[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

: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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3dbe42d79250bf65dacc36d01bb0a3dd"><img src="https://joss.theoj.org/papers/3dbe42d79250bf65dacc36d01bb0a3dd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3dbe42d79250bf65dacc36d01bb0a3dd/status.svg)](https://joss.theoj.org/papers/3dbe42d79250bf65dacc36d01bb0a3dd)

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

@adi3 & @PierreGuilbertF, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz 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 ✨

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?

danielskatz commented 3 years ago

@whedon remind @danielskatz and @antviro in 16 days

Just to see how things are going at that point after @antviro has had a chance to work on their review

whedon commented 3 years ago

Reminder set for @danielskatz and @antviro in 16 days

danielskatz commented 3 years ago

👋 @antviro - Do you think you will be able get started soon?

antviro commented 3 years ago

Hi @danielskatz,

Up to now, I have reviewed paper and the descriptions in the repository. They seem clear and quite interesting, I think they are ready to be published. Perhaps I miss some written documentation of the functions (besides the figure). Is there any? Despite there are two Jupyter notebooks describing its uses, It could be interesting.

Before finishing, I want to check functionality. I plan to do it within this week. I have no anaconda installation (I usually use pip instead, but perhaps I will install on other computer to check "official installation"). @PacoCosta: Are there instructions to use it without any package provider (besides installing the prerequisites)?

Best regards, Antonio

PacoCosta commented 3 years ago

Hi @antviro, There aren't such instructions. If you have already installed python3.7 on your computer you can use pip to install the requirements, as you said. The good thing about using Anaconda is that you have a version of JupyterLab/Jupyter Notebook available there. Otherwise, if you want to go through the Tutorials, you have to install Jupyter separately. You don't need to install anything else, but the requirements and Jupyter to run the code. Please remember to download the first release of the code, as stated in the readme file on the repository. Thanks for your time and effort.

danielskatz commented 3 years ago

@antviro - I hope you saw the response from @PacoCosta above, and are able to proceed - let us know if not.

antviro commented 3 years ago

@PacoCosta You mean the last release, don't you? (0.91 in https://github.com/SWE-UniStuttgart/Qlunc/releases). Finally I installed anaconda so that I test it exactly as described. I am having issues following the instructions with the requeriments, particularly NETCDF fails to get installed. I reproduce it:

(base) XXX@XXX:~/anaconda3/2021_QLunc/Qlunc_last$ conda env create -f environment.yml 
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - netcdf

I have no experience using Anaconda, so I apologize if I committed some error in the procedure... If not, I guess it may be either some repository which is not currently available (I will try again later just in case) or the name of netcdf should be replaced perhaps with netcdf4 or something similar (in this case you should update readme or the environment.yml file).

PacoCosta commented 3 years ago

Hi @antviro, Yes, the problem is that new features have been added since the first release, where netcdf data conversion process was not needed at that point. When you download the first release "Qlunc-0.91" (and only this version), the code doesn't install this package since it is not in the requirements (environment.yml file in the repository), and the code doesn't need it at all. I've just downloaded the first release and the installation process properly worked out for me following the instructions. If you use this version, you don't need to install netcdf. Anyway, I updated, as you suggested, the environment.yml file in the latest code version with the netcdf version that the code installs. Please, let me know if, by downloading the first release "Qlunc-0.91", and following instructions you have problems again; perhaps we can arrange a short meeting to go through the process together.

danielskatz commented 3 years ago

👋 @antviro - any update on your side to the response from the author ☝️ ?

antviro commented 3 years ago

Yes, sorry for the delay and thank you for the guidance I thought I was sure that I downloaded 0.91, but I was wrong. After downloading such version I could go on and check tutorials. Everything seems to work properly. I only lack some more documentation on the functions, it would be nice to extend its use and allow others to contribute. Despite that, I suggest it to be published on its current state.

danielskatz commented 3 years ago

@antviro - we can't publish until your checklist is complete - so how should we handle the item

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

Can you state what specifically you think is needed so that the authors can work on it?

danielskatz commented 3 years ago

👋 @antviro - another ping on this - we're almost ready to complete this review...

antviro commented 2 years ago

wave @antviro - another ping on this - we're almost ready to complete this review...

Done, sorry for the delay! I have fulfil the last item in the checklist, so I guess review is now completed.

danielskatz commented 2 years ago

@PacoCosta - sorry for my missing the above comment. It looks like we are now mostly done. I'll proofread the paper now, then ask you to do some final steps.

danielskatz commented 2 years ago

@whedon check references

whedon commented 2 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 2 years ago

@whedon generate pdf

whedon commented 2 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 2 years ago

I'm suggesting some changes in https://github.com/SWE-UniStuttgart/Qlunc/pull/137.

Also, where you say "through a website", it would be good to say what that website is.

danielskatz commented 2 years ago

Once you've made these changes, could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

PacoCosta commented 2 years ago

I'm suggesting some changes in SWE-UniStuttgart/Qlunc#137.

Also, where you say "through a website", it would be good to say what that website is.

Still under development, not yet publicly available

PacoCosta commented 2 years ago

Tag of the reviewed version: v0.92
DOI: 10.5281/zenodo.5592248

danielskatz commented 2 years ago

@whedon set v0.92 as version

whedon commented 2 years ago

OK. v0.92 is the version.

danielskatz commented 2 years ago

@whedon set 10.5281/zenodo.5592248 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5592248 is the archive.

danielskatz commented 2 years ago

@whedon recommend accept

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

danielskatz commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 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

whedon commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2703

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2703, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 2 years ago

👋 @PacoCosta - Can you change the title and authors in the zenodo archive to match the paper?

archive:

paper:

PacoCosta commented 2 years ago

@danielskatz - I can't remove "SWE-UniStuttgart" since is the institution supporting the project. So, what do suggest instead?

danielskatz commented 2 years ago

When you say "I can't remove 'SWE-UniStuttgart'", I'm unsure what you mean by can't - Zenodo should allow you to change the title metadata to whatever you want.

And this is the software equivalent of the paper title so I don't see any reason you shouldn't make this the same as the paper title - this is the standard practice for JOSS papers and software archives.

PacoCosta commented 2 years ago

@danielskatz - Changes done successfully

[x] Title
[x] Authors

danielskatz commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 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

whedon commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2717

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2717, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2718
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03211
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @PacoCosta (F. Costa García) and co-authors!!

And thanks to @adi3 and @antviro for reviewing - we couldn't do this without you!

whedon commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.03211/status.svg)](https://doi.org/10.21105/joss.03211)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03211">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03211/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03211/status.svg
   :target: https://doi.org/10.21105/joss.03211

This is how it will look in your documentation:

We need your help!

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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

PacoCosta commented 2 years ago

Many thanks to all of you who have helped me in this process. @danielskatz, @antviro and @adi3. Congrats also to you!

PacoCosta commented 2 years ago

@danielskatz , One of the authors noticed that one of the references has a small mistake and we would like to fix it. Is it possible at this stage to change it? In this reference Vasiljevic, N., & Clifton, A. (2021). OntoStack. http://data.windenergy.dtu.dk/ontologies/ view/en/ the sole author is Vasiljevic, N. We need to remove Clifton, A.

danielskatz commented 2 years ago

Yes, please change the reference and then ping @arfon who can republish it.

PacoCosta commented 2 years ago

Hi @arfon, I changed the paper.bib at the repository to fix a small mistake in the following reference: Vasiljevic, N., & Clifton, A. (2021). OntoStack. http://data.windenergy.dtu.dk/ontologies/view/en/

Would you please republish the paper with the correct reference? Do I need to do something else?

openjournals / joss-reviews