Joss-reviews: [REVIEW]: Overlapping: a R package for Estimating Overlapping in Empirical Distributions

Created on 15 Oct 2018 · 66Comments · Source: openjournals/joss-reviews

Submitting author: @masspastore (MASSIMILIANO PASTORE)
Repository: https://github.com/masspastore/overlapping
Version: v1.5.0
Editor: @arfon
Reviewer: @soodoku, @russellpierce
Archive: 10.5281/zenodo.1920397

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/05da34b6ecffbbb8f8be61362989a757"><img src="http://joss.theoj.org/papers/05da34b6ecffbbb8f8be61362989a757/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/05da34b6ecffbbb8f8be61362989a757/status.svg)](http://joss.theoj.org/papers/05da34b6ecffbbb8f8be61362989a757)

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) 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

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

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @leeper know.

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

Review checklist for @soodoku

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (v1.5.0)?
[x] Authorship: Has the submitting author (@https://github.com/masspastore) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @russellpierce

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (v1.5.0)?
[x] Authorship: Has the submitting author (@https://github.com/masspastore) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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)?
[ ] Automated tests: Are there automated tests or manual steps described so that the function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

accepted published recommend-accept review

Source

whedon

All 66 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @soodoku, it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

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

watching

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

whedon on 15 Oct 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 15 Oct 2018

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

whedon on 15 Oct 2018

@soodoku, @russellpierce - please carry out your reviews in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

arfon on 15 Oct 2018

@masspator Nice to meet you. I've added several issues to your repo to cover items that I believe are in this checklist. Rather than giving you a lot of extra feedback at this time, I'll pause there and wait to see if that feedback seems useful. :)

russellpierce on 15 Oct 2018

@whedon commands

masspastore on 25 Oct 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name

whedon on 25 Oct 2018

@whedon generate pdf

masspastore on 25 Oct 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 25 Oct 2018

PDF failed to compile for issue #1023 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1023/paper/paper.md): control characters are not allowed at line 1 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon.rb:68:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/bin/whedon:52:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/bin/whedon:113:in 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

whedon on 25 Oct 2018

@whedon generate pdf

masspastore on 25 Oct 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 25 Oct 2018

PDF failed to compile for issue #1023 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon/author.rb:23:in strip_footnotes': undefined method[]' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon/author.rb:13:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon.rb:109:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon.rb:109:in block in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon.rb:106:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon.rb:106:in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon.rb:73:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/bin/whedon:52:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-8e8528b72684/bin/whedon:113:in 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

whedon on 25 Oct 2018

@masspastore - please update your paper YAML header to _exactly_ match the format of this example: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

Please note that YAML is whitespace sensitive.

arfon on 25 Oct 2018

Thanks @arfon

I unfortunately added a new reference in the bib file without checking it.
I updated the bib and the paper files, now I think it is correct.

masspastore on 26 Oct 2018

:wave: Hey @masspastore...

Letting you know, @arfon is currently OOO until Monday, October 29th 2018. :heart:

ooo[bot] on 26 Oct 2018

@whedon generate pdf

masspastore on 26 Oct 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 26 Oct 2018

PDF failed to compile for issue #1023 with the following error:

whedon on 26 Oct 2018

I updated the bib and the paper files, now I think it is correct.

No, I'm afraid the issue is with the YAML header of your paper. Please update your paper YAML header to match the format of this example: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

arfon on 26 Oct 2018

@whedon generate pdf

masspastore on 27 Oct 2018

Thanks @arfon

I updated the YAML header as of your suggestion.
I checked it in my computer and it works, I hope now it's fine.

masspastore on 27 Oct 2018

:wave: Hey @masspastore...

Letting you know, @arfon is currently OOO until Monday, October 29th 2018. :heart:

ooo[bot] on 27 Oct 2018

@masspastore - please merge this PR too: https://github.com/masspastore/overlapping/pull/9

arfon on 27 Oct 2018

@whedon generate pdf

arfon on 29 Oct 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 29 Oct 2018

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

whedon on 29 Oct 2018

Oh darn, @soodoku I might have checked items off your list when I meant to be checking off mine. My apologies!

russellpierce on 5 Nov 2018

No worries.

On Mon, Nov 5, 2018 at 7:53 AM Russell S. Pierce notifications@github.com
wrote:

Oh darn, @soodoku https://github.com/soodoku I might have checked items
off your list when I meant to be checking off mine. My apologies!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1023#issuecomment-435925934,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AAsCOhL6d9slN-YSuG0v66CSguUF7J-Kks5usF7ugaJpZM4Xcx0f
.

soodoku on 5 Nov 2018

@whedon generate pdf

russellpierce on 7 Nov 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 7 Nov 2018

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

whedon on 7 Nov 2018

@whedon generate pdf

russellpierce on 13 Nov 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 13 Nov 2018

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

whedon on 13 Nov 2018

@soodoku, @russellpierce - it looks like you're both making good progress with your reviews here. Do you think you might be able to complete them in the next week?

arfon on 19 Nov 2018

@whedon assign @arfon as editor

arfon on 19 Nov 2018

@whedon generate pdf

masspastore on 26 Nov 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 26 Nov 2018

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

whedon on 26 Nov 2018

@masspastore I added one more grammar correction under a git blame. Otherwise I think things are looking good. cc: @arfon

russellpierce on 28 Nov 2018

❤1

@soodoku - it looks like there are a few checkboxes un-checked for your review. Is there still work to be done by the author or are you happy to accept here?

arfon on 29 Nov 2018

@arfon: need to check a couple of things. i plan to get to it over the weekend. i will be in touch soonish.

soodoku on 29 Nov 2018

@soodoku thanks for giving it a thorough look. I'll admit that I've been through it enough at this point where I don't have as clear as view on the end result as I might have at the start. So, it is entirely possible I'm missing something. :) I.e. don't take my signoff as a need for less rigour.

russellpierce on 30 Nov 2018

hey @arfon: go for it.

soodoku on 3 Dec 2018

👍1

@masspastore - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

arfon on 3 Dec 2018

Thanks @arfon - Sure, just done; here is the link: https://zenodo.org/record/1920397#.XAZeVeLTU2x. Doi for Zenodo is 10.5281/zenodo.1920397

masspastore on 4 Dec 2018

@whedon set 10.5281/zenodo.1920397 as archive

arfon on 4 Dec 2018

OK. 10.5281/zenodo.1920397 is the archive.

whedon on 4 Dec 2018

@whedon accept

arfon on 4 Dec 2018

Attempting dry run of processing paper acceptance...

whedon on 4 Dec 2018

PDF failed to compile for issue #1023 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 12 0 12 0 0 170 0 --:--:-- --:--:-- --:--:-- 171
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/bibtex.rb:43:in make_citation': undefined methodhas_field?' for #<, %f>> (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/bibtex.rb:30:in block in generate_citations' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:ineach'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/bibtex.rb:29:ingenerate_citations'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:214:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/lib/whedon/processor.rb:91:incompile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:76:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-c44264c87f39/bin/whedon:113:in 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

whedon on 4 Dec 2018

@whedon accept

arfon on 4 Dec 2018

@whedon accept

arfon on 4 Dec 2018

Attempting dry run of processing paper acceptance...

whedon on 4 Dec 2018

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/100

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/100, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon on 4 Dec 2018

Hi @masspastore - from a quick inspection, lots of the references in this article likely have DOIs. Could you add a doi field to the bibtex file where possible please?

For example, this paper has the DOI 10.1016/j.csda.2005.01.014

arfon on 4 Dec 2018

Hi @arfon, I updated the bib file with all avaliable DOIs

Thanks

masspastore on 5 Dec 2018

👍1

@whedon accept

arfon on 5 Dec 2018

Attempting dry run of processing paper acceptance...

whedon on 5 Dec 2018

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/105

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/105, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon on 5 Dec 2018

@whedon accept deposit=true

arfon on 5 Dec 2018

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

whedon on 5 Dec 2018

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/106
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01023
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

whedon on 5 Dec 2018

@soodoku, @russellpierce - many thanks for your reviews here ✨

@masspastore - your paper is now accepted into JOSS :zap::rocket::boom:

arfon on 5 Dec 2018

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01023/status.svg)](https://doi.org/10.21105/joss.01023)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01023">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01023/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01023/status.svg
   :target: https://doi.org/10.21105/joss.01023

This is how it will look in your documentation:

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whedon on 5 Dec 2018

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