[REVIEW]: ProgPy: Python Packages for Prognostics and Health Management of Engineering Systems

[editorialbot]

Submitting author: @teubert (Chris Teubert)
Repository: https://github.com/nasa/prog_models
Branch with paper.md (empty if default branch): paper
Version: v1.5
Editor: @kellyrowland
Reviewers: @tbsexton, @nkrusch
Archive: 10.5281/zenodo.8097013

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/86cc587435ae9f766eb67e0b22d49a67/status.svg)](https://joss.theoj.org/papers/86cc587435ae9f766eb67e0b22d49a67)

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

@matthewjdaigle & @tbsexton, 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 @kellyrowland 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 @tbsexton

📝 Checklist for @nkrusch

[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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (544.0 files/s, 146713.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      12           2769           3087          11446
Python                          80           2196           3692           8265
CSS                              5            392             76           1505
HTML                             8            282              0           1349
YAML                             8             55             68            297
Markdown                         8             76              0            293
Jupyter Notebook                 1              0            784            181
TeX                              1              8              0             55
reStructuredText                14             17             17             40
-------------------------------------------------------------------------------
SUM:                           137           5795           7724          23431
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1142

[editorialbot]

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

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.36001/ijphm.2017.v8i2.2618 may be a valid DOI for title: A Generic Software Architecture for Prognostics (GSAP)
- 10.36001/phmconf.2022.v14i1.3238 may be a valid DOI for title: Enabling in-time prognostics with surrogate modeling through physics-enhanced Dynamic Mode Decomposition method

INVALID DOIs

- None

[matthewjdaigle]

Review checklist for @matthewjdaigle

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/nasa/prog_models?
• 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 (@teubert) 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?

[matthewjdaigle]

@kellyrowland Regarding COI policy, I'm a former colleague with the submitting author (5+ years ago), however, within the repository's readme I am credited as an author, since it is based on my previous work (which is also cited in the paper). So there is definitely a perception of a COI here. Let me know how to proceed.

[rtbs-dev]

Review checklist for @tbsexton

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/nasa/prog_models?
• 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 (@teubert) 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?

[kellyrowland]

@matthewjdaigle thanks for pointing that out - in the interest of impartiality it would probably be best that I remove you from the reviewer list. My apologies for not catching this in the pre-review stage.

Would you be able to recommend someone in the broader field who would be a good fit for reviewing this?

[matthewjdaigle]

@matthewjdaigle thanks for pointing that out - in the interest of impartiality it would probably be best that I remove you from the reviewer list. My apologies for not catching this in the pre-review stage.

Would you be able to recommend someone in the broader field who would be a good fit for reviewing this?

I'll check with my network and let you know.

[matthewjdaigle]

@kellyrowland I can recommend @samim91 as a reviewer.

[kellyrowland]

Thanks very much - @samim91 would you be interested in and available for reviewing this submission to JOSS?

@tbsexton thanks for getting started on your review - feel free to reach out if you have any questions.

[samim91]

Hi Kelly, Yes, would be happy to. Can you include my stanford address in copy? ***@***.*** Best, Samim Sent from Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Kelly L. Rowland ***@***.***> Sent: Monday, February 13, 2023 9:49:19 AM To: openjournals/joss-reviews ***@***.***> Cc: samim91 ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [REVIEW]: ProgPy: Python Packages for Prognostics and Health Management of Engineering Systems (Issue #5099) Thanks very much - @samim91<https://github.com/samim91> would you be interested in and available for reviewing this submission to JOSS? @tbsexton<https://github.com/tbsexton> thanks for getting started on your review - feel free to reach out if you have any questions. — Reply to this email directly, view it on GitHub<#5099 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKSWKEL3LHAANS5LCT6OVOTWXJXZ7ANCNFSM6AAAAAAUFUHRZ4>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[kellyrowland]

Hi @samim91 - thanks for the response and interest here. I think you may want to add your Stanford email address onto your Github profile to have it copied on messages; I'm not sure that I can ping it via commenting on the issue from the Github website.

The review process is done here in the Github issue; you'll generate a checklist and then check off those items as you progress through your review. Please let me know if you have any questions or concerns.

[kellyrowland]

@editorialbot add @samim91 as reviewer

[editorialbot]

@samim91 added to the reviewers list!

[teubert]

Hello @samim91, @tbsexton, Thank you both so much for reviewing this paper.

I wanted to check in- do you need anything from me at this point for the review?

[kellyrowland]

@editorialbot remove @matthewjdaigle from reviewers

[editorialbot]

@matthewjdaigle removed from the reviewers list!

[kellyrowland]

@tbsexton @samim91 please let me know whether or not you think you'll be able to make progress on your reviews in the near future so that I can start reaching out to other potential reviewers if needed.

[rtbs-dev]

Definitely, just had some obligations come up recently but I should get through a good amount this week

[samim91]

I will not be able to conduct the review without further changes to my system. It wouldn't be a bad idea to reach out to other potential reviewers.

[kellyrowland]

@editorialbot set 10.5281/zenodo.8097013 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8097013

[kellyrowland]

@editorialbot set v1.5 as version

[editorialbot]

Done! version is now v1.5

[kellyrowland]

@teubert thanks! Reading through the paper, my only minor comments are that "Python" and "TensorFlow" should be capitalized in the text. Happy to open an issue on the repo if that's useful.

[teubert]

Thanks @kellyrowland, I just pushed an update with the fixed capitalization.

What are the next steps?

[kellyrowland]

Great, thanks. I'll run one last EditoralBot to generate the final proofs and notify the editors-in-chief team that the paper is ready for final processing.

[kellyrowland]

@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

- 10.36001/ijphm.2017.v8i2.2618 is OK
- 10.36001/phmconf.2022.v14i1.3238 is OK
- 10.5281/zenodo.7329096 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/pe-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#4383, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

Hi @teubert, I'm doing some final checks before accepting.

It appears that the author/contributor list on Zenodo does not match the author list of the paper. These should usually match - is there a reason for this?

Also, I've made some typographic edits to the paper. Could you review and merge the PR? nasa/prog_models#574

Lastly, the Goebel et al. (2017) reference seems to be missing some details. Is that a book, or something else?

[teubert]

Thank you for the comments @kyleniemeyer

I just approved and merged your PR.

The author list for the paper are the individuals who contributed to the paper, which is a subset of the authors of the software itself. Should I add the other software authors to the paper?

Also, yes, the Goebel publication is a book. I'll see if I can find any other details (e.g., publisher) that I can add to the bibtex entry.

[teubert]

I just added the publisher to the Goebel book- Looking through I didn't see any other information that could be added.

[kyleniemeyer]

The author list for the paper are the individuals who contributed to the paper, which is a subset of the authors of the software itself. Should I add the other software authors to the paper?

@teubert yes, the author lists should match - the paper is really meant as a stand-in for the software itself. Please add the missing authors to the paper.

[teubert]

@kyleniemeyer Done! I added the two missing authors to the paper

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@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.

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: Teubert
  given-names: Christopher
  orcid: "https://orcid.org/0000-0001-6788-4507"
- family-names: Jarvis
  given-names: Katelyn
- family-names: Corbetta
  given-names: Matteo
  orcid: "https://orcid.org/0000-0002-7169-1051"
- family-names: Kulkarni
  given-names: Chetan
- family-names: Daigle
  given-names: Matthew
doi: 10.5281/zenodo.8097013
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Teubert
    given-names: Christopher
    orcid: "https://orcid.org/0000-0001-6788-4507"
  - family-names: Jarvis
    given-names: Katelyn
  - family-names: Corbetta
    given-names: Matteo
    orcid: "https://orcid.org/0000-0002-7169-1051"
  - family-names: Kulkarni
    given-names: Chetan
  - family-names: Daigle
    given-names: Matthew
  date-published: 2023-07-06
  doi: 10.21105/joss.05099
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5099
  title: "ProgPy: Python Packages for Prognostics and Health Management
    of Engineering Systems"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05099"
  volume: 8
title: "ProgPy: Python Packages for Prognostics and Health Management of
  Engineering Systems"

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]

🐘🐘🐘 👉 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.05099 joss-papers#4386
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05099
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...

[teubert]

Thank you @kyleniemeyer @kellyrowland

[kyleniemeyer]

Congratulations @teubert on your article's publication in JOSS! If you haven't already, please consider signing up to be a future reviewer.

Many thanks to @tbsexton and @nkrusch for reviewing this, and @kellyrowland for editing.

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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