editorialbot commented 6 months ago

Submitting author: !--author-handle-->@AlCap23@diehlpk<!--end-editor-- Reviewers: @KBodolai, @joshuaeh Archive: 10.5281/zenodo.12084055

Status

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Markdown: [![status](https://joss.theoj.org/papers/6f19f7ae5cffd207a843b2e3a3134a12/status.svg)](https://joss.theoj.org/papers/6f19f7ae5cffd207a843b2e3a3134a12)

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

@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. 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 @diehlpk 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 @joshuaeh

📝 Checklist for @KBodolai

editorialbot commented 6 months ago

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

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editorialbot commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

Paper file info:

📄 Wordcount for paper.md is 1253

✅ The paper includes a Statement of need section

editorialbot commented 6 months ago

License info:

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

editorialbot commented 6 months ago

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

joshuaeh commented 6 months ago

Review checklist for @joshuaeh

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/mathopt/DynamicOED.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 (@AlCap23) 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?

joshuaeh commented 5 months ago

Had an issue on installation: https://github.com/mathopt/DynamicOED.jl/issues/28#issue-2269343131

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 commented 5 months ago

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

diehlpk commented 5 months ago

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

AlCap23 commented 5 months ago

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 commented 5 months ago

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

KBodolai commented 5 months ago

Review checklist for @KBodolai

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/mathopt/DynamicOED.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 (@AlCap23) 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?

KBodolai commented 5 months ago

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:

I can't seem to reproduce the examples other than the example in the home section, more info in mathopt/DynamicOED.jl#30.
(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?
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 commented 5 months ago

Thanks for the review and the approval!

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.

(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?

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 https://github.com/mathopt/DynamicOED.jl/pull/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 commented 5 months ago

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 commented 4 months ago

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 commented 4 months ago

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

diehlpk commented 4 months ago

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

diehlpk commented 4 months ago

@editorialbot remove @imciner2 as reviewer

editorialbot commented 4 months ago

@imciner2 removed from the reviewers list!

diehlpk commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago

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 commented 4 months ago

@editorialbot commands

editorialbot commented 4 months ago

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


# List all available commands
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@editorialbot add @username as reviewer

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# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

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

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

# Set a value for repository
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# Set a value for the archive DOI
@editorialbot set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

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@editorialbot check repository

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@editorialbot check references

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@editorialbot generate pdf

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@editorialbot list reviewers

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@editorialbot create post-review checklist

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diehlpk commented 4 months ago

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
[x] Recommend acceptance with @editorialbot recommend-accept

diehlpk commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

diehlpk commented 4 months ago

Hi @AlCap23 I took a look at the paper as editor and here are my comments:

Figure 1: Please add a unit to the Time is it seconds or milliseconds?
Line 55 add a space between ModelingToolkit.jl and the reference.

diehlpk commented 4 months ago

@AlCap23 if you could address these comments, we could proceed with the paper.

AlCap23 commented 4 months ago

@AlCap23 if you could address these comments, we could proceed with the paper.

@diehlpk I've added the space. Unfortunately, time has no unit in given that it is from our viewpoint just a "scaling" factor ( see also the original publication ), so I would just leave it blank or add days if strictly necessary.

AlCap23 commented 4 months ago

@diehlpk We archived the version v0.1.2 on Zenodo and are good to go 👍 License, Orcid IDs and authors check out.

One minor comment based on my copy-pasta mistake : There is a 1 in the title of the paper hidden, would you be so kind to remove it? Thanks!

diehlpk commented 4 months ago

@editorialbot set v0.1.2 as version

editorialbot commented 4 months ago

Done! version is now v0.1.2

diehlpk commented 4 months ago

@AlCap23 can you please post the DOI for Zenodo?

diehlpk commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

diehlpk commented 4 months ago

@AlCap23 One minor comment based on my copy-pasta mistake : There is a 1 in the title of the paper hidden, would you be so kind to remove it? Thanks!

Not sure where this is happening. I think you should be able to fix that too.

AlCap23 commented 4 months ago

@AlCap23 can you please post the DOI for Zenodo?

10.5281/zenodo.12084055

AlCap23 commented 4 months ago

@AlCap23 One minor comment based on my copy-pasta mistake : There is a 1 in the title of the paper hidden, would you be so kind to remove it? Thanks!

Not sure where this is happening. I think you should be able to fix that too.

I've tried, but not found a way ( maybe it is irrelevant ). This happened during the initial submission

diehlpk commented 4 months ago

@editorialbot set 10.5281/zenodo.12084055 as archive

editorialbot commented 4 months ago

Done! archive is now 10.5281/zenodo.12084055

diehlpk commented 4 months ago

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

diehlpk commented 4 months ago

@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 commented 4 months ago

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 commented 4 months ago

@editorialbot check references

editorialbot commented 4 months ago

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 commented 4 months ago

@editorialbot recommend-accept

editorialbot commented 4 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 4 months ago

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

openjournals / joss-reviews

[REVIEW]: DynamicOED.jl: A Julia package for solving optimum1 experimental design problems #6605

Status

Reviewer instructions & questions

Checklists

Review checklist for @joshuaeh

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @KBodolai

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance