07 and @kvenkman, Thank you for reviewing this paper. I see @kvenkman has started the review. @Subho07, could you please update me on your review progress?

[Subho07]

Review checklist for @Subho07

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/actris-cloudnet/mwrpy?
• 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 (@tobiasmarke) 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?

[Subho07]

@editorialbot generate pdf

[editorialbot]

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

[Subho07]

@mengqi-z @editorialbot I think a exisitng program is not mentioned, i.e. PyRTlib. This particular module works with radiative transfer functions which may also include the radiometer data. What is the difference between PyRTlib and MWRpy? Can the processes not be solved by PyRTlib? A flow chart may be required in the manuscript to understand the connectivity among the modules used in the software. Can the algorithms be applied for all type of microwave frequencies or any other pre-processing is required for some particular microwave frequencies?
"is able to handle raw data from HATPRO manufactured by Radiometer Physics GmbH ": it sounds like the program is very specific to the product only, but can not be used for other products.
Otherwise the manuscript is well-written and easy to follow. The program also provides nice information on the installation procedure and has a test dataset that can be used to generate the test result for validation.

[mengqi-z]

Thank you, @Subho07!

@tobiasmarke Could you please address @Subho07 's comments above? The paper should also include a section describing how this software compares to others.

[tobiasmarke]

@editorialbot generate pdf

[editorialbot]

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

[tobiasmarke]

@Subho07 thanks for reviewing and your comments.

We are aware of PyRTlib, but it serves a different purpose. As you mentioned, the software is developed to simulate microwave brightness temperatures. On the other hand, MWRpy handles measured data by MWR, applies quality control and creates a common file format. Therefore, there is no overlap between the two software packages.

Another MWR processing software from a different European network (E-PROFILE) is now mentioned in the text. While E-PROFILE is focusing on near-real-time data provision and being hosted by the National Weather Services, ACTRIS is a research infrastructure with different scientific goals. There is an overlap in the data format, but there are for example differences in product generation and some stations might be part of both networks. Therefore the two approaches are needed.

A flowchart was added to the manuscript (and can also be found in the documentation).

Unlike PyRTlib, where a full spectrum can be simulated, MWRpy is restricted to the instrument configuration and supplied frequencies. But in general different frequency combinations are supported. "measured T_B at various frequencies" was added to the manuscript.

Regarding supported instruments: other instrument types can be added in the future, but the focus is on handling data in the ACTRIS network, where currently only one type (RPG HATPRO) exists.

I hope this clarifies your questions/comments.

[kvenkman]

Hi @tobiasmarke, could you clarify where the input MWR data path needs to be specified when running the command line tool mwrpy/cli.py? Could you add this to the documentation page, if it isn't already explicitly mentioned somewhere?

Also, following up on your previous comment, perhaps the paper would benefit from a brief mention of PyRTlib and how it's a simulation tool, compared to the data processing step that MWRpy serves.

The paper and software package look great otherwise 👍

[tobiasmarke]

Hi @kvenkman , thanks for reviewing.

The input data path can be specified in the configuration file mwrpy/site_config/hatpro.yaml. This is mentioned in the README under "Configuration" (including a link to an example file).
In addition, the documentation includes examples on how to run single modules and manually setting the data path (https://actris-cloudnet.github.io/mwrpy/mwrpy_processing.html). The information about the configuration file was added to the command line usage section (currently in the "docs" branch, but will be merged soon).

PyRTlib is now mentioned and referenced as an example for microwave radiative transfer calculations. Those will be needed for the retrieval development in the ACTRIS network.

[kvenkman]

@editorialbot generate pdf

[editorialbot]

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

[Subho07]

@editorialbot generate pdf

[tobiasmarke]

@mengqi-z thanks for the proofread. All suggested changes were incorporated in the manuscript.
The tag of the archived version is v1.0.0 and the DOI is https://zenodo.org/doi/10.5281/zenodo.11614185

[mengqi-z]

@editorialbot set 10.5281/zenodo.11614185 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11614185

[mengqi-z]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[mengqi-z]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.7973552 is OK
- 10.1175/BAMS-88-6-883 is OK
- 10.1175/BAMS-D-23-0064.1 is OK
- 10.21105/joss.02123 is OK
- 10.23919/URSIRSB.2004.7909438 is OK
- 10.1007/s42865-021-00033-w is OK
- 10.1109/TGRS.2006.888434 is OK
- 10.1029/2002RS002634 is OK
- 10.5194/amt-5-1121-2012 is OK
- 10.5194/gmd-17-2053-2024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @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#5497, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[mengqi-z]

@tobiasmarke Thank you for addressing all the comments from the reviewers!

@kvenkman @Subho07 Thank you for your reviews! I hope you enjoyed the process and look forward to working with you on future JOSS reviews.

[kthyng]

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

• Are checklists all checked off?
• Check that version was updated and make sure the version from JOSS matches github and Zenodo.
• Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
• Check paper.

[kthyng]

@tobiasmarke Paper looks good except please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example, "european" is not capitalized, but check for others.

[tobiasmarke]

@editorialbot generate pdf

[editorialbot]

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

[tobiasmarke]

@kthyng thank you for checking. The references are updated now.

[kthyng]

Ok everything is ready to go!

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Marke
  given-names: Tobias
  orcid: "https://orcid.org/0000-0001-7804-9056"
- family-names: Löhnert
  given-names: Ulrich
  orcid: "https://orcid.org/0000-0002-9023-0269"
- family-names: Tukiainen
  given-names: Simo
  orcid: "https://orcid.org/0000-0002-0651-4622"
- family-names: Siipola
  given-names: Tuomas
  orcid: "https://orcid.org/0009-0004-7757-0893"
- family-names: Pospichal
  given-names: Bernhard
  orcid: "https://orcid.org/0000-0001-9517-8300"
contact:
- family-names: Marke
  given-names: Tobias
  orcid: "https://orcid.org/0000-0001-7804-9056"
doi: 10.5281/zenodo.11614185
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Marke
    given-names: Tobias
    orcid: "https://orcid.org/0000-0001-7804-9056"
  - family-names: Löhnert
    given-names: Ulrich
    orcid: "https://orcid.org/0000-0002-9023-0269"
  - family-names: Tukiainen
    given-names: Simo
    orcid: "https://orcid.org/0000-0002-0651-4622"
  - family-names: Siipola
    given-names: Tuomas
    orcid: "https://orcid.org/0009-0004-7757-0893"
  - family-names: Pospichal
    given-names: Bernhard
    orcid: "https://orcid.org/0000-0001-9517-8300"
  date-published: 2024-06-20
  doi: 10.21105/joss.06733
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6733
  title: "MWRpy: A Python package for processing microwave radiometer
    data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06733"
  volume: 9
title: "MWRpy: A Python package for processing microwave radiometer
  data"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06733 joss-papers#5517
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06733
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congratulations on your new publication @tobiasmarke! Many thanks to @mengqi-z and to reviewers @Subho07 and @kvenkman for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

[editorialbot]

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06733/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.06733

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[kthyng]

@tobiasmarke If you're interested in reviewing for JOSS in the future, please register at https://reviewers.joss.theoj.org/.