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[REVIEW]: OMEGA-Py: Python Tools for OMEGA Data #6566

Open editorialbot opened 3 months ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@AStcherbinine<!--end-author-handle-- (Aurélien Stcherbinine) Repository: https://github.com/AStcherbinine/omegapy Branch with paper.md (empty if default branch): joss-paper Version: v3.0 Editor: !--editor-->@dfm<!--end-editor-- Reviewers: @Sierra-MC, @ryanbanderson Archive: Pending

Status

status

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HTML: <a href="https://joss.theoj.org/papers/15cf348a29d186e12f49a110f9f787f8"><img src="https://joss.theoj.org/papers/15cf348a29d186e12f49a110f9f787f8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/15cf348a29d186e12f49a110f9f787f8/status.svg)](https://joss.theoj.org/papers/15cf348a29d186e12f49a110f9f787f8)

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

@Sierra-MC, 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 @dfm 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 @Sierra-MC

📝 Checklist for @ryanbanderson

editorialbot commented 3 months ago

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

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

OK DOIs

- 10.1109/MCSE.2007.55 is OK
- 10.1016/j.icarus.2022.115366 is OK
- 10.1016/j.icarus.2021.114627 is OK
- 10.5194/epsc2022-847 is OK

MISSING DOIs

- No DOI given, and none found for title: OMEGA: Observatoire Pour La Minéralogie, l’Eau, Le...

INVALID DOIs

- None
editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (487.2 files/s, 172292.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6            354           2292           3072
SVG                              3              2             21           2285
Markdown                        14            383              0           1503
YAML                             4             14             44            185
TeX                              1              5              0             57
CSV                              1              0              0             38
-------------------------------------------------------------------------------
SUM:                            29            758           2357           7140
-------------------------------------------------------------------------------

Commit count by author:

   126  Aurélien Stcherbinine
    93  aurelien stcherbinine
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 638

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 3 months ago

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

dfm commented 3 months ago

@Sierra-MC — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate!

👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting @editorialbot generate my checklist on this issue ASAP. 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.

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#6566 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 the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible!

Sierra-MC commented 3 months ago

Review checklist for @Sierra-MC

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Sierra-MC commented 3 months ago

@AStcherbinine,

Would you be able to add a short summary in the paper of what the functionality of the original IDL script this is replacing does? Especially if this is targeting the younger generation of scientists who don't rely on IDL, there should be some explanation of what those routines did originally. While it may be obvious for users who used to use the IDL scripts and are moving to Python it is less so for new users of OMEGA data.

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:

dfm commented 2 months ago

@editorialbot add @ryanbanderson as reviewer

Thanks @ryanbanderson for agreeing to review! Please take a look at the info in the top comment of this thread, and my first comment for more info about how the review will progress. As soon as possible please comment @editorialbot generate my checklist to get your review checklist and see if you can go through the first couple of items quickly. Thanks again!!

editorialbot commented 2 months ago

@ryanbanderson added to the reviewers list!

ryanbanderson commented 2 months ago

Review checklist for @ryanbanderson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

AStcherbinine commented 2 months ago

@AStcherbinine,

Would you be able to add a short summary in the paper of what the functionality of the original IDL script this is replacing does? Especially if this is targeting the younger generation of scientists who don't rely on IDL, there should be some explanation of what those routines did originally. While it may be obvious for users who used to use the IDL scripts and are moving to Python it is less so for new users of OMEGA data.

@Sierra-MC thank you for raising this point. The second paragraph of the paper has been updated to include a brief statement of what the IDL SOFT10 routines are doing.

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:

Sierra-MC commented 2 months ago

@AStcherbinine, obviously you've made major contributions to the software (you are the only contributor on github prior to this review). However, assessing the full list of authors is more difficult. Would you be able to provide a quick description of the contributions of the other authors for the following review criteria to be assessed?:

Has the submitting author (@AStcherbinine) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Sierra-MC commented 2 months ago

The tests here are a bit weak in that they mainly revolve around confirming installation and turn users to the basic usage rather than confirming the output of the functions being used are accurate. However they do exist as a manual walk-through.

AStcherbinine commented 2 months ago

@AStcherbinine, obviously you've made major contributions to the software (you are the only contributor on github prior to this review). However, assessing the full list of authors is more difficult. Would you be able to provide a quick description of the contributions of the other authors for the following review criteria to be assessed?:

Has the submitting author (@AStcherbinine) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

@Sierra-MC sure. So I am the only contributor for writing the Python code of the module but here are how other authors contributed to this work:

dfm commented 2 months ago

@ryanbanderson — Just checking in here to make sure that this remains on your radar. Thanks!!

ryanbanderson commented 2 months ago

Yep, I haven't forgotten, just working on some other deadlines first!

ryanbanderson commented 1 month ago

@AStcherbinine I'm doing my review today, looks like a very useful tool! I just created an issue with a suggestion to enable a recursive option when searching for OMEGA data. Or maybe that option already exists and I just missed it... https://github.com/AStcherbinine/omegapy/issues/9

ryanbanderson commented 1 month ago

@AStcherbinine Opened another issue: it would be nice to put the function BD_Omega that is shown in the documentation into useful_functions.py so that users can import it. https://github.com/AStcherbinine/omegapy/issues/10

ryanbanderson commented 1 month ago

@AStcherbinine In the checklist it is asking whether there is a "statement of need" in the documentation. You have one in the paper, but it would be good to copy it over to the docs as well to expand on what is already there.

ryanbanderson commented 1 month ago

The tests here are a bit weak in that they mainly revolve around confirming installation and turn users to the basic usage rather than confirming the output of the functions being used are accurate. However they do exist as a manual walk-through.

I agree, it would be nice if there were tests confirming output values. Maybe this could be addressed by providing a "demo script" that new users can run that automatically ingests data, corrects it, calculates some band depths, and visualizes. (Basically just taking the steps from the examples and putting them in a .py file) The documentation is great, but I suspect many users would appreciate having it all together in a script that can be run. That way it serves as both a form of test and a tutorial.

AStcherbinine commented 1 month ago

@AStcherbinine In the checklist it is asking whether there is a "statement of need" in the documentation. You have one in the paper, but it would be good to copy it over to the docs as well to expand on what is already there.

@ryanbanderson thanks for pointing that, the statement of need has been added in the online documentation homepage in the Why this module? section with commit 5dcf7b0 https://astcherbinine.github.io/omegapy/#why-this-module

AStcherbinine commented 1 month ago

The tests here are a bit weak in that they mainly revolve around confirming installation and turn users to the basic usage rather than confirming the output of the functions being used are accurate. However they do exist as a manual walk-through.

I agree, it would be nice if there were tests confirming output values. Maybe this could be addressed by providing a "demo script" that new users can run that automatically ingests data, corrects it, calculates some band depths, and visualizes. (Basically just taking the steps from the examples and putting them in a .py file) The documentation is great, but I suspect many users would appreciate having it all together in a script that can be run. That way it serves as both a form of test and a tutorial.

As suggested by reviewer @ryanbanderson, a full example script that can be run to [ load / apply atm & thermal corrections / compute band depth / and display the maps from the examples ] has been added as part of the test in commit f568fe9, and the documentation has been updated accordingly: https://astcherbinine.github.io/omegapy/tests/#test-to-process-and-display-an-omega-observation

Test script file: example_test_script.py

AStcherbinine commented 2 weeks ago

Hello @dfm @ryanbanderson did you have time to check the updates made to address the reviewer's comments?

Thanks

dfm commented 2 weeks ago

Thanks for the ping, @AStcherbinine!

@ryanbanderson — Can you take a look at the updates @AStcherbinine has made soon? Thanks!!

ryanbanderson commented 1 week ago

Sorry for the delay, I'll take a look soon!