[REVIEW]: hessQuik: Fast Hessian computation of composite functions

whedon commented 2 years ago

Submitting author: !--author-handle-->@elizabethnewman@jbytecode<!--end-editor-- Reviewers: @GregaVrbancic, @yhtang Archive: 10.5281/zenodo.6478757

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/126dc76c56d70524ac58b47a9bee7460"><img src="https://joss.theoj.org/papers/126dc76c56d70524ac58b47a9bee7460/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/126dc76c56d70524ac58b47a9bee7460/status.svg)](https://joss.theoj.org/papers/126dc76c56d70524ac58b47a9bee7460)

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

@GregaVrbancic & @yhtang, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode 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 ✨

Review checklist for @GregaVrbancic

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@elizabethnewman) 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

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 and who the target audience is?
[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?

Review checklist for @yhtang

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@elizabethnewman) 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

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 and who the target audience is?
[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?

jbytecode commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

jbytecode commented 2 years ago

Dear @elizabethnewman

It seems okay now.

[ ] Please read the paper pdf carefully, one more time.
[ ] Create a tagged release in the software repository. Report the version here. The version should be in form of vx.y.z, e.g. v1.2.3.
[ ] Create a Zenodo archive in https://zenodo.org/
[ ] The Zenodo archive should have the correct metadata, e.g. author names, ORCIDs, the title of the archive. Despite it is not a rigid requirement, please set the archive title as the paper title.
[ ] Please provide the tagged release version id, zenodo archive DOI, zenodo archive url here.

Thank you in advance.

elizabethnewman commented 2 years ago

Dear @elizabethnewman

It seems okay now.

[x] Please read the paper pdf carefully, one more time.

[x] Create a tagged release in the software repository. Report the version here. The version should be in form of vx.y.z, e.g. v1.2.3.

[x] Create a Zenodo archive in https://zenodo.org/

[x] The Zenodo archive should have the correct metadata, e.g. author names, ORCIDs, the title of the archive. Despite it is not a rigid requirement, please set the archive title as the paper title.

[x] Please provide the tagged release version id, zenodo archive DOI, zenodo archive url here.

Thank you in advance.

Dear @jbytecode

I believe I have followed all of the steps you have outlined above. Here is the requested information:

tagged release version id: v1.0.0 zenodo archive DOI: 10.5281/zenodo.6478757 zenodo archive url: https://zenodo.org/record/6478757#.YmMyAfPMK3J

Please let me know if you need any other information. Thank you!

jbytecode commented 2 years ago

@editorialbot set v1.0.0 as version

editorialbot commented 2 years ago

Done! version is now v1.0.0

jbytecode commented 2 years ago

@editorialbot set 10.5281/zenodo.6478757 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6478757

jbytecode commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/gamm.202100008 is OK
- 10.1109/cvpr.2016.90 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1109/EuroSP.2016.36 is OK
- 10.1007/978-1-4842-4470-8_7 is OK
- 10.1137/1.9781611973808 is OK
- 10.1073/pnas.1922204117 is OK
- 10.1137/07070111X is OK
- 10.1007/s40304-017-0103-z is OK
- 10.1088/1361-6420/aa9a90 is OK
- 10.1073/pnas.1916634117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

jbytecode commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/gamm.202100008 is OK
- 10.1109/cvpr.2016.90 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1109/EuroSP.2016.36 is OK
- 10.1007/978-1-4842-4470-8_7 is OK
- 10.1137/1.9781611973808 is OK
- 10.1073/pnas.1922204117 is OK
- 10.1137/07070111X is OK
- 10.1007/s40304-017-0103-z is OK
- 10.1088/1361-6420/aa9a90 is OK
- 10.1073/pnas.1916634117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

jbytecode commented 2 years ago

@openjournals/dev - could you please help us with the compilation issue above?

arfon commented 2 years ago

I think the issue is that this is actually an ISSN not ISBN: https://github.com/elizabethnewman/hessQuik/blob/main/paper/paper.bib#L179 and so the current value is failing the XML validation.

jbytecode commented 2 years ago

Dear @elizabethnewman

I have just send a new pull request (https://github.com/elizabethnewman/hessQuik/pull/7) that possibly fixes the compilation task. Could you please review and apply it?

Thank you.

jbytecode commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/gamm.202100008 is OK
- 10.1109/cvpr.2016.90 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1109/EuroSP.2016.36 is OK
- 10.1007/978-1-4842-4470-8_7 is OK
- 10.1137/1.9781611973808 is OK
- 10.1073/pnas.1922204117 is OK
- 10.1137/07070111X is OK
- 10.1007/s40304-017-0103-z is OK
- 10.1088/1361-6420/aa9a90 is OK
- 10.1073/pnas.1916634117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/gamm.202100008 is OK
- 10.1109/cvpr.2016.90 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1109/EuroSP.2016.36 is OK
- 10.1007/978-1-4842-4470-8_7 is OK
- 10.1137/1.9781611973808 is OK
- 10.1073/pnas.1922204117 is OK
- 10.1137/07070111X is OK
- 10.1007/s40304-017-0103-z is OK
- 10.1088/1361-6420/aa9a90 is OK
- 10.1073/pnas.1916634117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

jbytecode commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/gamm.202100008 is OK
- 10.1109/cvpr.2016.90 is OK
- 10.1016/j.jcp.2018.10.045 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1109/EuroSP.2016.36 is OK
- 10.1007/978-1-4842-4470-8_7 is OK
- 10.1137/1.9781611973808 is OK
- 10.1073/pnas.1922204117 is OK
- 10.1137/07070111X is OK
- 10.1007/s40304-017-0103-z is OK
- 10.1088/1361-6420/aa9a90 is OK
- 10.1073/pnas.1916634117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3169

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3169, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

👋 @elizabethnewman - can you please edit the zenodo metadata to change your name from your account name to your actual name? (i.e. "Elizabeth Newman", not "elizabethnewman")

danielskatz commented 2 years ago

Once that's done, I (as the AEiC this week) will be pleased to publish this submission; I see no other changes needed.

elizabethnewman commented 2 years ago

👋 @elizabethnewman - can you please edit the zenodo metadata to change your name from your account name to your actual name? (i.e. "Elizabeth Newman", not "elizabethnewman")

Dear @danielskatz

Done! Please let me know if you need any other information and thanks for your help!

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3170
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04171
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @elizabethnewman (Elizabeth Newman) and co-author!!

And thanks to @GregaVrbancic and @yhtang for reviewing, and to @jbytecode for editing! We couldn't do this without you

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.04171/status.svg)](https://doi.org/10.21105/joss.04171)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04171">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04171/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04171/status.svg
   :target: https://doi.org/10.21105/joss.04171

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews