[REVIEW]: CRNPy: An Open-Source Python Library for Cosmic Ray Neutron Probe Data Processing

[editorialbot]

Submitting author: @joaquinperaza (Joaquin Peraza Rud)
Repository: https://github.com/soilwater/crnpy
Branch with paper.md (empty if default branch): JOSS
Version: v0.6.1
Editor: @elbeejay
Reviewers: @jlarsen-usgs, @danpower101
Archive: 10.5281/zenodo.11090077

Status

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Markdown: [![status](https://joss.theoj.org/papers/e65c1bb5fee58c39289efc4547d1fd10/status.svg)](https://joss.theoj.org/papers/e65c1bb5fee58c39289efc4547d1fd10)

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

@jlarsen-usgs & @danpower101, 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 @elbeejay 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 @danpower101

📝 Checklist for @jlarsen-usgs

[editorialbot]

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

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[editorialbot]

Software report:

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JavaScript                      33           1013           1272           4924
SVG                              2             76              2           2203
Python                           6            383            570            629
Jupyter Notebook                 6              0           3365            378
Markdown                         6            118              0            202
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YAML                             2             11              6             58
XML                              1              0              0             38
CSS                              1              6              6             24
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-------------------------------------------------------------------------------
SUM:                            67           5533           5227          21751
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1064

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.2136/vzj2017.04.0086 may be a valid DOI for title: Status and perspectives on the cosmic-ray neutron method for soil moisture estimation and other environmental science applications
- 10.1029/2009wr008726 may be a valid DOI for title: Nature’s neutron probe: Land surface hydrology at an elusive scale with cosmic rays
- 10.1002/2014wr016443 may be a valid DOI for title: An empirical vegetation correction for soil water content quantification using cosmic ray probes
- 10.1007/978-3-319-69539-6_2 may be a valid DOI for title: In Situ Destructive Sampling
- 10.22323/1.358.1149 may be a valid DOI for title: Re-examination of the First Five Ground-Level Events
- 10.1029/2008gl035655 may be a valid DOI for title: Measuring soil moisture content non-invasively at intermediate spatial scale using cosmic-ray neutrons
- 10.1029/2012wr011871 may be a valid DOI for title: Measurement depth of the cosmic ray soil moisture probe affected by hydrogen from various sources
- 10.3389/frwa.2020.00009 may be a valid DOI for title: Practical data products from cosmic-ray neutron sensing for hydrological applications
- 10.5194/hess-12-1323-2008 may be a valid DOI for title: From near-surface to root-zone soil moisture using an exponential filter: an assessment of the method based on in-situ observations and model simulations
- 10.1002/saj2.20319 may be a valid DOI for title: Predicting rootzone soil moisture from surface observations in cropland using an exponential filter
- 10.5194/egusphere-egu2020-8488 may be a valid DOI for title: Error estimation for soil moisture measurements with cosmic ray neutron sensing and implications for rover surveys

INVALID DOIs

- https://doi.org/10.1175/JHM-D-12-0120.1 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[elbeejay]

Thanks @jlarsen-usgs and @danpower101 for agreeing to review this submission to JOSS.

This is the official "review" issue, please let me know if you have any questions about the process, I believe instructions are auto-generated by the bot in the first comment including the comment you need to make to generate your reviewer checklist. It'd be great if you could complete your first passes of the software in 6 weeks, I will have the bot send us reminders in 3 weeks time.

[elbeejay]

@editorialbot remind @jlarsen-usgs in three weeks

[editorialbot]

Reminder set for @jlarsen-usgs in three weeks

[elbeejay]

@editorialbot remind @danpower101 in three weeks

[editorialbot]

Reminder set for @danpower101 in three weeks

[editorialbot]

👋 @jlarsen-usgs, please update us on how your review is going (this is an automated reminder).

[editorialbot]

👋 @danpower101, please update us on how your review is going (this is an automated reminder).

[jlarsen-usgs]

First day back from vacation (was gone most of November). I've read through the article and have time blocked out this week to begin my review.

[elbeejay]

Sounds good, thanks for the update @jlarsen-usgs.

@danpower101 if you don't mind letting us know of any plans or timeline you have for getting around to this review that'd be great, thanks

[danpower101]

@elbeejay apologies for the delay, I've been transitioning into a new job/city this past month. I'm aiming to finish the review by the end of this week.

[danpower101]

Review checklist for @danpower101

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/soilwater/crnpy?
• 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 (@joaquinperaza) 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?

[elbeejay]

@elbeejay apologies for the delay, I've been transitioning into a new job/city this past month. I'm aiming to finish the review by the end of this week.

Fantastic, thank you for the update @danpower101

[jlarsen-usgs]

Review checklist for @jlarsen-usgs

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/soilwater/crnpy?
• 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 (@joaquinperaza) 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?

[editorialbot]

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

OK DOIs

- 10.5194/hess-16-4079-2012 is OK
- 10.1175/JHM-D-12-0120.1 is OK
- 10.2136/vzj2017.04.0086 is OK
- 10.1029/2009WR008726 is OK
- 10.1002/2014WR016443 is OK
- 10.1007/978-3-319-69539-6_2 is OK
- 10.1029/2017WR021719 is OK
- 10.22323/1.358.1149 is OK
- 10.1002/2017WR021692 is OK
- 10.1029/2008GL035655 is OK
- 10.1029/2012WR011871 is OK
- 10.1002/2015WR017169 is OK
- 10.3389/frwa.2020.00009 is OK
- 10.5194/hess-12-1323-2008 is OK
- 10.1002/saj2.20319 is OK
- 10.3389/frwa.2020.00010 is OK
- 10.5194/hess-21-5009-2017 is OK
- 10.1002/2013WR015138 is OK
- 10.1029/2022WR033889 is OK
- 10.5194/gmd-14-7287-2021 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.25080/Majora-92bf1922-00a 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: WWW.NMDB.EU: The real-time Neutron Monitor databas...
- No DOI given, and none found for title: Volume 16: how to detect and handle outliers
- No DOI given, and none found for title: Geomagnetic cutoff rigidity computer program: Theo...
- No DOI given, and none found for title: CORNish PASDy - COsmic-Ray Neutron flavored PASDy

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#5332, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[andres-patrignani]

@elbeejay I checked the final proof and everything looks good. We want to also thank you and the two reviewers (@jlarsen-usgs and @danpower101) for the constructive feedback and guidance, which greatly enhanced the quality of the library and the associated manuscript. The review process on Github was very dynamic, providing an excellent and refreshing reviewing experience.

[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]

@joaquinperaza I see your name isn't quite the same between the JOSS paper and the Zenodo archive — is there a reason for that?

Also, please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example, "australia" and "python".

[andres-patrignani]

@editorialbot generate pdf

[editorialbot]

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

[joaquinperaza]

@kthyng I have address the issue with my name in the Zenodo archive and @andres-patrignani has solved the issues in the JOSS paper.

[kthyng]

Great, looks good!

[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: Peraza Rud
  given-names: Joaquin A.
  orcid: "https://orcid.org/0009-0007-9337-830X"
- family-names: Ochsner
  given-names: Tyson E.
  orcid: "https://orcid.org/0000-0003-0875-4491"
- family-names: Patrignani
  given-names: Andres
  orcid: "https://orcid.org/0000-0001-5955-5877"
doi: 10.5281/zenodo.11090077
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Peraza Rud
    given-names: Joaquin A.
    orcid: "https://orcid.org/0009-0007-9337-830X"
  - family-names: Ochsner
    given-names: Tyson E.
    orcid: "https://orcid.org/0000-0003-0875-4491"
  - family-names: Patrignani
    given-names: Andres
    orcid: "https://orcid.org/0000-0001-5955-5877"
  date-published: 2024-05-24
  doi: 10.21105/joss.06025
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6025
  title: "CRNPy: An Open-Source Python Library for Cosmic-Ray Neutron
    Probe Data Processing"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06025"
  volume: 9
title: "CRNPy: An Open-Source Python Library for Cosmic-Ray Neutron
  Probe Data Processing"

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.06025 joss-papers#5380
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06025
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...

[andres-patrignani]

@kthyng I noticed that the citation in JOSS shows as "A. et al., (2024)", but it should be "Peraza Rud et al., (2024)". If we fix/upload the .cff file, will this change? Any suggestions on how to get the citation correct would be greatly appreciated.

[kthyng]

@openjournals/dev Could you help with this ⬆️ ?

[kthyng]

In the meantime...

Congratulations on your new publication @joaquinperaza! Many thanks to @elbeejay and to reviewers @jlarsen-usgs and @danpower101 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

[xuanxu]

Citation string fixed!

[kthyng]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5406

[kthyng]

@andres-patrignani Please take a look to make sure everything is in order.

@xuanxu Thank you!

[andres-patrignani]

@kthyng everything looks good. Thanks @xuanxu for fixing the issue with the citation. Thanks everyone for the refreshing peer-review process! The active community of editors and reviewers made it a great experience. Keep up the awesome work!

[editorialbot]

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06025/status.svg)](https://doi.org/10.21105/joss.06025)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06025">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06025/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06025/status.svg
   :target: https://doi.org/10.21105/joss.06025

This is how it will look in your documentation:

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