[REVIEW]: Qlunc: Quantification of lidar uncertainty

whedon commented 3 years ago

Submitting author: @PacoCosta (F. Costa García) Repository: https://github.com/SWE-UniStuttgart/Qlunc Version: v0.92 Editor: @danielskatz Reviewers: @adi3, @antviro Archive: 10.5281/zenodo.5592248

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✨ 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 ✨

Review checklist for @adi3

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 repository url?
[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 (@PacoCosta) 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

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 and who the target audience is?
[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 @PierreGuilbertF

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 repository url?
[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 (@PacoCosta) 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

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

[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).
[ ] 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 and who the target audience is?
[ ] 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?

Review checklist for @antviro

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 repository url?
[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 (@PacoCosta) 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

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 and who the target audience is?
[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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @adi3, @PierreGuilbertF it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.36 s (97.7 files/s, 19675.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            359            631            944
YAML                            10            204            218            676
Jupyter Notebook                 4              0           2933            582
Markdown                         5             81              0            275
TeX                              1             15              0            133
-------------------------------------------------------------------------------
SUM:                            35            659           3782           2610
-------------------------------------------------------------------------------

Statistical information for the repository 'f337ee7233c8f9bc2ed041b8' was
gathered on 2021/04/22.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Costa                           62          4017           4223           33.60
Francisco Costa                137          3717           4628           34.03
PacoCosta                       67          5033           2903           32.36

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Costa                       333            8.3          5.9                9.61
Francisco Costa            1622           43.6          1.5               14.80

whedon commented 3 years ago

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

whedon commented 3 years ago

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

OK DOIs

- 10.5281/zenodo.3414197 is OK
- 10.5281/zenodo.4432136 is OK
- 10.5281/zenodo.3580749 is OK
- 10.5281/zenodo.3823878 is OK
- 10.5281/zenodo.1212538 is OK
- 10.1175/1520-0450(1968)007<0105:TDOKPO>2.0.CO;2 is OK
- 10.3390/rs10030406 is OK
- 10.13140/RG.2.1.1658.2005 is OK
- 10.3390/rs9060561 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 3 years ago

👋 @adi3 and @PierreGuilbertF - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

Please read the first couple of comments in this issue carefully, so that you can accept the invitation from JOSS and be able to check items, and so that you don't get overwhelmed with notifications from other activities in JOSS.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3211 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

PacoCosta commented 3 years ago

Fixing Figure1. Qlunc basic structure. Power module components were wrong. No issue regarding this.

PacoCosta commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

whedon commented 3 years ago

:wave: @adi3, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

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

danielskatz commented 3 years ago

👋 @adi3 & @PierreGuilbertF - how are your reviews going?

adi3 commented 3 years ago

@danielskatz I'm juggling with a few things right now so I'll move forward with my review in a couple of weeks. Sorry for the delay!

danielskatz commented 3 years ago

👋 @adi3 & @PierreGuilbertF - Just checking again: how are your reviews going?

danielskatz commented 3 years ago

👋 @adi3 & @PierreGuilbertF - Just checking again: how are your reviews going?

adi3 commented 3 years ago

@PacoCosta Can you please edit your paper to write Qlunc in regular font instead of as a code block? In addition, can this be installed via pip or conda? I don't see it mentioned in the installation instructions.

adi3 commented 3 years ago

@PacoCosta A few more points.

Please remove the Usage and Tutorials section from your paper. These do not go in a JOSS paper.
Please combine the Summary and Qlun's capabilities section. As it is, the Summary section a is bit too verbose right now and I would recommend you in condensing it. Thereafter, add the content from Qlun's capabilities under Summary and ensure there is no repetition.
The last line of your current Summary section is not needed. Please remove it. The JOSS paper will have a link to your repository anyway.

PacoCosta commented 3 years ago

@adi3, Thanks for your comments. In response to them:

No, it can't be installed via pip nor conda. All along with the paper, neither conda nor pip is named as installers.

A few more points.

[x] 1. Please remove the Usage and Tutorials section from your paper. These do not go in a JOSS paper
[x] 2. Please combine the Summary and Qlun's capabilities section. As it is, the Summary section a is bit too verbose right now and I would recommend you in condensing it. Thereafter, add the content from Qlun's capabilities under Summary and ensure there is no repetition.
[x] 3. The last line of your current Summary section is not needed. Please remove it. The JOSS paper will have a link to your repository anyway.

@whedon generate pdf

PacoCosta commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

danielskatz commented 3 years ago

👋 @adi3 - Can you let us know where this in your opinion? What is blocking you from moving forward?

danielskatz commented 3 years ago

👋 @PierreGuilbertF - It doesn't seem like you've started your review - can you let us know when you will?

danielskatz commented 3 years ago

👋 @PacoCosta - Can you let us know where this in your opinion?

PacoCosta commented 3 years ago

@danielskatz - Following @adi3 suggestions, the points are updated. I am waiting for reviewers' new suggestions or comments

danielskatz commented 3 years ago

👋 @PierreGuilbertF - It doesn't seem like you've started your review - can you let us know when you will?

danielskatz commented 3 years ago

👋 @adi3 - Can you let us know where this in your opinion? What is blocking you from moving forward?

danielskatz commented 3 years ago

👋 @adi3 & @PierreGuilbertF - this review is dragging a bit. Can you update us on your status?

danielskatz commented 3 years ago

@whedon re-invite @PierreGuilbertF as reviewer

whedon commented 3 years ago

@pierreguilbertf already has access.

adi3 commented 3 years ago

@danielskatz I've been making progress through my list. Haven't had the opportunity to finish with the Documentation review. Will attempt to finish this week.

adi3 commented 3 years ago

@PacoCosta I'm almost finished with my review. I see only one item still outstanding. Could you please community guidelines for third parties wishing to

Contribute to the software
Report issues or problems with the software
Seek support

This can either be done by adding a CONTRIBUTING.md file and linking it in the README, or adding the content directly in the main repo README. Thanks!

danielskatz commented 3 years ago

👋 @PierreGuilbertF - Can you provide an update on when you will be able to get started? (or if you have started, when you will start checking off items in the review)

PacoCosta commented 3 years ago

https://github.com/openjournals/joss-reviews/issues/3211#issuecomment-869146287: Done. I added a section (Contributions) in the README in the repository. Thanks.

adi3 commented 3 years ago

Thank you @PacoCosta.

@danielskatz I have finished my review and I happily recommend this paper for publication. Thanks for your patience!

PierreGuilbertF commented 3 years ago

@danielskatz I started the review a week ago. I should be done by the end of the week.

danielskatz commented 3 years ago

👋 @PierreGuilbertF - Do you have any update for us on your review?

danielskatz commented 2 years ago

👋 @PierreGuilbertF - Do you have any update for us on your review?

danielskatz commented 2 years ago

I've pinged @PierreGuilbertF by email

danielskatz commented 2 years ago

And again - If there's no response in another week (as this is a holiday period for many), I'll start planning other options.

danielskatz commented 2 years ago

Ok, I apologize for the delays, but I'm going to remove @PierreGuilbertF as a reviewer once I can find another. I hope this isn't too much work, since we already have one positive review from @adi3, meaning we've worked through at least some potential issues. If anyone here has any suggestions for another review, please let me know, and I'm also working on this outside of this issue

PacoCosta commented 2 years ago

Ok, thank you very much @danielskatz. I don't have any other suggestions for another reviewer. As far as I know, there is a list of available reviewers. Maybe, if you can send it to me I can suggest a new suitable one.

danielskatz commented 2 years ago

See https://bit.ly/joss-reviewers

danielskatz commented 2 years ago

And if you suggest people, please do it without tagging them (don't use the @ in their usernames)

PacoCosta commented 2 years ago

At a glance, I can see some people with knowledge of lidar and wind energy, which is what the topic is about. Also, python skills. These two seems suitable choices to me :

Scivision (python, lidar, remote sensing, data science)
antviro (python, wind power)

danielskatz commented 2 years ago

👋 @antviro & @Scivision - Would either of you be able to step in and review this submission for JOSS - I hope this isn't too much work, since we already have one positive review from @adi3, meaning we've worked through at least some potential issues. If you cannot review, and have suggestions for colleagues who might be suitable, that would also be great.

antviro commented 2 years ago

Hi @danielskatz, I am at the moment on holidays, and I have a few workdays during august which are quite full of tasks. I could do it during the first week of September, although perhaps it is too late. What do you think?

danielskatz commented 2 years ago

Thanks @antviro - Given the delays up to this point, I'm in favor of a little more delay followed by a good review by a willing person than seeking someone else, I'm going assign you for now, and if someone else appears who can do this more quickly, I'll switch to that person.

I'll go ahead and invite you now, and if you can accept the invitation at https://github.com/openjournals/joss-reviews/invitations soon, it would be great - if not, it will expire and you will be unable to check off items when you are ready to start.

danielskatz commented 2 years ago

@whedon add @antviro as reviewer

whedon commented 2 years ago

OK, @antviro is now a reviewer

danielskatz commented 2 years ago

@whedon remove @PierreGuilbertF as reviewer

whedon commented 2 years ago

OK, @PierreGuilbertF is no longer a reviewer

openjournals / joss-reviews