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[REVIEW]: IPART: A Python Package for Image-Processing based Atmospheric River Tracking #2407

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whedon opened this issue Jun 29, 2020 · 12 comments
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@whedon
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@whedon whedon commented Jun 29, 2020

Submitting author: @Xunius (Guangzhi XU)
Repository: https://github.com/ihesp/IPART
Version: v1.0
Editor: @kbarnhart
Reviewer: @sadielbartholomew, @rabernat
Archive: Pending

⚠️ 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/e5e7c126fe26a82ab717e7d2ce70a1e1"><img src="https://joss.theoj.org/papers/e5e7c126fe26a82ab717e7d2ce70a1e1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e5e7c126fe26a82ab717e7d2ce70a1e1/status.svg)](https://joss.theoj.org/papers/e5e7c126fe26a82ab717e7d2ce70a1e1)

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

@sadielbartholomew & @rabernat, 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 @kbarnhart know.

Please try and complete your review in the next six weeks

Review checklist for @sadielbartholomew

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

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: Do the authors clearly state 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 @rabernat

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

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: Do the authors clearly state 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
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@whedon whedon commented Jun 29, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sadielbartholomew, @rabernat 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:

watching

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

notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf
@whedon
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@whedon whedon commented Jun 29, 2020

PDF failed to compile for issue #2407 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2407 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:119:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

@kbarnhart kbarnhart changed the title [REVIEW]: AR tracker: A Python package for detecting and tracking atmospheric rivers using image-processing [REVIEW]: IPART: A Python Package for Image-Processing based Atmospheric River Tracking Jun 29, 2020
@kbarnhart
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@kbarnhart kbarnhart commented Jun 29, 2020

@whedon generate pdf

@whedon
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@whedon whedon commented Jun 29, 2020

PDF failed to compile for issue #2407 with the following error:

Can't find any papers to compile :-(

@kbarnhart
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@kbarnhart kbarnhart commented Jun 29, 2020

@arfon / @openjournals/joss-eics could you help me ensure the repository is linked correctly to this review issue. Issues may have cropped up because the authors changed the title of the submission and the repository address during the pre-review stage (#2197).

I can edit the title/comments on this thread... @whedon could find the paper in the review issue (e.g., here)

repo: https://github.com/ihesp/IPART
title: "IPART: A Python Package for Image-Processing based Atmospheric River Tracking"

thanks!

@danielskatz
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@danielskatz danielskatz commented Jun 29, 2020

@whedon generate pdf

@whedon
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@whedon whedon commented Jun 29, 2020

PDF failed to compile for issue #2407 with the following error:

Can't find any papers to compile :-(

@danielskatz
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@danielskatz danielskatz commented Jun 29, 2020

👋 @openjournals/dev - can you take a look at this?

@xuanxu
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@xuanxu xuanxu commented Jun 29, 2020

@whedon generate pdf

@whedon
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@whedon whedon commented Jun 29, 2020

@xuanxu
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@xuanxu xuanxu commented Jun 29, 2020

It was the bold markup in the repo link. It was confusing for Whedon. I removed it and now it works.

@kbarnhart
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@kbarnhart kbarnhart commented Jun 29, 2020

@xuanxu thank you! Pretty confident that was my fault.

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