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[REVIEW]: CRNPy: An Open-Source Python Library for Cosmic Ray Neutron Probe Data Processing #6025

Closed editorialbot closed 5 months ago

editorialbot commented 1 year ago

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

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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 commented 1 year ago

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

For a list of things I can do to help you, just type:

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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 commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (268.1 files/s, 130086.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             8           3905              6          13118
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
TeX                              1             21              0            176
YAML                             2             11              6             58
XML                              1              0              0             38
CSS                              1              6              6             24
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            67           5533           5227          21751
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1064

editorialbot commented 1 year ago 
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 commented 1 year ago

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

elbeejay commented 1 year ago

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 commented 1 year ago

@editorialbot remind @jlarsen-usgs in three weeks

editorialbot commented 1 year ago

Reminder set for @jlarsen-usgs in three weeks

elbeejay commented 1 year ago

@editorialbot remind @danpower101 in three weeks

editorialbot commented 1 year ago

Reminder set for @danpower101 in three weeks

editorialbot commented 11 months ago

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

editorialbot commented 11 months ago

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

jlarsen-usgs commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

@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 commented 11 months ago

Review checklist for @danpower101

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

elbeejay commented 11 months ago

@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 commented 11 months ago

Review checklist for @jlarsen-usgs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

danpower101 commented 11 months ago

@elbeejay I've completed my initial review.

In summary, I think it's a nice well structured set of code that can process Cosmic-Ray Neutron Sensor raw data to soil moisture data. The documentation is clear and I was easily able to run it on my own machine and work through the examples.

I've made some more specific points as separate issues in the repository that I feel should be addressed before acceptance.

If you need clarification on anything just let me know!

jlarsen-usgs commented 11 months ago

@elbeejay

I've finished my review and have linked it from CRNPy to this issue. Overall, the software is well documented and I was able to run the examples.

I've compiled a list of review comments for the author to address. Most of these comments are relatively minor, however I do think that testing could be improved some.

elbeejay commented 11 months ago

Great, thanks @danpower101 and @jlarsen-usgs for taking the time to conduct your reviews, and doubly thanks for linking those review issues to this over-arching issue thread.

@joaquinperaza if you could take a look at the review comments to make an initial assessment and get back to us here with an estimated timeframe for your revisions that'd be great. I took a look and as both reviewers stated above the software is well documented and the examples work, and so most of the comments are fairly minor. The most time-consuming are potentially the code formatting and test suite comments.

Thanks all!

elbeejay commented 10 months ago

@joaquinperaza we are looking for some sort of plan or tentative schedule for making these minor changes. Please let us know here, thanks.

joaquinperaza commented 10 months ago

Thanks for your valuable feedback @danpower101 @jlarsen-usgs, I went over the review and already started working on the suggestions.

I apologize for the delay in my response. I estimate to address them in less than 2 weeks considering the required changes.

I am planning to create a new branch to address all the mentioned issues as a new version, I can reference commits for each of them in the different issues threads, please let me know if you have any preference on this.

elbeejay commented 10 months ago

Thanks for your valuable feedback @danpower101 @jlarsen-usgs, I went over the review and already started working on the suggestions.

I apologize for the delay in my response. I estimate to address them in less than 2 weeks considering the required changes.

I am planning to create a new branch to address all the mentioned issues as a new version, I can reference commits for each of them in the different issues threads, please let me know if you have any preference on this.

That sounds fantastic, thanks for the update @joaquinperaza

elbeejay commented 10 months ago

@joaquinperaza just wanted to check-in on the revisions. I realize we've just had some holidays so maybe it will take a little longer than expected. Just let us all know when you've completed them please.

elbeejay commented 9 months ago

@joaquinperaza - reaching out here to ask if you've got a status update for us

joaquinperaza commented 9 months ago

@elbeejay I apologize for the delay; I already finished implementing the proposed changes into the library and addressed some bugs in my last commits today. Over the next week, I plan to work on the library manuscript to finish the submission.

elbeejay commented 9 months ago

Great, thanks for the update.

joaquinperaza commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

elbeejay commented 9 months ago

@joaquinperaza - I've noticed that you've been making changes and tying your commits to reviewer issues, great! Can you let us know where those stand; are you done revising your manuscript and making changes to the software?

I think it'd be most clear if you replied with a comment in the various issues that are open to state how you've addressed it. This might help our reviewers more easily track whether the change has been made.

Thanks!

joaquinperaza commented 9 months ago

@elbeejay I finished working on the library software; I am still working on the manuscript, and I would like to have a last round of revisions with the coauthors this week. I will update it here once we are done with that part. Thanks for your understanding, and again, thank the reviewers for their feedback on this submission.

joaquinperaza commented 8 months ago

@elbeejay, I just submitted the last revision of the manuscript to https://github.com/soilwater/crnpy/tree/JOSS. Addressing the comments about the text from #8, #10, #11 . The software changes were all implemented in the branch 0.6.0

Please let me know if anything else is needed from our side, and thanks for your support!

elbeejay commented 8 months ago

Great, thanks @joaquinperaza - I'd ask @jlarsen-usgs and @danpower101, if you both could review the changes relevant to your open issues and confirm that your comments have been addressed that would be great. Once the issues are closed (and presumably the branch is merged) we can discuss the next steps @joaquinperaza.

I'll have the bot render the new PDF below for our review.

elbeejay commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

elbeejay commented 8 months ago

@joaquinperaza to make things easier on @jlarsen-usgs and @danpower101 would you mind summarizing your revisions in response to their comments in the appropriate issues? Thanks - and @jlarsen-usgs and @danpower101 when y'all get a chance if you could check and potentially close the issues you'd opened that'd be great

elbeejay commented 7 months ago

@jlarsen-usgs and @danpower101 - could you please let us know when you'll have a chance to take a second look at this submission now that @joaquinperaza has made revisions? Please see your review issues and comment/close those as appropriate.

Thanks!

elbeejay commented 7 months ago

Thanks @danpower101 for your follow-up comments in both https://github.com/soilwater/crnpy/issues/9 and https://github.com/soilwater/crnpy/issues/10. @jlarsen-usgs when you get a chance if you could revisit https://github.com/soilwater/crnpy/issues/11 that'd be much appreciated.

jlarsen-usgs commented 7 months ago

@elbeejay I'll look through the revisions this week and approve or provide follow up comments.

andres-patrignani commented 7 months ago

@elbeejay We made several updates based on the revisions made by @danpower101. We would greatly appreciate if the editor and the reviewers can take another look at the changes.

elbeejay commented 7 months ago

Thanks @andres-patrignani and @joaquinperaza for making revisions.

Checking in here with @danpower101 and @jlarsen-usgs.

@danpower101 it looks like some additional changes have been made in https://github.com/soilwater/crnpy/issues/9

@jlarsen-usgs if you could revisit https://github.com/soilwater/crnpy/issues/11 when you get a chance that'd be great.

Thank you both for reviewing and continuing to engage with the submitting authors throughout this process!

danpower101 commented 6 months ago

@elbeejay I've made some comments on the two issues. Still some minor adjustments needed there.

elbeejay commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

andres-patrignani commented 6 months ago

@elbeejay, @joaquinperaza and I addressed the issue with the weighting function and we updated the Statement of Need to better reflect prior libraries.

jlarsen-usgs commented 6 months ago

@editorialbot commands

editorialbot commented 6 months ago

Hello @jlarsen-usgs, here are the things you can ask me to do:


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jlarsen-usgs commented 6 months ago

@elbeejay all of my issues have been addressed. Consider my review as approved.

elbeejay commented 6 months ago

@editorialbot generate pdf