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[REVIEW]: itmlogic: Longley Rice Irregular Terrain Model #2266

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @edwardoughton (Edward J. Oughton) Repository: https://github.com/edwardoughton/itmlogic Version: v1.1 Editor: @danielskatz Reviewer: @gorlapraveen, @garrettj403 Archive: 10.5281/zenodo.3931350

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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

@gorlapraveen & @garrettj403, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @gorlapraveen

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @garrettj403

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @gorlapraveen, @garrettj403 it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1016/j.tele.2019.01.003 is OK
- 10.1109/ACCESS.2019.2949460 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

👋 @gorlapraveen & @garrettj403 - thanks for agreeing to review this submission. Please be sure to read the comments above, and let me know if you have any questions. Basically, your job is to check the article proof and repository and check items off your checklist above.

If you see small problems that need to be discussed, feel free to discuss them here. But if you can, create a new issue in the target repository and link to this review thread in that issue to create corresponding breadcrumb trail here.

I look forward to seeing how this review goes

garrettj403 commented 4 years ago

Hello @edwardoughton,

I have a couple comments on your paper:

Overall, the paper was very well-written. The software was also easy to install on my computer and I hope to finish reviewing the code in the next couple days. Note: I had the same issue as @gorlapraveen that he raised in issue #34 (missing rasterstats package).

danielskatz commented 4 years ago

Thanks @garrettj403 - if you and @gorlapraveen can add a link to this issue (https://github.com/openjournals/joss-reviews/issues/2266) in any issues you open in the source repo, the will be flagged here and anyone looking at this issue will be able to tell if they are open or closed as well.

edwardoughton commented 4 years ago

Thank you for the review feedback @garrettj403 and @gorlapraveen, we're working to turn these corrections around.

edwardoughton commented 4 years ago

Hello @edwardoughton,

I have a couple comments on your paper:

  • You wrote "... access to disparate user base ...". Do you mean "dispersed user base"?
  • I think that "Longley-Rice" should be hyphenated.
  • You should check the capitalization of the titles in your references. E.g., "The its irregular terrain model..." should be changed to "The ITS Irregular Terrain Model...".
  • The final reference is wonky. You have the Institute for Telecommunication Sciences listed as the author.

Overall, the paper was very well-written. The software was also easy to install on my computer and I hope to finish reviewing the code in the next couple days. Note: I had the same issue as @gorlapraveen that he raised in issue #34 (missing rasterstats package).

@garrettj403 I've now made most of those changes. I'm not sure the reference is wonky for the last entry in the bib as this is a citation of the website that releases the code. I think ITS seems like the right author, as it's their website, but I'm happy to be convinced otherwise.

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

the bib problem is in formatting - please merge https://github.com/edwardoughton/itmlogic/pull/39 to fix it (and some other bib problems)

danielskatz commented 4 years ago

then you can put in a new comment here with @whedon generate pdf to regenerate the pdf.

gorlapraveen commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

@gorlapraveen - we need changes in the repo before it's useful to regenerate the pdf.

edwardoughton commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

edwardoughton commented 4 years ago

@gorlapraveen @garrettj403 @danielskatz I think that fixed the bibliography ordering plus capitalizations. Please let me know if there is anything else.

danielskatz commented 4 years ago

I'm not sure why you made changes manually rather than just merging the PR. You missed the {}s around MHz and GHz. Otherwise, it looks ok to me.

edwardoughton commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

edwardoughton commented 4 years ago

I'm not sure why you made changes manually rather than just merging the PR. You missed the {}s around MHz and GHz. Otherwise, it looks ok to me.

Apologies Daniel, I missed the PR! Thanks for that. I hope this is resolved now.

danielskatz commented 4 years ago

no problem

garrettj403 commented 4 years ago

Hi @edwardoughton

I like that you provided two examples in the scripts/ directory, but I think that they need a bit more explanation. For example, scripts/area.py doesn't have any inline comments past line 107, which makes it difficult to follow along. I raised this issue in #43.

The testing looks good (I think), but again it's very difficult to follow along without any comments. For example, I'm looking at the test for lrprop (test_lrprop.py). Where does setup_expected_prop_to_test_lrprop come from? Were these results generated by the previous FORTRAN/C++/MATLAB code? I think that you should have a short docstring in each file to describe the general idea behind the test. I raised this issue in #44.

Outside the scope of the JOSS review, I have a few general comments about the package:

Overall, the package looks very useful. I think if you add a couple more comments to the scripts/ and tests/ directories, it will help new users to understand how the package works and ensure that the package is maintainable. I'll be ready to sign off once issue #43 and issue #44 are addressed. Also, it looks like the build is failing right now, so that should be taken care of.

danielskatz commented 4 years ago

👋 @edwardoughton - This is just to make sure you've seen the comments and are working on responding to them...

edwardoughton commented 4 years ago

👋 @edwardoughton - This is just to make sure you've seen the comments and are working on responding to them...

Most of this is now complete @danielskatz, I'm just waiting for the authorship team to agree all the changes, and then I'll integrate the branch for @garrettj403 to review. I'm hoping this will be done by tomorrow.

edwardoughton commented 4 years ago

@danielskatz @garrettj403

We've now completed our corrections and look forward to your response.

Best wishes,

Ed et al.

danielskatz commented 4 years ago

👋 @gorlapraveen & @garrettj403 - can you take a look at the changes, and see what else (if anything) you think needs to be done?

garrettj403 commented 4 years ago

Hi @edwardoughton, the changes look great! The additional comments will definitely help new users get started with your code.

@danielskatz, I'm ready to recommend publication. itmlogic was easy to install on my computer and all of the unit tests run smoothly without any errors. The package also has detailed documentation, which is hosted online. Overall, it looks like a very useful package with clear applications.

Great job!

danielskatz commented 4 years ago

thanks @garrettj403!

I now look forward to hearing from @gorlapraveen

gorlapraveen commented 4 years ago

Hi @edwardoughton, the functionality and the use of algorithms is technically quite satisfying. However, I would also suggest you to document where User inputs can be given. Such as where to change the operating frequencies for different modes. This would be my final comment and we can proceed for publication.

edwardoughton commented 4 years ago

@gorlapraveen I've now adapted the example running scripts and the documentation to reflect the main user defined parameters. This includes having a dict which contains the main parameters which the user can concisely state before calling the itmfunction. Hopefully this makes things clearer.

I also separated out the example scripts which use either 1 DEM tile or 2 DEM tiles, to overcome the issue of working across large areas which some users will need to deal with. The documentation also now reflects these changes.

Thanks for the review feedback, Ed

gorlapraveen commented 4 years ago

@edwardoughton Thanks for the changes. Looks great! @danielskatz I also recommend for publishing.

edwardoughton commented 4 years ago

Fantastic, thanks for the review @gorlapraveen.

danielskatz commented 4 years ago

thanks @gorlapraveen!

danielskatz commented 4 years ago

@edwardoughton - at this point, please:

I can then move forward with accepting the submission, which will include me proofreading the paper and the references.

edwardoughton commented 4 years ago

@edwardoughton - at this point, please:

  • [x] Make a tagged release of your software, and list the version tag of the archived version here.
  • [x] Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
  • [x] 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.
  • [x] Please list the DOI of the archived version here.

I can then move forward with accepting the submission, which will include me proofreading the paper and the references.

Thanks @danielskatz, I should now have completed those tasks. Please let me know if I missed anything.

DOI: 10.5281/zenodo.3931350

Zonodo link: https://zenodo.org/record/3931350#.XwLumihKh9M

danielskatz commented 4 years ago

@whedon set v1.1 as version

whedon commented 4 years ago

OK. v1.1 is the version.

danielskatz commented 4 years ago

@whedon set 10.5281/zenodo.3931350 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3931350 is the archive.

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1016/j.tele.2019.01.003 is OK
- 10.1109/ACCESS.2019.2949460 is OK
- 10.1108/DPRG-02-2018-0004 is OK
- 10.1016/j.telpol.2017.07.009 is OK
- 10.1016/j.compenvurbsys.2020.101515 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 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/1548

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1548, 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 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦