[REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6189

editorialbot · 2024-01-08T17:16:54Z

Submitting author: @lrnv (Oskar Laverny)
Repository: https://github.com/lrnv/Copulas.jl
Branch with paper.md (empty if default branch):
Version: v0.1.21
Editor: @osorensen
Reviewers: @lucaferranti, @AnderGray
Archive: 10.5281/zenodo.6652672

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/98fa5d88d0d8f27038af2da00f210d45"><img src="https://joss.theoj.org/papers/98fa5d88d0d8f27038af2da00f210d45/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/98fa5d88d0d8f27038af2da00f210d45/status.svg)](https://joss.theoj.org/papers/98fa5d88d0d8f27038af2da00f210d45)

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

@lucaferranti & @AnderGray, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ 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 ✨

Checklists

📝 Checklist for @lucaferranti

📝 Checklist for @AnderGray

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-01-08T17:16:58Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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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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editorialbot · 2024-01-08T17:16:59Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1276.2 files/s, 94660.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           46            410            194           2448
TeX                              3             19              2            890
Markdown                        21            350              0            806
TOML                             3            136              1            593
YAML                             7              1              7            134
CSS                              1              0              0             17
-------------------------------------------------------------------------------
SUM:                            81            916            204           4888
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-01-08T17:17:00Z

Wordcount for paper.md is 915

editorialbot · 2024-01-08T17:17:03Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.1201/9780367803896 is OK
- 10.1201/b18674 is OK
- 10.1214/07-AOS556 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-01-08T17:18:21Z

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

lucaferranti · 2024-01-12T03:36:32Z

Review checklist for @lucaferranti

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/lrnv/Copulas.jl?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lrnv) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
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?

osorensen · 2024-01-31T14:21:38Z

👋 @AnderGray, could you please update us on how it's going with your review?

lucaferranti · 2024-02-04T09:12:18Z

Hi @osorensen and @lrnv 👋 , overall very nice work and I definitely recommend acceptance, here are some comments.

Paper

Overall the paper is clear and gives a good motivation to the package.

It would be good to add a reference for DataGenCopulaBased.jl and BivariateCopulas.jl, especially since both are registered in zenodo.
At line 40 a pretty strong statement is made

Copulas.jl is clearly the must fully featured, and brings, as a key feature, the complience with the broader ecosystem.

it is not clear to me from tha paper alone that Copulas.jl is the most feature complete of the three and would be good to give some more arguments in the paper. Ideally, a table comparing features of the three would be nice to have.

Documentation

Overall the API is well documented and gives a lot of background knowledge. A few improvement suggestions

Currently the documentation feels to have more theory than code, it would be nice to expand the Examples section with a few more examples of how to use the code, ideally within some applications of how to solve some "real-world" problems. E.g. applying Copulas.jl to some popular datasets and concrete example problems.
In the turing integration example, the code ends with a plot, would be good to include the resulting image in the documentation. If possible, some visual representation would also be nice to have for the example of the README
The contribution guidelines section is very short, but I think this is enough. Since you have the colprac badge, you could add a sentence there saying that more info can be found in the ColPrac guide.

Typos

I spotted a few typos, you may consider using a tool like typos-cli to check more systematically. This could also be setup on CI (actually the julia repo does it) but it might be an overkill.

line 40 of the paper must -> most
line 41 of the paper complience -> compliance
line 46 of the paper specify -> specifies
line 55 folloiwng -> following (I also think consists of is the grammatically correct form, instead of is consisting of but I am not native)
line 63 exploit -> exploits
Documentation navbar Exemples -> Examples
here in the "Unfinished work" box, wtill -> still

Unicode

The paper has some issues rendering some unicode characters

lrnv · 2024-02-04T10:46:59Z

@lucaferranti Thanks a lot for your time and your review. I definitely agree with all the points you mentioned, 100%.

I will split your review into issues on Copulas.jl to be able to start working on each of them with my co-author @Santymax98. @osorensen it might take a while, but I think it is definitely worth it.

lucaferranti · 2024-02-04T17:35:19Z

@editorialbot generate pdf

editorialbot · 2024-02-04T17:36:32Z

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

lrnv · 2024-02-04T18:58:27Z

@editorialbot generate pdf

editorialbot · 2024-02-04T18:59:40Z

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

AnderGray · 2024-02-05T08:52:43Z

@osorensen @lrnv Hi 👋 you can expect my review this week. Overall, looks good

AnderGray · 2024-02-05T08:52:56Z

Review checklist for @AnderGray

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/lrnv/Copulas.jl?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@lrnv) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
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?

Editorial comment on [JOSS submission](openjournals/joss-reviews#6189)

lrnv · 2024-02-23T19:55:27Z

@AnderGray Maybe you could help with lrnv/Copulas.jl#176 ?

lrnv · 2024-02-24T07:52:48Z

@editorialbot set v0.1.21 as version

editorialbot · 2024-02-24T07:52:50Z

Done! version is now v0.1.21

osorensen · 2024-02-24T19:06:44Z

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

Read the text of the paper and offer comments/corrections (as either a list or a pull request)
Check that the archive title, author list, version tag, and the license are correct
Set archive DOI with @editorialbot set <DOI here> as archive
Set version with @editorialbot set <version here> as version
Double check rendering of paper with @editorialbot generate pdf
Specifically check the references with @editorialbot check references and ask author(s) to update as needed
Recommend acceptance with @editorialbot recommend-accept

osorensen · 2024-02-24T19:12:50Z

@lrnv, can you now please complete these tasks?

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

lrnv · 2024-02-24T19:16:01Z

So :

ORCIDS and affilition are OK for both authors.
Release is 0.1.21 as already told to editorialbot.
Zenodo record for the release is there : https://zenodo.org/records/10699969 with DOI https://doi.org/10.5281/zenodo.10699969
I have checked that title and authors list, including orcid, match from the archive to the JOSS paper. (It did not, I edited the archive)
I have checked that the licence match (MIT Licence, I also edited the archive).

osorensen · 2024-02-24T19:57:12Z

@editorialbot set 10.5281/zenodo.6652672 as archive

editorialbot · 2024-02-24T19:57:15Z

Done! archive is now 10.5281/zenodo.6652672

osorensen · 2024-02-24T19:57:33Z

@editorialbot recommend-accept

editorialbot · 2024-02-24T19:57:35Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-02-24T19:58:12Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.1201/9780367803896 is OK
- 10.1201/b18674 is OK
- 10.1214/07-AOS556 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK
- 10.5281/zenodo.7944064 is OK
- 10.5281/zenodo.10412898 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-24T19:58:45Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5048, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon · 2024-02-29T10:07:19Z

@editorialbot accept

editorialbot · 2024-02-29T10:07:29Z

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

editorialbot · 2024-02-29T10:14:08Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Laverny
  given-names: Oskar
  orcid: "https://orcid.org/0000-0002-7508-999X"
- family-names: Jimenez
  given-names: Santiago
  orcid: "https://orcid.org/0000-0002-8198-3656"
contact:
- family-names: Laverny
  given-names: Oskar
  orcid: "https://orcid.org/0000-0002-7508-999X"
doi: 10.5281/zenodo.6652672
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Laverny
    given-names: Oskar
    orcid: "https://orcid.org/0000-0002-7508-999X"
  - family-names: Jimenez
    given-names: Santiago
    orcid: "https://orcid.org/0000-0002-8198-3656"
  date-published: 2024-02-29
  doi: 10.21105/joss.06189
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6189
  title: "Copulas.jl: A fully Distributions.jl-compliant copula package"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06189"
  volume: 9
title: "Copulas.jl: A fully Distributions.jl-compliant copula package"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-02-29T10:14:11Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-02-29T10:14:12Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06189 joss-papers#5070
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06189
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

From Joss openjournals/joss-reviews#6189 (comment)

…182) * Create CITATION.cff From Joss openjournals/joss-reviews#6189 (comment) * Update CITATION.bib * Update README.md * Update index.md

lrnv · 2024-02-29T10:28:46Z

Thanks a lot to @osorensen , @lucaferranti and @AnderGray for this review, the package and its documentation LARGELY improved from the comments and remarks that you brought tot he table, and we still have very good projects for further improvements thanks to @AnderGray.

editorialbot · 2024-02-29T10:53:25Z

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

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

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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06189">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06189/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06189/status.svg
   :target: https://doi.org/10.21105/joss.06189

This is how it will look in your documentation:

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editorialbot added Julia review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Jan 8, 2024

editorialbot assigned osorensen Jan 8, 2024

editorialbot mentioned this issue Jan 8, 2024

[PRE REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6074

Closed

lrnv pushed a commit to lrnv/Copulas.jl that referenced this issue Feb 23, 2024

Remove parentheses in citation (#172)

e5f8d79

Editorial comment on [JOSS submission](openjournals/joss-reviews#6189)

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 24, 2024

editorialbot added accepted published Papers published in JOSS labels Feb 29, 2024

lrnv added a commit to lrnv/Copulas.jl that referenced this issue Feb 29, 2024

Create CITATION.cff

c1a0d80

From Joss openjournals/joss-reviews#6189 (comment)

lrnv mentioned this issue Feb 29, 2024

[Paper] Change citations guidelines to take the paper into account. lrnv/Copulas.jl#182

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[REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6189

[REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6189

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[REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6189

[REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6189

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Documentation

Software paper

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Software paper

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Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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