[REVIEW]: CalibrateEmulateSample.jl: Accelerated Parametric Uncertainty Quantification

[editorialbot]

Submitting author: @odunbar (Oliver Dunbar)
Repository: https://github.com/CliMA/CalibrateEmulateSample.jl
Branch with paper.md (empty if default branch):
Version: v0.5.1
Editor: @sappelhoff
Reviewers: @matt-graham, @Vaibhavdixit02, @nluetts
Archive: 10.5281/zenodo.10946875

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c761e46a8a82ce342fad84a2f3e1ae69"><img src="https://joss.theoj.org/papers/c761e46a8a82ce342fad84a2f3e1ae69/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c761e46a8a82ce342fad84a2f3e1ae69/status.svg)](https://joss.theoj.org/papers/c761e46a8a82ce342fad84a2f3e1ae69)

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

@matt-graham & @Vaibhavdixit02 & @nluetts, 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 @sappelhoff 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 @matt-graham

📝 Checklist for @nluetts

📝 Checklist for @Vaibhavdixit02

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (701.2 files/s, 115307.0 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Julia                            36           1453           1228           6686
Markdown                         24            632              0           2558
YAML                              8             50              7            319
TeX                               1             26              0            248
TOML                             11             10              0            160
SVG                               1              0              0             71
Bourne Again Shell                1             10             15             11
--------------------------------------------------------------------------------
SUM:                             82           2181           1250          10053
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1514

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.21105/joss.04869 is OK
- 10.1029/2022MS002994 is OK
- 10.1109/TPAMI.2021.3097011 is OK
- 10.1214/13-STS421 is OK
- 10.21105/joss.04561 is OK
- 10.1137/19M1304891 is OK
- 10.1093/bioinformatics/btaa078 is OK
- 10.1088/1361-6420/ac99fa is OK
- 10.1029/2022MS003245 is OK
- 10.22541/essoar.170365299.96491153/v1 is OK

MISSING DOIs

- 10.1088/0266-5611/29/4/045001 may be a valid DOI for title: Ensemble Kalman methods for inverse problems
- 10.1109/allerton.2008.4797607 may be a valid DOI for title: Uniform approximation of functions with random bases
- 10.1214/10-sts327 may be a valid DOI for title: The Random Walk Metropolis: Linking Theory and Practice Through a Case Study

INVALID DOIs

- https://doi.org/10.1016/j.jcp.2020.109716 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2020MS002454 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2021MS002735 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1029/2022MS002997 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[sappelhoff]

Hello again! 👋


@matt-graham, @Vaibhavdixit02, @nluetts

FYI @odunbar

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to #6372 so that a link is created to this thread. That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread if you are unsure about something!

🎯 We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. NOTE: I am aware that some of you asked for some additional time due to having other obligations for now. That's no problem, please just communicate with me if your schedule for this review changes.

[nluetts]

Review checklist for @nluetts

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/CliMA/CalibrateEmulateSample.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 (@odunbar) 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?

[matt-graham]

Review checklist for @matt-graham

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/CliMA/CalibrateEmulateSample.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 (@odunbar) 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?

[Vaibhavdixit02]

Review checklist for @Vaibhavdixit02

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/CliMA/CalibrateEmulateSample.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 (@odunbar) 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?

[sappelhoff]

@Vaibhavdixit02 if you are done with your review (seems like it from your checkmarks), I'd appreciate if you could write a short summary whether you recommend this paper for acceptance or/and if some points still need to be addressed.

Same for @matt-graham once you are finished, please 🙏

@nluetts I know that you will only be able to really get started on this in early March, please keep me updated should anything change with that.

[Vaibhavdixit02]

@sappelhoff the package is quite well-developed and has comprehensive documentation and usage tutorials. It is a novel implementation as well so from my end it is a clear accept. The points raised by Matt are reasonable and I am following those issues barring which I don't have any other comments here.

[nluetts]

@nluetts I know that you will only be able to really get started on this in early March, please keep me updated should anything change with that.

All fine, @sappelhoff , I just started with the review.

[sappelhoff]

@matt-graham may I ask you for an update on your ongoing review, please? What are the outstanding points, and the approximate timeline for them?

[matt-graham]

@sappelhoff - I've currently got no spare capacity due to other commitments so will not be able to look at this again till next week. I saw that the authors responded to the issues I previously raised but haven't had a chance to look through their responses to two of the issues yet. I also have some minor feedback on the paper which I haven't yet had a chance to transcribe in to an issue.

[sappelhoff]

@matt-graham @nluetts just to check in with you: Are there any blockers that are holding you back from completing your reviews? Are you able to share an approximate date with us of when you might finish the last steps? Thanks!

[nluetts]

@sappelhoff The cold season has taken its toll on me a little, but I resumed the review now and have some time during this week, so I try to provide all my feedback by Friday. Apropos feedback, when I have questions and feedback to the JOSS paper draft itself, am I supposed to open an issue over at https://github.com/CliMA/CalibrateEmulateSample.jl or comment in this issue?

[sappelhoff]

Sorry to hear that, get well soon @nluetts! Thanks for your updated schedule as well. Please open issues at https://github.com/CliMA/CalibrateEmulateSample.jl also when it's about the JOSS paper draft 🙏

[matt-graham]

Apologies for the delay in finishing off my review. I have opened an issue with some minor suggestions for changes to text to paper (and have therefore left a couple of items on reviewer checklist unticked but just to be clear I don't have any concerns about overall quality of writing). @odunbar has addressed everything in the other issues I raised so from my perspective it is only the minor changes to the paper that are outstanding.

[editorialbot]

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

Element doi: [facet 'pattern'] The value '1721.1/145140' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

[sappelhoff]

@openjournals/dsais-eics I wanted to recommend this paper for acceptance, but I get the above error for a DOI: 1721.1/145140 ... However, this DOI does seem to resolve correctly: https://doi.org/1721.1/145140

How shall we proceed?

[sappelhoff]

@odunbar for your information, I have contacted the editor in chief for this problem also on a separate channel, but it seems they are currently busy. I am sure they will reply as soon as possible, and once this problem is resolved we can swiftly go on to publication of your paper. Until then, we will have to wait. Sorry for the delay.

[arfon]

@xuanxu – I wonder if we need some kind of 'accept ignoring errors' command here? The XML validation is overly-prescriptive here (i.e., wrong!)

[xuanxu]

@arfon We can add that command yeah, but we have to take into account that this error comes from the Crossref XML schema validator so it means that if we ignore the errors we will try to deposit with Crossref a metadata file that they will consider invalid (I'm not sure if they will accept it anyway or reject the deposit).

[arfon]

@xuanxu – let's try and see what happens. What's the command to override?

[xuanxu]

@arfon it should be accept ignoring errors

[arfon]

@editorialbot accept ignoring errors

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance (ignoring metadata errors)...

[editorialbot]

⚠️ Ignoring errors that could prevent acceptance The generated Crossref XML v5.3.1 metadata file is invalid.

Element doi: [facet 'pattern'] The value '1721.1/145140' is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

[arfon]

@xuanxu – Crossref failed to deposit the DOI :-(

@odunbar – can you please remove the BibTeX entry with 1721.1/145140 as the DOI?

[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: Dunbar
  given-names: Oliver R. A.
  orcid: "https://orcid.org/0000-0001-7374-0382"
- family-names: Bieli
  given-names: Melanie
- family-names: Garbuno-Iñigo
  given-names: Alfredo
  orcid: "https://orcid.org/0000-0003-3279-619X"
- family-names: Howland
  given-names: Michael
  orcid: "https://orcid.org/0000-0002-2878-3874"
- family-names: Souza
  given-names: Andre Nogueira
  name-particle: de
  orcid: "https://orcid.org/0000-0002-9906-7824"
- family-names: Mansfield
  given-names: Laura Anne
  orcid: "https://orcid.org/0000-0002-6285-6045"
- family-names: Wagner
  given-names: Gregory L.
  orcid: "https://orcid.org/0000-0001-5317-2445"
- family-names: Efrat-Henrici
  given-names: N.
contact:
- family-names: Dunbar
  given-names: Oliver R. A.
  orcid: "https://orcid.org/0000-0001-7374-0382"
doi: 10.5281/zenodo.10946875
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Dunbar
    given-names: Oliver R. A.
    orcid: "https://orcid.org/0000-0001-7374-0382"
  - family-names: Bieli
    given-names: Melanie
  - family-names: Garbuno-Iñigo
    given-names: Alfredo
    orcid: "https://orcid.org/0000-0003-3279-619X"
  - family-names: Howland
    given-names: Michael
    orcid: "https://orcid.org/0000-0002-2878-3874"
  - family-names: Souza
    given-names: Andre Nogueira
    name-particle: de
    orcid: "https://orcid.org/0000-0002-9906-7824"
  - family-names: Mansfield
    given-names: Laura Anne
    orcid: "https://orcid.org/0000-0002-6285-6045"
  - family-names: Wagner
    given-names: Gregory L.
    orcid: "https://orcid.org/0000-0001-5317-2445"
  - family-names: Efrat-Henrici
    given-names: N.
  date-published: 2024-05-06
  doi: 10.21105/joss.06372
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6372
  title: "CalibrateEmulateSample.jl: Accelerated Parametric Uncertainty
    Quantification"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06372"
  volume: 9
title: "CalibrateEmulateSample.jl: Accelerated Parametric Uncertainty
  Quantification"

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.06372 joss-papers#5313
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06372
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]

It seems like this should be reported to Crossref, since the DOI does resolve.

[xuanxu]

Crossref failed to deposit the DOI :-(

The Crossref API response was OK: https://github.com/openjournals/joss-papers/actions/runs/8973048619/job/24642364367#step:7:76

[arfon]

It seems like this should be reported to Crossref, since the DOI does resolve.

Crossref did OK. We knowingly submitted slightly bad XML (which it rejected). Waiting on an update from the author (@odunbar) to their BibTeX for this to be fixed.

[arfon]

@odunbar – this is the PR we need you to merge please CliMA/CalibrateEmulateSample.jl#307

[danielskatz]

How was our XML bad? If it was just that we have a DOI that Crossref doesn't like, that's what I think should be reported to Crossref, as the DOI is valid.

[arfon]

How was our XML bad? If it was just that we have a DOI that Crossref doesn't like, that's what I think should be reported to Crossref, as the DOI is valid.

Right. It's the Crossref validation getting caught up on 1721.1/145140

[odunbar]

Sorry - missed a lot of this discussion. I have merged CliMA/CalibrateEmulateSample.jl#307

[arfon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5317

[arfon]

@matt-graham, @Vaibhavdixit02, @nluetts – many thanks for your reviews here and to @sappelhoff for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@odunbar – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06372/status.svg)](https://doi.org/10.21105/joss.06372)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06372/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06372/status.svg
   :target: https://doi.org/10.21105/joss.06372

This is how it will look in your documentation:

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[odunbar]

Thanks everyone for the reviews, editing and to the JOSS team for sifting through DOI errors! It is much appreciated on our end!

Cheers,
Ollie