[REVIEW]: pyGeo: A geometry package for multidisciplinary design optimization #5319

editorialbot · 2023-03-31T14:58:19Z

Submitting author: @hajdik (Hannah Hajdik)
Repository: https://github.com/mdolab/pygeo
Branch with paper.md (empty if default branch): main
Version: v1.13.0
Editor: @drvinceknight
Reviewers: @HaoZeke, @zhaowei0566
Archive: 10.5281/zenodo.8027706

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4e9c207dac16a07c9aca05eead19c45a"><img src="https://joss.theoj.org/papers/4e9c207dac16a07c9aca05eead19c45a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4e9c207dac16a07c9aca05eead19c45a/status.svg)](https://joss.theoj.org/papers/4e9c207dac16a07c9aca05eead19c45a)

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

@HaoZeke & @zhaowei0566, 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 @drvinceknight 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 @zhaowei0566

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

editorialbot · 2023-03-31T14:58:21Z

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

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editorialbot · 2023-03-31T14:58:25Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.31 s (367.9 files/s, 124343.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          80           6016          10046          19067
SVG                              3              0             21           1737
reStructuredText                19            279            259            519
TeX                              2             38              0            343
Markdown                         4             55              0            211
DOS Batch                        1             23              1            166
YAML                             2              4              4             37
Bourne Shell                     3              3              3             15
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           115           6422          10341          22104
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-03-31T14:58:27Z

Wordcount for paper.md is 1782

editorialbot · 2023-03-31T14:58:53Z

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

OK DOIs

- 10.2514/6.2010-9231 is OK
- 10.2514/6.2022-0004 is OK
- 10.2514/6.2013-3073 is OK
- 10.1145/15886.15903 is OK
- 10.2514/1.29958 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.2514/1.C032150 is OK
- 10.2514/1.J052255 is OK
- 10.2514/2.1391 is OK
- 10.21105/joss.02564 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/6.2021-3032 is OK
- 10.2514/1.j053813 is OK
- 10.2514/6.2022-3931 is OK
- 10.1145/838250.838251 is OK
- 10.2514/1.J056550 is OK
- 10.1007/s00366-020-01247-w is OK
- 10.2514/6.2022-2177 is OK
- 10.1016/j.oceaneng.2022.112051 is OK
- 10.2514/1.C036216 is OK
- 10.1016/j.compstruct.2021.113937 is OK
- 10.2514/6.2022-1289 is OK
- 10.5194/wes-4-163-2019 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/1.C036103 is OK
- 10.1017/9781108980647 is OK
- 10.2514/3.58379 is OK
- 10.2514/1.C032491 is OK
- 10.2514/1.J058366 is OK
- 10.2514/6.2023-0726 is OK
- 10.1016/j.actaastro.2018.02.011 is OK
- 10.2514/1.J057294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-31T14:59:41Z

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

danielskatz · 2023-04-20T17:56:07Z

👋 @drvinceknight - how is this review coming along? I can't tell if anything has happened since it started.

zhaowei0566 · 2023-04-30T23:12:27Z

@danielskatz This is a very powerful package for the airplane outer model line design, which enables a high-fidelity MDAO study. I have followed this optimization framework for a while. I have no problem with the manuscript just a minor question about the claim given in Line 54, “Design variables formulated from groupings of FFD control points often exhibit ill conditioning”, do you have any relevant reference to support this, or was it studied in Wu et al. 2022?

The manuscript has covered relevant information and meets the JOSS criteria, https://joss.readthedocs.io/en/latest/review_criteria.html. Good work!

drvinceknight · 2023-05-01T09:16:33Z

@zhaowei0566 would you be able to complete your review checklist please?

@editorialbot generate my checklist

Likewise, @HaoZeke if you could let me know how the review is going that would be appreciated.

zhaowei0566 · 2023-05-01T21:15:21Z

Review checklist for @zhaowei0566

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/mdolab/pygeo?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@hajdik) 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?

hajdik · 2023-05-12T19:54:59Z

@editorialbot generate pdf

editorialbot · 2023-05-12T19:56:47Z

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

hajdik · 2023-05-12T20:07:46Z

just a minor question about the claim given in Line 54, “Design variables formulated from groupings of FFD control points often exhibit ill conditioning”, do you have any relevant reference to support this, or was it studied in Wu et al. 2022?

This was studied in Wu et al. 2022. I moved the reference to clarify this @zhaowei0566.

zhaowei0566 · 2023-05-13T16:43:04Z

Thanks, @hajdik, I have no further question.

drvinceknight · 2023-05-17T13:59:15Z

Thanks @zhaowei0566, can I double check that all the points in your checklist are now complete?

zhaowei0566 · 2023-05-22T20:30:18Z

@drvinceknight Yes, I have completed the checklist.

drvinceknight · 2023-05-23T08:00:11Z

Great, thanks @zhaowei0566.

drvinceknight · 2023-05-23T08:00:40Z

@editorialbot check references

editorialbot · 2023-05-23T08:00:49Z

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

OK DOIs

- 10.2514/6.2010-9231 is OK
- 10.2514/6.2022-0004 is OK
- 10.2514/6.2013-3073 is OK
- 10.1145/15886.15903 is OK
- 10.2514/1.29958 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.2514/1.C032150 is OK
- 10.2514/1.J052255 is OK
- 10.2514/2.1391 is OK
- 10.21105/joss.02564 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/6.2021-3032 is OK
- 10.2514/1.j053813 is OK
- 10.2514/6.2022-3931 is OK
- 10.1145/838250.838251 is OK
- 10.2514/1.J056550 is OK
- 10.1007/s00366-020-01247-w is OK
- 10.2514/6.2022-2177 is OK
- 10.1016/j.oceaneng.2022.112051 is OK
- 10.2514/1.C036216 is OK
- 10.1016/j.compstruct.2021.113937 is OK
- 10.2514/6.2022-1289 is OK
- 10.5194/wes-4-163-2019 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/1.C036103 is OK
- 10.1017/9781108980647 is OK
- 10.2514/3.58379 is OK
- 10.2514/1.C032491 is OK
- 10.2514/1.J058366 is OK
- 10.2514/6.2023-0726 is OK
- 10.1016/j.actaastro.2018.02.011 is OK
- 10.2514/1.J057294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

drvinceknight · 2023-05-23T08:05:12Z

@editorialbot generate pdf

editorialbot · 2023-05-23T08:06:57Z

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

drvinceknight · 2023-05-23T08:43:30Z

This looks good to me. Could you make a tagged release and archive, and report the version number and archive DOI in the review thread. Please make sure the archive deposit has the correct metadata (title and author list) which must match the paper.

ewu63 · 2023-06-12T17:06:32Z

Hi @drvinceknight, we have released a version which is archived on zenodo.
version number: v1.13.0
DOI: 10.5281/zenodo.8027706

The paper branch has also changed to main now that we have merged mdolab/pygeo#203.
Please let us know if there's anything else you need.

editorialbot · 2023-07-02T03:13:15Z

Done! branch is now main

ewu63 · 2023-07-02T03:13:23Z

@editorialbot generate pdf

editorialbot · 2023-07-02T03:14:58Z

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

drvinceknight · 2023-07-07T15:22:22Z

Thanks for your patience, taking care of this now.

drvinceknight · 2023-07-07T15:24:08Z

@editorialbot set 10.5281/zenodo.8027706 as archive

editorialbot · 2023-07-07T15:24:10Z

Done! archive is now 10.5281/zenodo.8027706

drvinceknight · 2023-07-07T15:24:58Z

@editorialbot set v1.13.0 as version

editorialbot · 2023-07-07T15:25:01Z

Done! version is now v1.13.0

drvinceknight · 2023-07-07T15:25:21Z

@editorialbot recommend-accept

editorialbot · 2023-07-07T15:25:22Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-07-07T15:25:30Z

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

OK DOIs

- 10.2514/6.2010-9231 is OK
- 10.2514/6.2022-0004 is OK
- 10.2514/6.2013-3073 is OK
- 10.1145/15886.15903 is OK
- 10.2514/1.29958 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.2514/1.C032150 is OK
- 10.2514/1.J052255 is OK
- 10.2514/2.1391 is OK
- 10.21105/joss.02564 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/6.2021-3032 is OK
- 10.2514/1.j053813 is OK
- 10.2514/6.2022-3931 is OK
- 10.1145/838250.838251 is OK
- 10.2514/1.J056550 is OK
- 10.1007/s00366-020-01247-w is OK
- 10.2514/6.2022-2177 is OK
- 10.1016/j.oceaneng.2022.112051 is OK
- 10.2514/1.C036216 is OK
- 10.1016/j.compstruct.2021.113937 is OK
- 10.2514/6.2022-1289 is OK
- 10.5194/wes-4-163-2019 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/1.C036103 is OK
- 10.1017/9781108980647 is OK
- 10.2514/3.58379 is OK
- 10.2514/1.C032491 is OK
- 10.2514/1.J058366 is OK
- 10.2514/6.2023-0726 is OK
- 10.1016/j.actaastro.2018.02.011 is OK
- 10.2514/1.J057294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-07T15:27:33Z

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

ID ref-Brelje2021a already defined

hajdik · 2023-07-07T18:50:32Z

paper.bib has been updated to remove the duplicate citation.

drvinceknight · 2023-07-19T10:18:40Z

@editorialbot recommend-accept

editorialbot · 2023-07-19T10:18:41Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-07-19T10:18:46Z

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

OK DOIs

- 10.2514/6.2010-9231 is OK
- 10.2514/6.2022-0004 is OK
- 10.2514/6.2013-3073 is OK
- 10.1145/15886.15903 is OK
- 10.2514/1.29958 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.2514/1.C032150 is OK
- 10.2514/1.J052255 is OK
- 10.2514/2.1391 is OK
- 10.21105/joss.02564 is OK
- 10.2514/6.2021-1132 is OK
- 10.2514/6.2021-3032 is OK
- 10.2514/1.j053813 is OK
- 10.2514/6.2022-3931 is OK
- 10.1145/838250.838251 is OK
- 10.2514/1.J056550 is OK
- 10.1007/s00366-020-01247-w is OK
- 10.2514/6.2022-2177 is OK
- 10.1016/j.oceaneng.2022.112051 is OK
- 10.2514/1.C036216 is OK
- 10.1016/j.compstruct.2021.113937 is OK
- 10.2514/6.2022-1289 is OK
- 10.5194/wes-4-163-2019 is OK
- 10.2514/1.C036103 is OK
- 10.1017/9781108980647 is OK
- 10.2514/3.58379 is OK
- 10.2514/1.C032491 is OK
- 10.2514/1.J058366 is OK
- 10.2514/6.2023-0726 is OK
- 10.1016/j.actaastro.2018.02.011 is OK
- 10.2514/1.J057294 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-07-19T10:20:42Z

👋 @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#4410, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-07-19T16:48:41Z

@hajdik - I'm now proofreading this paper to get ready to process it further towards publication. While I do so, I notice that the zenodo archive doesn't have any ORCIDs for the authors, while the paper does. If you want to, you can edit the Zenodo metadata to add ORCIDs. This is up to you to decide.

danielskatz · 2023-07-19T16:51:16Z

@editorialbot accept

This all looks good, so I'm going forward with accepting it (the zenodo metadata can still be changed, if you want, as it's independent)

editorialbot · 2023-07-19T16:51:18Z

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

editorialbot · 2023-07-19T16:53:06Z

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: Hajdik
  given-names: Hannah M.
  orcid: "https://orcid.org/0000-0002-5103-7159"
- family-names: Yildirim
  given-names: Anil
  orcid: "https://orcid.org/0000-0002-1814-9191"
- family-names: Wu
  given-names: Neil
  orcid: "https://orcid.org/0000-0001-8856-9661"
- family-names: Brelje
  given-names: Benjamin J.
  orcid: "https://orcid.org/0000-0002-9819-3028"
- family-names: Seraj
  given-names: Sabet
  orcid: "https://orcid.org/0000-0002-7364-0071"
- family-names: Mangano
  given-names: Marco
  orcid: "https://orcid.org/0000-0001-8495-3578"
- family-names: Anibal
  given-names: Joshua L.
  orcid: "https://orcid.org/0000-0002-7795-2523"
- family-names: Jonsson
  given-names: Eirikur
  orcid: "https://orcid.org/0000-0002-5166-3889"
- family-names: Adler
  given-names: Eytan J.
  orcid: "https://orcid.org/0000-0002-8716-1805"
- family-names: Mader
  given-names: Charles A.
  orcid: "https://orcid.org/0000-0002-2744-1151"
- family-names: Kenway
  given-names: Gaetan K. W.
  orcid: "https://orcid.org/0000-0003-1352-5458"
- family-names: Martins
  given-names: Joaquim R. R. A.
  orcid: "https://orcid.org/0000-0003-2143-1478"
doi: 10.5281/zenodo.8027706
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hajdik
    given-names: Hannah M.
    orcid: "https://orcid.org/0000-0002-5103-7159"
  - family-names: Yildirim
    given-names: Anil
    orcid: "https://orcid.org/0000-0002-1814-9191"
  - family-names: Wu
    given-names: Neil
    orcid: "https://orcid.org/0000-0001-8856-9661"
  - family-names: Brelje
    given-names: Benjamin J.
    orcid: "https://orcid.org/0000-0002-9819-3028"
  - family-names: Seraj
    given-names: Sabet
    orcid: "https://orcid.org/0000-0002-7364-0071"
  - family-names: Mangano
    given-names: Marco
    orcid: "https://orcid.org/0000-0001-8495-3578"
  - family-names: Anibal
    given-names: Joshua L.
    orcid: "https://orcid.org/0000-0002-7795-2523"
  - family-names: Jonsson
    given-names: Eirikur
    orcid: "https://orcid.org/0000-0002-5166-3889"
  - family-names: Adler
    given-names: Eytan J.
    orcid: "https://orcid.org/0000-0002-8716-1805"
  - family-names: Mader
    given-names: Charles A.
    orcid: "https://orcid.org/0000-0002-2744-1151"
  - family-names: Kenway
    given-names: Gaetan K. W.
    orcid: "https://orcid.org/0000-0003-1352-5458"
  - family-names: Martins
    given-names: Joaquim R. R. A.
    orcid: "https://orcid.org/0000-0003-2143-1478"
  date-published: 2023-07-19
  doi: 10.21105/joss.05319
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5319
  title: "pyGeo: A geometry package for multidisciplinary design
    optimization"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05319"
  volume: 8
title: "pyGeo: A geometry package for multidisciplinary design
  optimization"

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 · 2023-07-19T16:53:10Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-07-19T16:53:11Z

🚨🚨🚨 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.05319 joss-papers#4413
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05319
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2023-07-19T16:58:46Z

Congratulations to @hajdik (Hannah Hajdik) and co-authors on your publication!!

And thanks to @HaoZeke and @zhaowei0566 for reviewing, and to @drvinceknight for editing!
We couldn't do this without your voluntary efforts

editorialbot · 2023-07-19T16:58:48Z

🎉🎉🎉 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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</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05319/status.svg
   :target: https://doi.org/10.21105/joss.05319

This is how it will look in your documentation:

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editorialbot · 2024-05-08T12:54:41Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5322

editorialbot added Python review Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Mar 31, 2023

editorialbot assigned drvinceknight Mar 31, 2023

editorialbot mentioned this issue Mar 31, 2023

[PRE REVIEW]: pyGeo: A geometry package for multidisciplinary design optimization #5239

Closed

hajdik mentioned this issue May 24, 2023

Add JOSS paper mdolab/pygeo#203

Merged

13 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 19, 2023

editorialbot added accepted published Papers published in JOSS labels Jul 19, 2023

danielskatz closed this as completed Jul 19, 2023

[REVIEW]: pyGeo: A geometry package for multidisciplinary design optimization #5319

[REVIEW]: pyGeo: A geometry package for multidisciplinary design optimization #5319

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editorialbot commented Mar 31, 2023 •

edited

zhaowei0566 commented May 1, 2023 •

edited