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[REVIEW]: SEEDPOD Ground Risk: A Python application and library for Uncrewed Aerial Systems ground risk analysis and risk-aware path finding #4079

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whedon opened this issue Jan 21, 2022 · 59 comments
Closed
40 tasks done

[REVIEW]: SEEDPOD Ground Risk: A Python application and library for Uncrewed Aerial Systems ground risk analysis and risk-aware path finding #4079

whedon opened this issue Jan 21, 2022 · 59 comments
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@danielskatz @AustinTSchaffer @kylebeggs
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accepted Inno Setup published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX

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@whedon
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whedon commented Jan 21, 2022 •
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Submitting author: @aliaksei135 (Aliaksei Pilko)
Repository: https://github.com/aliaksei135/seedpod_ground_risk/
Branch with paper.md (empty if default branch):
Version: v0.15.1
Editor: @danielskatz
Reviewers: @kylebeggs, @AustinTSchaffer
Archive: 10.5281/zenodo.6363635

⚠️ JOSS reduced service mode ⚠️

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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b26d16f767693e3905b645aae9b72834"><img src="https://joss.theoj.org/papers/b26d16f767693e3905b645aae9b72834/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b26d16f767693e3905b645aae9b72834/status.svg)](https://joss.theoj.org/papers/b26d16f767693e3905b645aae9b72834)

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

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

  1. Make sure you're logged in to your GitHub account
  2. 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 @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

  • 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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • 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 @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

  • 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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • 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?
@whedon whedon mentioned this issue Jan 21, 2022
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whedon commented Jan 21, 2022

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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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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whedon commented Jan 21, 2022

Wordcount for paper.md is 713

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whedon commented Jan 21, 2022 

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

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whedon commented Jan 21, 2022 

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
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whedon commented Jan 21, 2022

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@danielskatz
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@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
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whedon commented Feb 4, 2022

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

@whedon
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whedon commented Feb 4, 2022

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

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

@AustinTSchaffer
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AustinTSchaffer commented Feb 7, 2022 via email

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

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

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

@kylebeggs kylebeggs mentioned this issue Feb 15, 2022
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@AustinTSchaffer AustinTSchaffer mentioned this issue Feb 16, 2022
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@AustinTSchaffer
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@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
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👋 @kylebeggs and @AustinTSchaffer - I'm just checking in once again to see how your reviews are coming along

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

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

@kylebeggs
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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
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👋 @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?

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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
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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

@aliaksei135
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All merged, thank you

@danielskatz
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@editorialbot recommend-accept

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

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

@danielskatz
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@editorialbot set v0.15.1 as version

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Done! version is now v0.15.1

@danielskatz
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@editorialbot set 10.5281/zenodo.6363635 as archive

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Done! Archive is now 10.5281/zenodo.6363635

@danielskatz
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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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

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

Check final proof 👉 openjournals/joss-papers#3067

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3067, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Mar 17, 2022
@danielskatz
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@editorialbot accept

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

@editorialbot
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04079 joss-papers#3068
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04079
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Mar 17, 2022
@danielskatz
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Congratulations to @aliaksei135 and co-author!!

And thanks to @kylebeggs and @AustinTSchaffer for reviewing!
We couldn't do this without you!

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.04079/status.svg)](https://doi.org/10.21105/joss.04079)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04079">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04079/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04079/status.svg
   :target: https://doi.org/10.21105/joss.04079

This is how it will look in your documentation:

DOI

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The 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:

@arfon arfon reopened this Mar 17, 2022
@arfon arfon closed this as completed Mar 17, 2022
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.04079/status.svg)](https://doi.org/10.21105/joss.04079)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04079">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04079/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04079/status.svg
   :target: https://doi.org/10.21105/joss.04079

This is how it will look in your documentation:

DOI

We need your help!

The 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:

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