[REVIEW]: DynamicOED.jl: A Julia package for solving optimum1 experimental design problems

[editorialbot]

Submitting author: @AlCap23 (Julius Martensen)
Repository: https://github.com/mathopt/DynamicOED.jl
Branch with paper.md (empty if default branch):
Version: v0.1.2
Editor: @diehlpk
Reviewers: @KBodolai, @joshuaeh
Archive: 10.5281/zenodo.12084055

Status

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Reviewers and authors:

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Reviewer instructions & questions

@KBodolai & @imciner2 & @joshuaeh, 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 @joshuaeh

📝 Checklist for @KBodolai

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[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.7738525 is OK
- 10.11588/heidok.00002980 is OK
- 10.1007/978-3-319-93031-2_27 is OK
- 10.1016/S0168-9274(99)00020-3 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.1137/110835098 is OK
- 10.1007/s10107-004-0559-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1292.5 files/s, 113404.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           14            262            168           1395
Markdown                         7            143              0            421
YAML                             6              9              4            141
TeX                              1              8              0            118
TOML                             3              5              0             46
-------------------------------------------------------------------------------
SUM:                            31            427            172           2121
-------------------------------------------------------------------------------

Commit count by author:

    61	JuliusMartensen
    48	Christoph Plate

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1253

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[joshuaeh]

Review checklist for @joshuaeh

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/mathopt/DynamicOED.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 (@AlCap23) 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?

[joshuaeh]

Had an issue on installation: mathopt/DynamicOED.jl#28 (comment)

Resolved problem was on my end. Looks good from my perspective. One minor note that I would add how to add while not in the registry: ] add https://github.com/mathopt/DynamicOED.jl and keep it even when in the registry just as a helpful redundancy

[diehlpk]

Hi @KBodolai, @imciner2 how is your review going?

[diehlpk]

Hi @KBodolai, @imciner2 how is your review going?

[AlCap23]

Hey @diehlpk . Thanks for your efforts!

If needed, I asked two people I know of if they could jump in for a review:

• @mohamed82008 ; Areas of expertise include OED, Optimization in general and MINLP; Full disclosure: I am working with him on another project within Pumas
• @baggepinnen ; Areas of expertise include Control, Modeling and Inference; He is also working on ModelingToolkit.jl.

Let me know if I can provide any more help on this.

[KBodolai]

Hi @diehlpk , apologies for the delay, finally moving forward with it!

[KBodolai]

Review checklist for @KBodolai

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/mathopt/DynamicOED.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 (@AlCap23) 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?

[KBodolai]

Overall I'm quite happy with the submission, the text in the paper reads well and the software looks solid!

A couple of small things that I noticed while reviewing, preventing me from ticking the last two boxes:

1. I can't seem to reproduce the examples other than the example in the home section, more info in MethodError in examples. mathopt/DynamicOED.jl#30.
2. (A bit more of a nitpick) As for the community guidelines tickbox, I've not seen any guidelines in the documentation referring to contributions. (issues and support can easily be reported through the gh issues). @AlCap23 , could it be possible to add a contributing.md file, or anything in the docs clarifying this?
3. There seems to be an error rendering the figure in the paper. I'm not entirely sure, but it may be because it's a pdf. I did a quick test with a screenshot and it renders well saved as a png, so I'd suggest exporting paper/figures/lotka.pdf as a png and replacing it. (I'd do a pull request with it, but it's probably best to export it directly as a png to preserve image quality)

[AlCap23]

Thanks for the review and the approval!

1. I can't seem to reproduce the examples other than the example in the home section, more info in MethodError in examples. mathopt/DynamicOED.jl#30.
2. (A bit more of a nitpick) As for the community guidelines tickbox, I've not seen any guidelines in the documentation referring to contributions. (issues and support can easily be reported through the gh issues). @AlCap23 , could it be possible to add a contributing.md file, or anything in the docs clarifying this?
3. There seems to be an error rendering the figure in the paper. I'm not entirely sure, but it may be because it's a pdf. I did a quick test with a screenshot and it renders well saved as a png, so I'd suggest exporting paper/figures/lotka.pdf as a png and replacing it. (I'd do a pull request with it, but it's probably best to export it directly as a png to preserve image quality)

Should be handled via mathopt/DynamicOED.jl#31
Instead of a seperate contribution guide, we choose to follow the ColPrac given by SciML ( as we are already closely related to this part of Julias Ecosystem ).

[KBodolai]

fantastic, thanks for checking so quickly! I've verified that the examples are now working and provide the expected results.

Good to hear about the separate contribution guide, it could be a good idea to mention it in the docs though (thinking of people that may be newer to the Julia ecosystem).

[diehlpk]

Hi @imciner2 the other two reviewers finished their reviews. Do you think you can finish your review in the next two weeks? If not I will go ahead with the other two reviews.

[diehlpk]

Hi @KBodolai and @joshuaeh. Thanks for finishing your reviews.

[diehlpk]

Hi @imciner2 can you please estimate when you will finish your review?

[diehlpk]

@editorialbot remove @imciner2 as reviewer

[editorialbot]

@imciner2 removed from the reviewers list!

[diehlpk]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.7738525 is OK
- 10.11588/heidok.00002980 is OK
- 10.1007/978-3-319-93031-2_27 is OK
- 10.1016/S0168-9274(99)00020-3 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.1137/110835098 is OK
- 10.1007/s10107-004-0559-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

[diehlpk]

@AlCap23 The title is wrong on Zendodo. Can you please change the tittle to match with the paper?

[diehlpk]

@AlCap23 if you log in to Zenodo, you should be able to edit the title and other meta data. See the screenshot below with one from my projects. I do not have access to your project to change that.

[AlCap23]

I've changed the title to

DynamicOED.jl: A Julia package for solving optimum1 experimental design problems

without the typo :) . Does this work for you @diehlpk ?

[diehlpk]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.7738525 is OK
- 10.11588/heidok.00002980 is OK
- 10.1007/978-3-319-93031-2_27 is OK
- 10.1016/S0168-9274(99)00020-3 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.1137/110835098 is OK
- 10.1007/s10107-004-0559-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

[diehlpk]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.7738525 is OK
- 10.11588/heidok.00002980 is OK
- 10.1007/978-3-319-93031-2_27 is OK
- 10.1016/S0168-9274(99)00020-3 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.1137/110835098 is OK
- 10.1007/s10107-004-0559-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

[diehlpk]

@AlCap23 you are good now and I recommended the paper for acceptance.

[editorialbot]

👋 @openjournals/csism-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#5512, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@AlCap23 - as the track editor, I've proofread the paper, and suggest the changes in mathopt/DynamicOED.jl#33 Please merge this, or let me know what you disagree with, then we can continue to acceptance and publication.

[AlCap23]

Thanks @danielskatz. I've approved the changes and merged.

And also thanks to @diehlpk for his guidance and management throughout the review process and @joshuaeh and @KBodolai for the reviews and suggestions!

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.5281/zenodo.7738525 is OK
- 10.11588/heidok.00002980 is OK
- 10.1007/978-3-319-93031-2_27 is OK
- 10.1016/S0168-9274(99)00020-3 is OK
- 10.48550/arXiv.2103.05244 is OK
- 10.1137/110835098 is OK
- 10.1007/s10107-004-0559-y is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#5513, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Martensen
  given-names: Carl Julius
  orcid: "https://orcid.org/0000-0003-4143-3040"
- family-names: Plate
  given-names: Christoph
  orcid: "https://orcid.org/0000-0003-0354-8904"
- family-names: Sager
  given-names: Sebastian
  orcid: "https://orcid.org/0000-0002-0283-9075"
contact:
- family-names: Martensen
  given-names: Carl Julius
  orcid: "https://orcid.org/0000-0003-4143-3040"
doi: 10.5281/zenodo.12084055
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Martensen
    given-names: Carl Julius
    orcid: "https://orcid.org/0000-0003-4143-3040"
  - family-names: Plate
    given-names: Christoph
    orcid: "https://orcid.org/0000-0003-0354-8904"
  - family-names: Sager
    given-names: Sebastian
    orcid: "https://orcid.org/0000-0002-0283-9075"
  date-published: 2024-06-19
  doi: 10.21105/joss.06605
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6605
  title: "DynamicOED.jl: A Julia package for solving optimum
    experimental design problems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06605"
  volume: 9
title: "DynamicOED.jl: A Julia package for solving optimum experimental
  design problems"

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.

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[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06605 joss-papers#5514
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2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @AlCap23 (Julius Martensen) and co-authors on your publication!!

And thanks to @KBodolai and @joshuaeh for reviewing, and to @diehlpk for editing!
JOSS depends on volunteers and we couldn't do this with you

[editorialbot]

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