[REVIEW]: MOLE: Mimetic Operators Library Enhanced

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@jcorbino@jedbrown<!--end-editor-- Reviewers: @jakelangham, @victorapm Archive: 10.5281/zenodo.12752946

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/a19d0799c87be56f189e125a12fb748a"><img src="https://joss.theoj.org/papers/a19d0799c87be56f189e125a12fb748a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/a19d0799c87be56f189e125a12fb748a/status.svg)](https://joss.theoj.org/papers/a19d0799c87be56f189e125a12fb748a)

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

@jakelangham & @victorapm, 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 @jedbrown 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 @jakelangham

📝 Checklist for @victorapm

editorialbot commented 9 months ago

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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 commented 9 months ago

Software report:

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gitinspector failed to run statistical information for the repository

editorialbot commented 9 months ago

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

OK DOIs

- 10.1016/j.cam.2019.06.042 is OK
- 10.1080/21681163.2021.1914733 is OK
- 10.1016/j.procs.2013.05.210 is OK
- 10.1190/geo2013-0371.1 is OK
- 10.1111/j.1365-246X.2007.03651.x is OK
- 10.1201/b14575 is OK
- 10.1137/S0895479801398025 is OK
- 10.21105/joss.00026 is OK
- 10.1016/j.cam.2013.12.046 is OK
- 10.1590/S1807-03022011000300012 is OK
- 10.1016/j.compfluid.2020.104746 is OK
- 10.5206/mase/10874 is OK
- 10.1016/j.compfluid.2023.105817 is OK
- 10.13140/RG.2.2.31741.95204 is OK
- 10.13140/RG.2.2.19919.25767 is OK
- 10.13140/RG.2.2.26630.14400 is OK
- 10.13140/RG.2.2.28307.86561 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

Wordcount for paper.md is 1012

editorialbot commented 9 months ago

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

jedbrown commented 9 months ago

Hi, @jakelangham and @victorapm :wave: Welcome to JOSS and thanks for agreeing to review! The comments from @editorialbot above outline the review process, which takes place in this thread (possibly with issues filed in the MOLE repository). I'll be watching this thread if you have any questions.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention this issue so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or two. Please let me know if you require some more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

jakelangham commented 9 months ago

Review checklist for @jakelangham

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/jcorbino/mole?
[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 (@jcorbino) 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?

victorapm commented 9 months ago

Review checklist for @victorapm

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/jcorbino/mole?
[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 (@jcorbino) 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?

jedbrown commented 7 months ago

Hi, @jcorbino :wave: I wanted to check in about how things are going. I see the issues that were opened, but don't know who is waiting on whom at this point.

jcorbino commented 6 months ago

Hello @jedbrown - Apologies for the delayed response. I'm currently addressing the issues raised by Jake Langham. I think I'll have those ready by the end of this month.

At the same time, I see that a good portion of his checklist has non-checked items (unrelated to the issues he mentioned in the repo), such as the ones in the "Software paper" section. I don't know the status of that. I assume he's been busy, and he'll review those once I integrate the suggested modifications.

Thank you for your patience.

jakelangham commented 6 months ago

@jcorbino @jedbrown I am getting back to this presently. Actually I wasn't sure whether the right thing to do was wait for updates on the open issues or not, but I agree that other things (e.g. the paper) can be reviewed independently.

jcorbino commented 6 months ago

@editorialbot generate pdf

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:

jcorbino commented 6 months ago

@editorialbot generate pdf

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:

jcorbino commented 6 months ago

@editorialbot generate pdf

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:

jakelangham commented 6 months ago

@jedbrown @jcorbino I have finished working my way through the review bullet points. From what I can see, MOLE is a nice piece of software that should be useful to numerical analysts and any scientists working in applications that would particularly benefit from solving PDEs via mimetic operators.

I have left some points unchecked for now, which relate to issues raised in the repository's tracker. Some of these are substantial. Nevertheless, I would recommend acceptance on their resolution.

Finally, I note that the C++ integration tests are failing at the moment, according to github. Looks like an easy issue, but suppose this should be fixed before any decision on publication!

jedbrown commented 6 months ago

Thanks, @jakelangham. @jcorbino Let us know your timeline for addressing these issues. I see @victorapm has left one unchecked item (Example usage) -- do you need clarification of what he's looking for?

jcorbino commented 6 months ago

Thanks, @jedbrown

I have all the information I need from the reviewers to finish the pending tasks. I've been quite busy with my job, so I estimate this will take me until the end of the month.

jedbrown commented 6 months ago

Sounds good, thanks!

victorapm commented 5 months ago

Hi Jed, I finished my review and would like to recommend publication. Thank you!

jedbrown commented 5 months ago

Thanks @victorapm!

@jcorbino Please let us know when you're ready for @jakelangham to have another look.

jcorbino commented 5 months ago

Hi @jedbrown , I believe it's ready now, so @jakelangham , please take another look whenever you have the time. Thanks!

jakelangham commented 5 months ago

Hi both, @jcorbino @jedbrown I have been away for a bit but am looking at this now.

jakelangham commented 5 months ago

@jcorbino @jedbrown I think there is still more to do regarding testing/functionality (cf https://github.com/jcorbino/mole/issues/12) but upon resolution of this I would gladly recommend acceptance.

jcorbino commented 5 months ago

Thank you, @jakelangham , for the feedback! I just pushed the updated version of the tests (both flavors) so they cover different orders of accuracy and grid resolutions. I hope this is sufficient to fulfill this requirement. @jedbrown , please let me know if anything else is required.

jcorbino 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:

jakelangham commented 4 months ago

@jcorbino @jedbrown Hi both - I've finished my review now and think it's ready for publication. Thanks.

jcorbino commented 4 months ago

@jakelangham @victorapm Thank you both for reviewing the article and the library. @jedbrown, please let me know if anything else is required from my side.

jedbrown commented 4 months ago

Thanks for your patience. Please have a look at https://github.com/jcorbino/mole/pull/18 and merge if you feel it is acceptable. Then proceed to:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

jcorbino commented 4 months ago

Not a problem! Thank you @jedbrown 👍🏻

I merged the PR, and here's the requested information:

Tagged release: v1.0 https://github.com/jcorbino/mole/releases/tag/v1.0
Zenodo: https://zenodo.org/records/12752946
DOI: https://doi.org/10.5281/zenodo.12752946

jedbrown commented 3 months ago

Thanks. I just want to confirm that you are intentionally clobbering the previous v1.0 tag (there were previous tags up to v5.0) with this new versioning scheme. If so, I think you should update your CITATION.cff (which currently has version: v2.0 from last year). An alternative is to call this v6.0 than to start over with a new versioning scheme.

jcorbino commented 3 months ago

Thank you, @jedbrown - I completely overlooked that. I've now updated the CITATION.cff with the new version and DOI. I prefer keeping this as version 1.0. Thanks again for pointing that out! 👍🏻

jedbrown commented 3 months ago

@editorialbot set v1.0 as version

editorialbot commented 3 months ago

Done! version is now v1.0

jedbrown commented 3 months ago

@editorialbot set 10.5281/zenodo.12752946 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.12752946

jedbrown commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.1016/j.cam.2019.06.042 is OK
- 10.1145/1089014.1089017 is OK
- 10.1080/21681163.2021.1914733 is OK
- 10.1016/j.procs.2013.05.210 is OK
- 10.1190/geo2013-0371.1 is OK
- 10.1111/j.1365-246X.2007.03651.x is OK
- 10.1201/b14575 is OK
- 10.1137/S0895479801398025 is OK
- 10.21105/joss.00026 is OK
- 10.1016/j.cam.2013.12.046 is OK
- 10.1590/S1807-03022011000300012 is OK
- 10.1016/j.compfluid.2020.104746 is OK
- 10.5206/mase/10874 is OK
- 10.1016/j.compfluid.2023.105817 is OK
- 10.13140/RG.2.2.31741.95204 is OK
- 10.13140/RG.2.2.19919.25767 is OK
- 10.13140/RG.2.2.26630.14400 is OK
- 10.13140/RG.2.2.28307.86561 is OK

MISSING DOIs

- No DOI given, and none found for title: OpenBLAS: An Optimized BLAS Library

INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5640, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 3 months ago

👋 @jcorbino - as the track chair, I've proofread this submission, and have a couple of small suggestions in https://github.com/jcorbino/mole/pull/19. Please merge this, or let me know what you disagree with.

jcorbino commented 3 months ago

Hi @danielskatz - Thank you for the PR; I just merged it 👍🏻

danielskatz commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.1016/j.cam.2019.06.042 is OK
- 10.1145/1089014.1089017 is OK
- 10.1080/21681163.2021.1914733 is OK
- 10.1016/j.procs.2013.05.210 is OK
- 10.1190/geo2013-0371.1 is OK
- 10.1111/j.1365-246X.2007.03651.x is OK
- 10.1201/b14575 is OK
- 10.1137/S0895479801398025 is OK
- 10.21105/joss.00026 is OK
- 10.1016/j.cam.2013.12.046 is OK
- 10.1590/S1807-03022011000300012 is OK
- 10.1016/j.compfluid.2020.104746 is OK
- 10.5206/mase/10874 is OK
- 10.1016/j.compfluid.2023.105817 is OK
- 10.13140/RG.2.2.31741.95204 is OK
- 10.13140/RG.2.2.19919.25767 is OK
- 10.13140/RG.2.2.26630.14400 is OK
- 10.13140/RG.2.2.28307.86561 is OK

MISSING DOIs

- No DOI given, and none found for title: OpenBLAS: An Optimized BLAS Library

INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5643, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 3 months ago

@editorialbot accept

openjournals / joss-reviews