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[REVIEW]: scikit-eo: A Python package for Remote Sensing Data Analysis #6692

Closed editorialbot closed 2 months ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@ytarazona<!--end-author-handle-- (Yonatan Tarazona Coronel) Repository: https://github.com/yotarazona/scikit-eo Branch with paper.md (empty if default branch): main Version: 0.2.31 Editor: !--editor-->@mikemahoney218<!--end-editor-- Reviewers: @dbuscombe-usgs, @KBodolai Archive: 10.5281/zenodo.12688708

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/46bccc5be81d7ea886e05807cfe6790c"><img src="https://joss.theoj.org/papers/46bccc5be81d7ea886e05807cfe6790c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/46bccc5be81d7ea886e05807cfe6790c/status.svg)](https://joss.theoj.org/papers/46bccc5be81d7ea886e05807cfe6790c)

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

@dbuscombe-usgs & @KBodolai, 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 @mikemahoney218 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 @dbuscombe-usgs

📝 Checklist for @KBodolai

editorialbot commented 5 months 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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 5 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1226.4 files/s, 229444.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18           1089            894           1567
Markdown                        26           1167              0           1393
Jupyter Notebook                16              0           6400            502
YAML                             7             19             16            227
TeX                              1             12              0            164
HTML                             1              2              0              9
CSV                              1              0              0              6
XML                              1              0              0              2
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            72           2289           7310           3871
-------------------------------------------------------------------------------

Commit count by author:

   232  Yonatan Tarazona
     9  Fernando Benitez-Paez
     5  Jakub Nowosad
     5  mfbenitezp
editorialbot commented 5 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/07038992.2021.1941823 is OK
- 10.1016/j.rsase.2020.100337 is OK
- 10.1016/j.ecolind.2018.07.012 is OK
- 10.1016/j.rse.2014.02.015 is OK
- 10.1016/j.isprsjprs.2021.04.015 is OK
- 10.3390/rs12183062 is OK
- 10.1080/10095020.2019.1710438 is OK
- 10.1038/nclimate1908 is OK
- 10.1038/s41559-022-01702-5 is OK
- 10.1016/J.RSE.2021.112577 is OK
- 10.5281/ZENODO.3233986 is OK
- 10.1038/s41558-017-0049-x is OK
- 10.1038/s41586-021-03436-z is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1668

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 5 months ago

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

mikemahoney218 commented 5 months ago

👋🏼 @ytarazona, @dbuscombe-usgs, @KBodolai: this is the review thread for the paper. Just about all of our communications should will happen here from now on. :smile:

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6692 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.

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns.

yotarazona commented 5 months ago

@mikemahoney218 and reviewers, thank you so much for taking your time during this process. We will keep an eye on the thread.

mikemahoney218 commented 4 months ago

Just as a quick note: I'm going to be traveling and generally less available until May 20th. I'll still be checking GitHub and email intermittently (so feel free to reach out with any questions or concerns), but apologies if it takes me a bit longer to respond than usual!

mikemahoney218 commented 4 months ago

Hi @dbuscombe-usgs and @KBodolai ! I wanted to bump this now that we're about a month into the review window, and ask how your reviews were progressing/if you're still expecting to complete your reviews on the original timeline.

Just as a reminder, the first step in the review is to post @editorialbot generate my checklist as the start of a new comment in this thread, which will generate a review checklist for you to use!

dbuscombe-usgs commented 4 months ago

Review checklist for @dbuscombe-usgs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

dbuscombe-usgs commented 4 months ago

Hi @dbuscombe-usgs and @KBodolai ! I wanted to bump this now that we're about a month into the review window, and ask how your reviews were progressing/if you're still expecting to complete your reviews on the original timeline.

Just as a reminder, the first step in the review is to post @editorialbot generate my checklist as the start of a new comment in this thread, which will generate a review checklist for you to use!

Sorry for the delay, and thanks for the reminder. I was able to devote all day to this today, reading and testing everything. This is mostly great and mostly works as described, but I have a few issues I'd like to see tackled, and one requested edit for the paper. I'd be an end-user of this software for sure, and I'm sure it will be valuable for the community. I'll be in touch soon!

mikemahoney218 commented 4 months ago

Thank you so much @dbuscombe-usgs !

mikemahoney218 commented 3 months ago

Hi @KBodolai ! I wanted to reach back out to ask how your review is progressing, and to see if you've got any questions/comments about the process!

Just as a reminder, the first step in the review is to post @editorialbot generate my checklist as the start of a new comment in this thread, which will generate a review checklist for you to use. Thanks!

KBodolai commented 3 months ago

Hi @mikemahoney218 , apologies for the delay, I set aside some time later this week to do it, so hopefully will be done by the end of the week!

mikemahoney218 commented 3 months ago

Fantastic, thank you!

KBodolai commented 3 months ago

Review checklist for @KBodolai

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mikemahoney218 commented 3 months ago

Thank you so much for starting your review @KBodolai ! I wanted to bump this issue to ask how you're progressing with the review, and to ask @yotarazona how they're doing in addressing @dbuscombe-usgs ' comments from their initial review.

yotarazona commented 3 months ago

Hi @mikemahoney218, @dbuscombe-usgs and @KBodolai, thanks a lot for your effort and time spent reviewing this python package. Very grateful for that!. There are only two missing issues regarding the paper that we will finish during the following days. Let us know if any additional issue needs to be addressed.

dbuscombe-usgs commented 3 months ago

I have completed my review of the manuscript and software. Thanks to @yotarazona and team for being responsive. All my previous issues have been satisfactorily resolved (except a minor one involving updating website links). I have completed my checklist above. Details have been added about the deep learning model and links to previous research. Some bugs have been fixed, and clearer instructions are provided for new users. So, I am happy to sign off on my review. I think this will become a valuable contribution to the remote sensing software community for both teaching and research.

yotarazona commented 3 months ago

Thank you very much @dbuscombe-usgs for your time and effort to review the package. I am sure that step by step the python package will be used by the remote sensing community, that is the idea. I am glad to have contributed with this small package (scikit-eo). Thank you so much!.

mikemahoney218 commented 3 months ago

Thank you so much for your review @dbuscombe-usgs !

KBodolai commented 3 months ago

Good morning @mikemahoney218 @yotarazona , apologies for the delay, I was on holiday last week - I'm now going through the review - I expect to finish (now for real!) in the following couple of days.

I think I've gotten through most of it (I'm missing to go through a few more of the examples in detail and review a couple of modules). I've raised some issues above :)

mikemahoney218 commented 3 months ago

Thank you so much, @KBodolai ! Am I right to think that you've finished the initial review, and we're now waiting for @yotarazona 's response?

yotarazona commented 3 months ago

Hi @mikemahoney218 and @KBodolai, We will finish with the responses in the following days (3 days maximum). I am so sorry for the delay.

mikemahoney218 commented 3 months ago

No worries! I'm just making sure I'm keeping track of where we are in the process :smile:

mikemahoney218 commented 3 months ago

Hi @yotarazona , just wanted to check back in to see how revisions are going!

yotarazona commented 3 months ago

Hi @mikemahoney218 and @KBodolai. We have sent responses to the issues and suggestions made by @KBodolai . We are grateful for these suggestions and comments that improved the package. We look forward to hearing from you if you have any other questions.

Again, thank you very much for your time during this entire review process!. :)

mikemahoney218 commented 2 months ago

Thank you @yotarazona ! My next question then is for @KBodolai -- would you be able to look at the responses to your comments and either check off the last of your checklist (and let me know that you've finished your review), or open new issues about anything else you've found? Thank you again for reviewing for us!

KBodolai commented 2 months ago

Hi everyone,

I'm happy with all the edits and responses by @yotarazona , thank you very much for taking the time and for your thoughtful responses!

Everything is checked and all issues are closed, I believe, so I'm happy for the process to continue .

mikemahoney218 commented 2 months ago

@editorialbot post-review checklist

editorialbot commented 2 months ago

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

@editorialbot commands

mikemahoney218 commented 2 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

mikemahoney218 commented 2 months ago

Awesome! Thank you so much @dbuscombe-usgs and @KBodolai for your thoughtful reviews here.

@yotarazona , at this point could you please complete the checklist above (making sure to link your archive and mention your final version number here)?

I can then move forward with recommending acceptance of the submission.

As a bit of housekeeping, I'll be offline the rest of this week so it may be a few days before I can finalize this review.

yotarazona commented 2 months ago

Hi @mikemahoney218 , sure. I can give it a final check considering the above points. I'll let you know in the next couple of days.

Thank you very much for handling this paper!!!

yotarazona commented 2 months ago

Hi @mikemahoney218, some checks below:

  1. Read the text of the paper and offer comments/corrections (as either a list or a pull request). In the new version, some comments to clarify some ideas were added. (DONE)
  2. Check that the archive title, author list, version tag, and the license are correct. The new version of the paper is within v0.2.28 (https://github.com/yotarazona/scikit-eo/tree/main/paper). License as Apache Software License 2.0 (DONE)

Let me know if this helps you.

mikemahoney218 commented 2 months ago

Sorry @yotarazona -- I'm asking you to do the top checklist ("Additional Author Tasks After Review is Complete") -- I'll take care of the editor checklist once you've finished that (including giving me the final version ID, your archive link, etc)

yotarazona commented 2 months ago

Sorry @mikemahoney218, a little mistake of mine. Checklist below:

Please, let me know if there is anything else missing.

mikemahoney218 commented 2 months ago

@editorialbot set archive as 10.5281/zenodo.12688708

editorialbot commented 2 months ago

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

@editorialbot commands

mikemahoney218 commented 2 months ago

@editorialbot set 10.5281/zenodo.12688708 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.12688708

mikemahoney218 commented 2 months ago

@editorialbot set 0.2.31 as version

editorialbot commented 2 months ago

Done! version is now 0.2.31

mikemahoney218 commented 2 months ago

@editorialbot generate pdf

mikemahoney218 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1080/07038992.2021.1941823 is OK
- 10.1016/j.rsase.2020.100337 is OK
- 10.1016/j.ecolind.2018.07.012 is OK
- 10.1016/j.rse.2014.02.015 is OK
- 10.1016/j.isprsjprs.2021.04.015 is OK
- 10.3390/rs12183062 is OK
- 10.1080/10095020.2019.1710438 is OK
- 10.1038/nclimate1908 is OK
- 10.1038/s41559-022-01702-5 is OK
- 10.1016/J.RSE.2021.112577 is OK
- 10.5281/ZENODO.3233986 is OK
- 10.1038/s41558-017-0049-x is OK
- 10.1038/s41586-021-03436-z is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 months ago

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

mikemahoney218 commented 2 months ago

Running through my checklist now:

@yotarazona , can you explain why the Zenodo archive doesn't have the same list of authors as your paper? Normally we expect that both the software archive and software paper should share an author list. Is this intentional?

The license of the Zenodo archive should be the same as the software itself (APL-2.0). The current license, CC-BY-4.0, is not an open source license and we cannot accept it.

Below are my comments on the paper. The top section needs to get fixed before I could recommend acceptance, the second section are suggestions I believe would improve the paper but aren't blockers.

Requested changes

Fig 1: the figure in the published paper is going to look just like the one in the draft. Can you provide a higher resolution figure, potentially with larger text?

Citations:

Other suggestions

Line 18: Consider breaking this into two sentences ("Applications that integrate... impact on urbanization levels. A particular area of interest is measuring and monitoring climate change impacts, including..."). As it is, this one sentence takes 7 lines and uses 5 commas, which makes it a bit hard to follow.

Line 67: I'm pretty confused by this sentence. Consider rephrasing -- maybe breaking it into two sentences, for instance "Its comprehensive features make it well-suited for various applications, from university teaching to cutting-edge research using the most recent machine learning and deep learning techniques. Whether the users are students seeking insights from a satellite image analysis or an experienced researcher looking for advanced tools, scikit-eo offers a valuable resource to support the most valuable methods for environmental studies."

Line 114 and 115: consider "classroom" instead of "lecture room".

Thanks!

yotarazona commented 2 months ago

Hi @mikemahoney218, I am new to zenodo :). I had to edit the author list to add the other authors and modify the license as well. Now you can verify that both the authors and the license were fixed: https://doi.org/10.5281/zenodo.12688708.

Requested changes: DONE. Thank you very much for these suggestions. Other suggestions: DONE. Thank you again for these suggestions. I agree and I think they improve the flow of the reading. You can see the changes in the updated paper.md https://github.com/yotarazona/scikit-eo/blob/main/paper/paper.md.

About the Fig. 1, we have two higher resolution figures in the paper folder: https://github.com/yotarazona/scikit-eo/tree/main/paper.

Let me know if you have any other comments.