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[REVIEW]: thresholdmodeling: A Python package for modeling excesses over a threshold using the Peak-Over-Threshold Method and the Generalized Pareto Distribution #2013

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whedon opened this issue Jan 13, 2020 · 69 comments
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@whedon whedon commented Jan 13, 2020

Submitting author: @iagolemos1 (Iago Lemos)
Repository: https://github.com/iagolemos1/thresholdmodeling
Version: v0.0.1
Editor: @drvinceknight
Reviewer: @bahung, @kellieotto
Archive: 10.5281/zenodo.3661338

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ed29ca0eb021662682a366adffb87f6c"><img src="https://joss.theoj.org/papers/ed29ca0eb021662682a366adffb87f6c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ed29ca0eb021662682a366adffb87f6c/status.svg)](https://joss.theoj.org/papers/ed29ca0eb021662682a366adffb87f6c)

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

@bahung & @kellieotto, 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 @drvinceknight know.

Please try and complete your review in the next two weeks

Review checklist for @bahung

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 (@iagolemos1) 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 @kellieotto

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 (@iagolemos1) 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?
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@whedon whedon commented Jan 13, 2020

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

⭐️ 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
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@whedon whedon commented Jan 13, 2020

Reference check summary:

OK DOIs

- 10.1007/978-1-4471-3675-0 is OK
- 10.1016/S0309-1708(02)00056-8 is OK
- 10.1017/CBO9780511529443 is OK
- 10.6028/jres.099.028 is OK
- 10.5194/os-2016-47 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Jan 13, 2020

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@iagolemos1 iagolemos1 commented Jan 15, 2020

I made some minimal corrections in the paper.

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@iagolemos1 iagolemos1 commented Jan 15, 2020

@whedon generate pdf

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@whedon whedon commented Jan 15, 2020

@kellieotto kellieotto mentioned this issue Jan 16, 2020
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@iagolemos1 iagolemos1 commented Jan 17, 2020

Modified paper considering @kellieotto corrections below.

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@iagolemos1 iagolemos1 commented Jan 17, 2020

@whedon generate pdf

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@whedon whedon commented Jan 17, 2020

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@iagolemos1 iagolemos1 commented Jan 19, 2020

Below, I tried to consider all the changes suggested by @bahung.

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@iagolemos1 iagolemos1 commented Jan 19, 2020

@whedon generate pdf

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@whedon whedon commented Jan 19, 2020

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@iagolemos1 iagolemos1 commented Jan 19, 2020

@whedon generate pdf

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@whedon whedon commented Jan 19, 2020

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@iagolemos1 iagolemos1 commented Jan 19, 2020

@whedon generate pdf

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@whedon whedon commented Jan 19, 2020

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@iagolemos1 iagolemos1 commented Jan 25, 2020

@whedon generate pdf

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@whedon whedon commented Jan 25, 2020

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@kellieotto kellieotto commented Jan 26, 2020

@drvinceknight I recommend the package for approval. @iagolemos1 has responded to all of my comments.

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@iagolemos1 iagolemos1 commented Jan 26, 2020

@kellieotto Thanks for the support and to help my paper to get better!

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@drvinceknight drvinceknight commented Jan 27, 2020

Thank you @kellieotto, I believe we are no waiting on @bahung to finish their review?

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@whedon whedon commented Feb 10, 2020

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@drvinceknight drvinceknight commented Feb 10, 2020

@drvinceknight Now I have to archive the repository in Zenodo, right?

That's right: and pleas report the DOI in the review thread. Could you make sure the Zenodo deposit has the correct metadata (title and author list).

Can you also confirm the version of the software please?

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@iagolemos1 iagolemos1 commented Feb 10, 2020

Version 0.0.1.

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@iagolemos1 iagolemos1 commented Feb 10, 2020

DOI in Zenodo:
10.5281/zenodo.3661338

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@drvinceknight drvinceknight commented Feb 10, 2020

@whedon set 10.5281/zenodo.3661338 as archive

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@whedon whedon commented Feb 10, 2020

OK. 10.5281/zenodo.3661338 is the archive.

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@drvinceknight drvinceknight commented Feb 10, 2020

@openjournals/joss-eics this paper is now ready to be accepted :) 👍 🎆

Thank you @bahung and @kellieotto for your time and effort reviewing the work. 👍

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@danielskatz danielskatz commented Feb 10, 2020

@whedon accept

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@whedon whedon commented Feb 10, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 10, 2020

Reference check summary:

OK DOIs

- 10.1007/978-1-4471-3675-0 is OK
- 10.1016/S0309-1708(02)00056-8 is OK
- 10.1017/CBO9780511529443 is OK
- 10.6028/jres.099.028 is OK
- 10.5194/os-2016-47 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Feb 10, 2020

Check final proof 👉 openjournals/joss-papers#1294

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1294, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Feb 10, 2020

👋 @iagolemos1 - please merge iagolemos1/thresholdmodeling#8 or let me know what parts of it you disagree with. Also, there is at least one case error in the .bib file, a pareto that should be {P}areto. Please check the bib entries as built in the pdf carefully, and make any other needed changes as well.

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@iagolemos1 iagolemos1 commented Feb 10, 2020

Hi @danielskatz. I merged the changes and made the changes in the .bib file. Thanks!

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@danielskatz danielskatz commented Feb 10, 2020

@whedon generate pdf

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@whedon whedon commented Feb 10, 2020

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@danielskatz danielskatz commented Feb 10, 2020

@whedon accept

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@whedon whedon commented Feb 10, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 10, 2020

Reference check summary:

OK DOIs

- 10.1007/978-1-4471-3675-0 is OK
- 10.1016/S0309-1708(02)00056-8 is OK
- 10.1017/CBO9780511529443 is OK
- 10.6028/jres.099.028 is OK
- 10.5194/os-2016-47 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Feb 10, 2020

Check final proof 👉 openjournals/joss-papers#1295

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1295, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Feb 10, 2020

@whedon accept deposit=true

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@whedon whedon commented Feb 10, 2020

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Feb 10, 2020
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@whedon whedon commented Feb 10, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Feb 10, 2020

🚨🚨🚨 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 👉 openjournals/joss-papers#1296
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02013
  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...

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@danielskatz danielskatz commented Feb 10, 2020

Thanks to @bahung, @kellieotto for reviewing!
And @drvinceknight for editing!
And congratulations to @iagolemos1 and co-authors!

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@whedon whedon commented Feb 10, 2020

🎉🎉🎉 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.02013/status.svg)](https://doi.org/10.21105/joss.02013)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02013">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02013/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02013/status.svg
   :target: https://doi.org/10.21105/joss.02013

This is how it will look in your documentation:

DOI

We need your help!

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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@iagolemos1 iagolemos1 commented Feb 10, 2020

@danielskatz I tried to reach the paper using the DOI and it's appearing "File not foud". It's because the DOI isn't ready yet?
image

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@danielskatz danielskatz commented Feb 10, 2020

The link https://doi.org/10.21105/joss.02013 works fine for me (and did before I closed the issue) - it might just be an issue of how new DOIs resolve and how this information is distributed. Please try again in a little bit and if it continue to not work for you, let us know.

As I look at this more carefully, the DOI is resolving for you, and bringing you to the right page. The problem you are having is that the PDF at that page is not displaying, which is likely a web caching issue. Again, however, waiting a little bit should work.

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@iagolemos1 iagolemos1 commented Feb 10, 2020

Ok, thanks!

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