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

[editorialbot]

Submitting author: !--author-handle-->@AkchurinDA<!--end-author-handle-- (Damir Akchurin) Repository: https://github.com/AkchurinDA/Fortuna.jl Branch with paper.md (empty if default branch): JOSS Version: v0.10.1 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @baxmittens, @rafaelorozco Archive: 10.5281/zenodo.13222060

Status

Status badge code:

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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

[editorialbot]

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

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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.12571719 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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1011.6 files/s, 113887.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           46            980            982           3282
SVG                              3              0              0           1813
Markdown                        22            447              0           1230
TeX                              2             25              0            339
YAML                             7              0              3            185
TOML                             2              4              0             39
CSS                              1              2              6              7
-------------------------------------------------------------------------------
SUM:                            83           1458            991           6895
-------------------------------------------------------------------------------

Commit count by author:

   214  Damir Akchurin
    15  CompatHelper Julia
    14  AkchurinDA
     2  dependabot[bot]

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 992

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[jbytecode]

@baxmittens, @rafaelorozco

This is the review thread. Firstly you can create you task list by typing

@editorialbot generate my checklist

Whenever you finish a task, you can check off of the corresponding task item. The review is interactive, so that means, you don't need to push a full review report after all the task finishes, rather, in each step you can ask questions, create pull requests in the target repo, and interact with the other reviewers and the editor.

Thank you in advance.

[baxmittens]

Review checklist for @baxmittens

Conflict of interest

• [x] 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

• [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 https://github.com/AkchurinDA/Fortuna.jl?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@AkchurinDA) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[baxmittens]

Hi @AkchurinDA

I ran Grammarly over your paper and created a pull request.

https://github.com/AkchurinDA/Fortuna.jl/pull/85

Double-check carefully before accepting the changes or rejecting them as you like.

I will continue to review it later this week. From what I have seen, it looks like an exciting package.

[AkchurinDA]

Hi @baxmittens,

Thank you very much for the suggestions. I have reviewed and merged your pull request.

[rafaelorozco]

Review checklist for @rafaelorozco

Conflict of interest

• [x] 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

• [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 https://github.com/AkchurinDA/Fortuna.jl?
• [x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@AkchurinDA) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] 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.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] 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

• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[AkchurinDA]

Hi @baxmittens and @rafaelorozco,

I just wanted to say thank you for starting the review process so quick!

[baxmittens]

Hi all, I was inactive for a while (vacation), I will continue with the revue tomorrow.

[AkchurinDA]

Hi @baxmittens,

Thanks for the heads up. Hope you had a good time off.

[rafaelorozco]

I have no such justification, I have been doing a couple checkmarks a day. I hope that my pace is acceptable!

I was thinking that community guidelines specifically for how to contribute to the software would be nice. I see you have a section in the readme for raising issue so maybe just add contribute guidelines there to make that clear.

[AkchurinDA]

Hi @rafaelorozco,

Thank you for the suggestion. I will add a simple contribution guideline in a few hours.

[AkchurinDA]

@rafaelorozco,

I have added a simple contribution guideline here. Please let me know if that works and if you want to see anything else in the repo.

[AkchurinDA]

@editorialbot generate pdf

[editorialbot]

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

[AkchurinDA]

Hi @baxmittens @rafaelorozco,

Hope your summer is going well!

I just wanted to kindly inquire about the status of the review process. If there is anything you would like to see in the package or its documentation to speed up the review, please do not hesitate to let me know. I would be more than happy to provide any necessary information ASAP!

Thank you!

[AkchurinDA]

Hi @jbytecode,

Hope you are doing well!

I wanted to ask a quick question. I want to push out a small non-breaking update to the package, is it somehow possible to update the version of the package referenced in the submission?

Thank you!

[baxmittens]

Hi @jbytecode,

Hope you are doing well!

I wanted to ask a quick question. I want to push out a small non-breaking update to the package, is it somehow possible to update the version of the package referenced in the submission?

Thank you!

As far as I know, you can do this without a problem. You have to create a Zenodo archive of the most recent version of your package after the paper is accepted. This archive is then linked with the paper together with the GitHub page of the package.

[baxmittens]

@AkchurinDA Can you add authors to your citation of SciML/Surrogates.jl? According to the Zenodo archive, it should be something like Bessi, L. et. al.

[AkchurinDA]

@baxmittens

@AkchurinDA Can you add authors to your citation of SciML/Surrogates.jl? According to the Zenodo archive, it should be something like Bessi, L. et. al.

Sure, I will update right now.

[baxmittens]

@AkchurinDA I will thoroughly review the documentation and reproduce a few examples with the software, and then I'm done. I should be able to do that by the beginning of next week.

[rafaelorozco]

Nothing on my side to speed up, i have been slowly going through the checklist. I just finished the checklist. I can send a short report soon but I can already say that I am satisfied with the current state of the package/writeup and recommend them for publication in JOSS.

[AkchurinDA]

@editorialbot generate pdf

@baxmittens - I have updated the author list for the reference on Surrogate.jl package. Thanks for catching it!

@rafaelorozco - Thank you very much for going over the checklist so quickly, I appreciate it!

[editorialbot]

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

[AkchurinDA]

@editorialbot commands

[editorialbot]

Hello @AkchurinDA, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[jbytecode]

@AkchurinDA - sure, merge your commits and provide the link of the changes here so we can track what's new.

[AkchurinDA]

@jbytecode - here is link to the PR that fixed a problem I had with the Latin Hypercube Sampling technique, which was failing for very large number of samples (>1E8). I have triggered the JuliaRegiatrator bot, new version (V0.10.1) should be up soon.

[baxmittens]

@AkchurinDA One thing I noticed in the documentation concerns the nomenclature. You create distributions from their moments...so far, so good, but why is the second moment the standard deviation and not the variance?

[AkchurinDA]

Hi @baxmittens,

This is a great question. This is actually done by design because all of the literature in the field of Structural and System Reliability Analysis typically report the statistic of random variables in terms of the mean $\mu$ and coefficient of variation $V = \sigma / \mu$ (or standard deviation $\sigma$) values. Here are just a few examples:

• https://ascelibrary.org/doi/full/10.1061/%28ASCE%29ST.1943-541X.0002011
• https://www.sciencedirect.com/science/article/pii/S0143974X23004376
• https://www.sciencedirect.com/science/article/pii/S0143974X23005540
• https://www.sciencedirect.com/science/article/pii/0167473082900121

Hope this answers your question.

[AkchurinDA]

@baxmittens - Apologies, I didn't think the reply through completely. Please let me know if you don't have access to the papers through your institution, I will organize a small Dropbox folder with their PDFs and share the link with you!

[AkchurinDA]

Hi @baxmittens,

Hope everything is well.

Here is a link to a Dropbox folder with the PDFs of the papers I have mentioned earlier.

Please let me know if there is anything else I can do to help speed up the review.

Thanks!

[AkchurinDA]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@baxmittens, @rafaelorozco - May I have a review update please?

[AkchurinDA]

HI @jbytecode,

I believe that @rafaelorozco has already recommended the package for publication.

Nothing on my side to speed up, i have been slowly going through the checklist. I just finished the checklist. I can send a short report soon but I can already say that I am satisfied with the current state of the package/writeup and recommend them for publication in JOSS.

[rafaelorozco]

Correct! The report would include nothing apart from what codes/examples I ran to justify my checkmarks. Sorry for the delay, I could make the report for posteriority tomorrow but my decision remains the same.

[jbytecode]

@baxmittens - may I have a review update please?

[baxmittens]

Sorry for the delay. I am done with my list and would recommend publication.

[AkchurinDA]

@rafaelorozco @baxmittens - thanks you for recommending the paper for publication! Appreciate you spending the time on the review.

@jbytecode - should I create a Zenodo archive of the latest version of the package?

[AkchurinDA]

@jbytecode - I took some liberty of creating a Zenodo archive, here is a link to the record to be referenced (13222060).

[jbytecode]

Please be patient, I will introduce the instructions soon.

[jbytecode]

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

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

[jbytecode]

@editorialbot check references

[editorialbot]

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]

Note for missing DOIs: I have performed a Crossref search but failed to find DOI's for those two citations