[REVIEW]: Fortuna.jl: Structural and System Reliability Analysis in Julia

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@AkchurinDA@jbytecode<!--end-editor-- Reviewers: @baxmittens, @rafaelorozco Archive: 10.5281/zenodo.13222060

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9df63bb9d4f1722272f85a0fc2249856"><img src="https://joss.theoj.org/papers/9df63bb9d4f1722272f85a0fc2249856/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9df63bb9d4f1722272f85a0fc2249856/status.svg)](https://joss.theoj.org/papers/9df63bb9d4f1722272f85a0fc2249856)

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

@baxmittens & @rafaelorozco, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

✨ 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 @baxmittens

📝 Checklist for @rafaelorozco

jbytecode commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jbytecode commented 1 month ago

@AkchurinDA - Now, I will check the manuscript and the bibliography in a great detail. Meanwhile I am proof-reading please

Create a tagged release of the software with a version number in form of vx.y.z, e.g. v0.10.2, with a caption describing it's belong to a JOSS submission
Please use that tagged release of the software, create a Zenodo archive. The archive should have the same metadata of off the submission, e.g. the title of the submisson, the list of authors, the ORCID's etc.
Please report me the tagged release, the link of the archive, and the DOI provided by the Zenodo.

Thank you in advance.

AkchurinDA commented 1 month ago

@jbytecode,

I have created a Zenodo archive based off the latest release I have (v0.10.1). All of the archive's metadata is based on the submission. Here is all the information you have requested:

Tagged release: v0.10.1 (I have added a note that my submission is based on this release in the release notes)
Link to the archive: https://zenodo.org/records/13222060
DOI provided by Zenodo: https://doi.org/10.5281/zenodo.13222060

Please let me know if there is anything else I should do.

Thanks again!

jbytecode commented 1 month ago

@editorialbot set v0.10.1 as version

editorialbot commented 1 month ago

Done! version is now v0.10.1

jbytecode commented 1 month ago

@editorialbot set 10.5281/zenodo.13222060 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13222060

jbytecode commented 1 month ago

@AkchurinDA - I've just sent a pull request (https://github.com/AkchurinDA/Fortuna.jl/pull/88). This PR includes minor fixes on the text. Please review the changes. If you're agreed with them, please merge. Thank you in advance.

AkchurinDA commented 1 month ago

@editorialbot generate pdf

@jbytecode - Thank you for suggestions, I have just merged the PR. Let us quickly check the paper one more time.

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

AkchurinDA commented 1 month ago

LGTM!

jbytecode commented 1 month ago

@AkchurinDA - When we say "x follows a Normal distribution with zero mean and a constant variance" the world normal is capitalized but it seems thing changes when it comes to saying "x is a standard normal variable", I thought the world normal would be capitalized but it seems leaving it as "normal" is okay.

jbytecode commented 1 month ago

@AkchurinDA - The manuscript and the bibliography seem okay to me. Please take a look at the paper and have a proof read one more time. When you've done with it, please ping me so we can go forward.

AkchurinDA commented 1 month ago

Yes, I understand what you mean, but based on all the literature on UQ I have read, there is no need to capitalize the word "normal" in this particular use case.

OK, I will go through the paper one more time and let you know. Thanks!

AkchurinDA commented 1 month ago

@jbytecode - I have finished the review, I think we can proceed forward.

jbytecode commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.1016/j.jcsr.2023.108327 is OK
- 10.1016/j.jocs.2020.101204 is OK
- 10.1016/j.jcsr.2023.108210 is OK
- 10.21105/joss.03349 is OK
- 10.1061/(ASCE)CP.1943-5487.0000002 is OK
- 10.18637/jss.v098.i16 is OK
- 10.21105/joss.05161 is OK
- 10.1137/141000671 is OK
- 10.1108/JSFE-07-2016-0010 is OK
- 10.1016/j.strusafe.2005.03.002 is OK
- 10.48550/ARXIV.1607.07892 is OK
- 10.21105/joss.06189 is OK
- 10.1016/j.ress.2012.10.008 is OK
- 10.5281/ZENODO.12571718 is OK

MISSING DOIs

- No DOI given, and none found for title: A Review of Recent Features and Improvements Added...
- No DOI given, and none found for title: Turing: A Language for Flexible Probabilistic Infe...

INVALID DOIs

- None

jbytecode commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jbytecode commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

OK DOIs

- 10.1016/j.jcsr.2023.108327 is OK
- 10.1016/j.jocs.2020.101204 is OK
- 10.1016/j.jcsr.2023.108210 is OK
- 10.21105/joss.03349 is OK
- 10.1061/(ASCE)CP.1943-5487.0000002 is OK
- 10.18637/jss.v098.i16 is OK
- 10.21105/joss.05161 is OK
- 10.1137/141000671 is OK
- 10.1108/JSFE-07-2016-0010 is OK
- 10.1016/j.strusafe.2005.03.002 is OK
- 10.48550/ARXIV.1607.07892 is OK
- 10.21105/joss.06189 is OK
- 10.1016/j.ress.2012.10.008 is OK
- 10.5281/ZENODO.12571718 is OK

MISSING DOIs

- No DOI given, and none found for title: A Review of Recent Features and Improvements Added...
- No DOI given, and none found for title: Turing: A Language for Flexible Probabilistic Infe...

INVALID DOIs

- None

editorialbot commented 1 month ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

No declaration for attribute displaystyle of element mfrac
No declaration for attribute displaystyle of element mfrac

jbytecode commented 1 month ago

@AkchurinDA - JOSS pdf compiler does not work well with dfrac instruction of LaTeX. Could you please merge the PR (https://github.com/AkchurinDA/Fortuna.jl/pull/89) that I've just sent? Thank you in advance.

AkchurinDA commented 1 month ago

@jbytecode - Thanks for the PR. I have merged it.

I have also decided to change the type of the input for the limit state function $g(\boldsymbol{x})$ in my example to AbstractVector. This is more general and better approach if the reader will use this example as a starting point for using the package. Hope that's OK.

jbytecode commented 1 month ago

@AkchurinDA - I agree with the change, AbstractVector will handle some other type of data types that inherit the AbstractVector now.

jbytecode commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jbytecode commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

OK DOIs

- 10.1016/j.jcsr.2023.108327 is OK
- 10.1016/j.jocs.2020.101204 is OK
- 10.1016/j.jcsr.2023.108210 is OK
- 10.21105/joss.03349 is OK
- 10.1061/(ASCE)CP.1943-5487.0000002 is OK
- 10.18637/jss.v098.i16 is OK
- 10.21105/joss.05161 is OK
- 10.1137/141000671 is OK
- 10.1108/JSFE-07-2016-0010 is OK
- 10.1016/j.strusafe.2005.03.002 is OK
- 10.48550/ARXIV.1607.07892 is OK
- 10.21105/joss.06189 is OK
- 10.1016/j.ress.2012.10.008 is OK
- 10.5281/ZENODO.12571718 is OK

MISSING DOIs

- No DOI given, and none found for title: A Review of Recent Features and Improvements Added...
- No DOI given, and none found for title: Turing: A Language for Flexible Probabilistic Infe...

INVALID DOIs

- None

editorialbot commented 1 month ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5723, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 month ago

@AkchurinDA - as track editor, I'll proofread this next and let you know what else, if anything, is needed from you.

AkchurinDA commented 1 month ago

@danielskatz - Great, thanks! Please let me know if there is anything else I can do.

danielskatz commented 1 month ago

@AkchurinDA - I'm suggesting changes in your paper in https://github.com/AkchurinDA/Fortuna.jl/pull/90 - please merge this, or let me know what you disagree with, then we can continue.

AkchurinDA commented 1 month ago

@danielskatz - Thank you for the suggestions. I have merged the PR with no amendments to its content.

danielskatz commented 1 month ago

@editorialbot recommend-accept

👋 @AkchurinDA - please check this once it is produced and let me know that none of the changes have hurt anything, then we can proceed

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 month ago

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

OK DOIs

- 10.1016/j.jcsr.2023.108327 is OK
- 10.1016/j.jocs.2020.101204 is OK
- 10.1016/j.jcsr.2023.108210 is OK
- 10.21105/joss.03349 is OK
- 10.1061/(ASCE)CP.1943-5487.0000002 is OK
- 10.18637/jss.v098.i16 is OK
- 10.21105/joss.05161 is OK
- 10.1137/141000671 is OK
- 10.1108/JSFE-07-2016-0010 is OK
- 10.1016/j.strusafe.2005.03.002 is OK
- 10.48550/ARXIV.1607.07892 is OK
- 10.21105/joss.06189 is OK
- 10.1016/j.ress.2012.10.008 is OK
- 10.5281/ZENODO.12571718 is OK

MISSING DOIs

- No DOI given, and none found for title: A Review of Recent Features and Improvements Added...
- No DOI given, and none found for title: Turing: A Language for Flexible Probabilistic Infe...

INVALID DOIs

- None

editorialbot commented 1 month ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5724, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

AkchurinDA commented 1 month ago

@danielskatz - LGTM, I think we can proceed forward.

danielskatz commented 1 month ago

@editorialbot accept

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

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

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CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Akchurin given-names: Damir orcid: "https://orcid.org/0000-0003-0849-4917" contact: - family-names: Akchurin given-names: Damir orcid: "https://orcid.org/0000-0003-0849-4917" doi: 10.5281/zenodo.13222060 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Akchurin given-names: Damir orcid: "https://orcid.org/0000-0003-0849-4917" date-published: 2024-08-05 doi: 10.21105/joss.06967 issn: 2475-9066 issue: 100 journal: Journal of Open Source Software publisher: name: Open Journals start: 6967 title: "Fortuna.jl: Structural and System Reliability Analysis in Julia" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06967" volume: 9 title: "Fortuna.jl: Structural and System Reliability Analysis in Julia" ```

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editorialbot commented 1 month ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 month ago

🚨🚨🚨 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/5725
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06967
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 1 month ago

Congratulations to @AkchurinDA (Damir Akchurin) on your publication!!

And thanks to @baxmittens and @rafaelorozco for reviewing, and to @jbytecode for editing! JOSS relies on volunteers like you to make this process of recognizing and improving open source software work

editorialbot commented 1 month ago

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AkchurinDA commented 1 month ago

Thank you all for putting in time and effort into reviewing and editing the submission, @danielskatz @jbytecode @baxmittens @rafaelorozco! I really appreciate it!

The review process in the Journal of Open Source Software is just great - it was such a great experience compared to more conventional journals!

openjournals / joss-reviews