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[REVIEW]: lidarSuit: A python package for retrieving wind profiles from Doppler lidar observations
Submitting author: @jdiasn (Dias Neto, José ) Repository: https://github.com/jdiasn/lidarSuit Branch with paper.md (empty if default branch): Version: v0.1.1 Editor: @elbeejay Reviewers: @tgoelles, @acocac, @bgailleton Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/28430a0c6a79e6d1ff33579ff13458f7"><img src="https://joss.theoj.org/papers/28430a0c6a79e6d1ff33579ff13458f7/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/28430a0c6a79e6d1ff33579ff13458f7)
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
@tgoelles & @acocac & @bgailleton, 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
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:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.06 s (731.8 files/s, 81453.6 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
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Python 17 917 938 1497
reStructuredText 12 130 81 166
Jupyter Notebook 4 0 794 101
make 2 25 6 79
Markdown 2 23 0 76
YAML 5 11 2 75
TeX 1 7 0 67
TOML 1 6 0 57
DOS Batch 1 8 1 27
INI 1 4 3 19
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SUM: 46 1131 1825 2164
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gitinspector failed to run statistical information for the repository
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1175/1520-0469(1962)019<0343:NOWVWD>2.0.CO;2 is OK
- 10.1175/1520-0426(1989)006<0809:DLMOPO>2.0.CO;2 is OK
- 10.5194/amt-8-729-2015 is OK
- 10.5281/zenodo.6926483 is OK
- 10.1007/s00585-000-0740-4 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @tgoelles, @acocac, @bgailleton thank you all again for agreeing to review this submission. I believe most of the instructions on how to conduct a JOSS review are included in the comment at the top of this issue. The gist of the process is the following:
- Comment in this issue to tell the @editorialbot to make your checklist
- Review the software and associated paper (this includes installing, running, trying examples), and mark items off on your reviewer checklist. If anything does not work, or if items mentioned in the checklist are not complete, please open an issue in the lidarSuit repository itself, and describe the situation, when doing that, please include a link to this review issue so that we keep things connected
- Once you have completed your initial review of the submission, please comment here with your overall impression so that both @jdiasn and myself know what the next steps need to be
We are currently giving our reviewers 6 weeks to complete their reviews. To help ensure this review doesn't slip off of anyone's to-do list, I am going to ask the bot to send out reminders in this issue in 3 weeks time, and I will follow up at that point as well. If you need an extension or if something comes up that prevents you from doing this review please let me know. We try to maintain a transparent review process here at JOSS, and open communication certainly helps with that.
Thanks again all for being part of this process. JOSS relies on everyone's efforts to improve and publish scientific software. Please do not hesitate to reach out to me with any questions.
Review checklist for @tgoelles
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the https://github.com/jdiasn/lidarSuit?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@jdiasn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- [x] 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.
- [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- [x] 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
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] 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?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] 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?
Review checklist for @acocac
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the https://github.com/jdiasn/lidarSuit?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@jdiasn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- [x] 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.
- [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- [x] 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
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] 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?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] 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?
Review checklist for @bgailleton
Conflict of interest
- [x] 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
- [x] I confirm that I read and will adhere to the JOSS code of conduct.
General checks
- [x] Repository: Is the source code for this software available at the https://github.com/jdiasn/lidarSuit?
- [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- [x] Contribution and authorship: Has the submitting author (@jdiasn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
- [x] 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.
- [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- [x] 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
- [x] Installation: Does installation proceed as outlined in the documentation?
- [x] Functionality: Have the functional claims of the software been confirmed?
- [x] 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
- [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
- [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- [x] 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
- [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
- [x] 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?
- [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- [x] 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?
In this paper authors present a new Python package, lidarSuit, whose main goal is to retrieve wind profiles from Doppler lidar systems. The paper is well-written with a good introduction and a clear statement of need. Authors claim the key difference to other commonly-used software is the support of 6-beam observations using the Fast Fourier Wind Vector Algorithm plus other functionalities i.e. computing the Reynold stress tensor. While the source code contains some useful notebooks examples, the documentation needs to be improved. In addition, I miss further details of other software (names at least) and their corresponding citations.
I strongly believe that lidarSuit has a great potential and could become a very useful Python package once the authors better describe the package and how to use it, both in the repository and in the paper. I have opened an issue in the source repository with some general and minor comments. Feel free to decide how to proceed.
Thanks @tgoelles, @bgailleton, and @acocac for taking the time to review this submission and open up relevant review issues in the lidarSuit repository. From what I can tell, it does not appear that any of the review comments are going to be barriers to future publication; most appear to be related to improving the clarity of the code and documentation. @jdiasn, it appears that you have seen some of these comments and have provided responses and are actively working on making changes so that is great. Please let us know once you believe the revisions you've made satisfy the comments, and be sure to tag the reviewers and myself.
Thanks all!
Thank you, @elbeejay, @acocac, @tgoelles and @bgailleton, for taking the time to review my submission. I will be working to address all comments as soon as possible. I think it will take some time for me to go over all suggestions, but I will do it.
@elbeejay I confirm that from my side, I consider my issue pretty minor and I recommend publication as soon as the documentation and examples improve. The contribution presents a python package gathering and combining multiple methods to retrieve wind profiles from LiDAR datasets. It brings to the community methods that were not as easily accessible before and is susceptible to improve scientific research in the field. I cannot really judge the academic value as this is a bit out of my field of expertise, but the code is well packaged, thoroughly commented, easy to install and delivers what the manuscript promise.
:wave: @tgoelles, please update us on how your review is going (this is an automated reminder).
:wave: @acocac, please update us on how your review is going (this is an automated reminder).
:wave: @bgailleton, please update us on how your review is going (this is an automated reminder).
Please disregard the bot reminders, @jdiasn is working to revise the software in response to all of your constructive comments.
Hi @kthyng, Thank you for asking! I am currently working to address the issues listed by the reviewers. I needed to slow down a bit to be able to work at other activities that I have to be involved at the university and also work at another paper review. I will come back to you to give a time estimation.
@jdiasn checking in here to follow-up and ask if you have an estimate as to when you'll be able to complete your revisions.
Thanks!
@elbeejay Thank you for asking! I want to complete the revision as soon as possible. I wish to suggest until the end of the current month. Sorry for taking this long to complete the revision. A few days before receiving the review feedback from the JOSS paper, I received comments from another paper. Then, I found myself trying to work on both revisions at the same time and getting more work at the university. Please let me know if the end of December is suitable.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left: