[REVIEW]: SEEDPOD Ground Risk: A Python application and library for Uncrewed Aerial Systems ground risk analysis and risk-aware path finding

whedon commented 2 years ago

Submitting author: !--author-handle-->@aliaksei135@danielskatz<!--end-editor-- Reviewers: @kylebeggs, @AustinTSchaffer Archive: 10.5281/zenodo.6363635

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Reviewer instructions & questions

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

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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 @kylebeggs

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@aliaksei135) 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 @AustinTSchaffer

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@aliaksei135) 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 2 years ago

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

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whedon commented 2 years ago

Wordcount for paper.md is 713

whedon commented 2 years ago

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

OK DOIs

- 10.1109/DASC.2017.8102039 is OK
- 10.1109/ICUAS48674.2020.9213990 is OK
- 10.2514/6.2017-3273 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.98 s (47.5 files/s, 4687.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          70           1240            725           5032
JSON                             5              0              0           1344
Qt                               3              0              0            465
Markdown                         4             66              0            177
YAML                             3             11             12             81
XML                              6              0              0             44
QML                              1              9              0             34
TeX                              1              2              0             31
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            94           1328            737           7214
-------------------------------------------------------------------------------

Statistical information for the repository '4171f2f6bddae50adde9fb0c' was
gathered on 2022/01/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Aliaksei Pilko                 391         12386           5139           92.94
Zach Tait                        8           794            411            6.39
Zach10a                          5            92             35            0.67

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
Aliaksei Pilko             6154           49.7          8.3                7.57
Zach Tait                   843          106.2          3.3                3.44

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

@kylebeggs and @AustinTSchaffer - 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#4079 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.

whedon commented 2 years ago

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

whedon commented 2 years ago

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

danielskatz commented 2 years ago

@kylebeggs & @AustinTSchaffer - how are things going in your reviews? Are there any problems I can help with?

AustinTSchaffer commented 2 years ago

Sorry, haven't gotten to it yet. It's on my to-do, but I was out of town this weekend. I'll take a look tonight.

On Mon, Feb 7, 2022, 10:02 AM Daniel S. Katz @.***> wrote:

@kylebeggs https://github.com/kylebeggs & @AustinTSchaffer https://github.com/AustinTSchaffer - how are things going in your reviews? Are there any problems I can help with?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4079#issuecomment-1031562485, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD3PHG4H5GC6ZVGLTZL5SRTUZ7NJLANCNFSM5MOE3A4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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kylebeggs commented 2 years ago

@danielskatz I am swamped with work right now. I will be able to get to it next week. If that is too long then we may have to find another reviewer. Apologies.

danielskatz commented 2 years ago

That's fine - I'm just checking in to make sure it doesn't get lost...

danielskatz commented 2 years ago

Hi @kylebeggs and @AustinTSchaffer - I'm just checking in again to see how your reviews are coming along

kylebeggs commented 2 years ago

@danielskatz Good, making my way through the source code. About to try running the software.

AustinTSchaffer commented 2 years ago

@danielskatz I'm so sorry, I didn't end up looking at this 9 days ago. I added a new issue regarding Lunux installation instructions, but I definitely have most of the review still to do. I'll do a little more work later this week.

danielskatz commented 2 years ago

👋 @kylebeggs and @AustinTSchaffer - I'm just checking in once again to see how your reviews are coming along

kylebeggs commented 2 years ago

Not great. Working through installation woes. It seems both Austin and I are on Linux and the package was more Windows focused.

danielskatz commented 2 years ago

Do you think you will be able to proceed through the review?

kylebeggs commented 2 years ago

Depends if the authors will be able to help my issues in a timely manner. Perhaps for the sake of time we should seek another reviewer.

danielskatz commented 2 years ago

👋 @aliaksei135 - What do you think?

Note that if we do need to find one or two new reviewers, this will basically be like starting the review process over once we do find them, which itself can take a little time for reviewers with Windows systems. But perhaps this is best?

aliaksei135 commented 2 years ago

I really appreciate the work put into the review thus far and I am keen to get this working on Linux as well, so I would rather not discard work already done on this review.

I've partitioned out and installed Ubuntu on my laptop and will be focusing on sorting out the dependencies again in a fresh environment.

danielskatz commented 2 years ago

👋 aliaksei135 - just a quick check in - I assume you are now working on this?

aliaksei135 commented 2 years ago

@danielskatz we've made a lot of progress updating docs and packaging for Linux. To my knowledge both reviewers can now run all commands in the CLI. I assume the review is now progressing

danielskatz commented 2 years ago

👋 @kylebeggs and @AustinTSchaffer, do you agree, and are you now making (or able to make) progress?

kylebeggs commented 2 years ago

Yes this is true.

danielskatz commented 2 years ago

👋 @kylebeggs and @AustinTSchaffer, it looks like things are getting close. Are there things currently blocking you from completing your reviews that I can help with? Or that @aliaksei135 can help with?

AustinTSchaffer commented 2 years ago

@danielskatz I have checked off the remainder of my items.

danielskatz commented 2 years ago

Thanks @AustinTSchaffer - so you are ok with this being published?

danielskatz commented 2 years ago

👋 @kylebeggs - just a ping on your part again...

AustinTSchaffer commented 2 years ago

Yes, I am ok with this being published.

On Wed, Mar 16, 2022, 12:32 PM Daniel S. Katz @.***> wrote:

Thanks @AustinTSchaffer https://github.com/AustinTSchaffer - so you are ok with this being published?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4079#issuecomment-1069326724, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD3PHGY7SWOCCNTA3WDJ53TVAIEKXANCNFSM5MOE3A4A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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kylebeggs commented 2 years ago

@danielskatz I just received help regarding the wiki info a few days ago, I will be finishing the review soon

kylebeggs commented 2 years ago

@danielskatz Ok, I've finished. Everything works as supposed to. I do think there is poor support/documentation for the CLI case, but its obvious this is not the intended audience so I will recommend to be published at this point.

danielskatz commented 2 years ago

Thanks!

danielskatz commented 2 years ago

👋 @aliaksei135 - I'll next proofread the paper

danielskatz commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/DASC.2017.8102039 is OK
- 10.1109/ICUAS48674.2020.9213990 is OK
- 10.2514/6.2017-3273 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 2 years ago

@editorialbot generate pdf

editorialbot 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

@aliaksei135 - I've suggested some small changes in https://github.com/aliaksei135/seedpod_ground_risk/pull/107 - please merge this, or let me know what you disagree with, then we can proceed.

aliaksei135 commented 2 years ago

All merged, thank you

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Paper is not ready for acceptance yet, the archive is missing

danielskatz commented 2 years ago

@aliaksei135 - At this point 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.

aliaksei135 commented 2 years ago

Tag is v0.15.1
DOI is 10.5281/zenodo.6363635 with updated metadata

danielskatz commented 2 years ago

@editorialbot set v0.15.1 as version

editorialbot commented 2 years ago

Done! version is now v0.15.1

danielskatz commented 2 years ago

@editorialbot set 10.5281/zenodo.6363635 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6363635

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

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