editorialbot commented 7 months ago

Submitting author: !--author-handle-->@mrava87@sappelhoff<!--end-editor-- Reviewers: @nirum, @ewu63 Archive: 10.5281/zenodo.10805997

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c953d2cc2f446d83595cc858baadb15d/status.svg)](https://joss.theoj.org/papers/c953d2cc2f446d83595cc858baadb15d)

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

@nirum & @ewu63, 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 @ewu63

📝 Checklist for @nirum

editorialbot commented 7 months ago

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 commented 7 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (911.3 files/s, 106775.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          79           1983           3798           4820
Markdown                         5            145              0            527
reStructuredText                12            300            277            387
YAML                             8             29             47            190
TeX                              1             12              0             95
CSS                              1             23              7             87
make                             2             18              8             48
TOML                             1              4              0             45
HTML                             1              6              0             32
-------------------------------------------------------------------------------
SUM:                           110           2520           4137           6231
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 7 months ago

Wordcount for paper.md is 1319

editorialbot commented 7 months ago

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

OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1561/2200000016 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1093/gji/ggab388 is OK
- 10.1109/GlobalSIP.2013.6737048 is OK
- 10.1190/tle42070457.1 is OK
- 10.3997/2214-4609.2022616015 is OK
- 10.3997/2214-4609.2021612003 is OK

MISSING DOIs

- 10.1109/tci.2024.3359178 may be a valid DOI for title: Interferometric Lensless Imaging: Rank-one Projections of Image Frequencies with Speckle Illuminations

INVALID DOIs

- None

editorialbot commented 7 months ago

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

sappelhoff commented 7 months ago

Hello again! 👋 

@nirum, @ewu63, @Leo-Simpson

FYI @mrava87

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 https://github.com/openjournals/joss-reviews/issues/6326 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.

ewu63 commented 6 months ago

Review checklist for @ewu63

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 http://github.com/pylops/pyproximal/?
[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 (@mrava87) 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?

sappelhoff commented 6 months ago

@ewu63 thanks for getting started!

@nirum @leo-simpson friendly reminder about your review in this thread. 🙂

nirum commented 6 months ago

Review checklist for @nirum

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 http://github.com/pylops/pyproximal/?
[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 (@mrava87) 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?

sappelhoff commented 6 months ago

@ewu63 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 @nirum once you are finished, please 🙏

@leo-simpson I haven't heard back from you in 3 weeks -- would you still like to review this paper? Please just let me know if you cannot make it so that I can find a potential replacement for you. It would be great to have all reviews finished within the next three weeks, approximately.

ewu63 commented 6 months ago

@sappelhoff I recommend this paper for acceptance, pending the following points to be addressed:

In the statement of need, it would be helpful to cite a few well-known packages in order to highlight the key distinguishing features of this package. This is already done in the repo README and can probably be reused.
One DOI is missing -- see https://github.com/openjournals/joss-reviews/issues/6326#issuecomment-1929141719 for the suggested DOI

This is tracked at PyLops/pyproximal#166

mrava87 commented 6 months ago

Thanks @ewu63, I have included now your comments as also written in the Github issue. Let me know if you agree or if you have any further suggestion :)

mrava87 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:

ewu63 commented 6 months ago

@sappelhoff the authors have addressed all my concerns, I recommend this paper for publication.

nirum commented 6 months ago

@mrava87 I really enjoyed reading through your repository. I especially appreciated the nice set of tutorials. Overall everything is clearly written and nicely documented. @sappelhoff I recommend for publication

mrava87 commented 6 months ago

@nirum thanks a lot!

sappelhoff commented 6 months ago

@ewu63 I see that you have changed your GitHub handle. Just FYI I will try to unassign the old handle (nwu63) from this review and assign your new one (@ewu63), so that the links will work and credit can be properly assigned to you as a reviewer.

sappelhoff commented 6 months ago

@editorialbot add @ewu63 as reviewer

editorialbot commented 6 months ago

@ewu63 added to the reviewers list!

sappelhoff commented 6 months ago

@editorialbot remove @nwu63 from reviewers

editorialbot commented 6 months ago

@nwu63 removed from the reviewers list!

sappelhoff commented 6 months ago

@Leo-Simpson I haven't heard back from you in 5 weeks now, so I am going to unassign you from the list of reviewers. I'd be happy to welcome you as a reviewer on another project, if the need of JOSS for a reviewer and your own time for volunteering should align again in the future.

@mrava87 we do not need to find another reviewer, as we have two full reviews ready and I judge this situation adequate to proceed.

sappelhoff commented 6 months ago

@editorialbot remove @Leo-Simpson from reviewers

editorialbot commented 6 months ago

@Leo-Simpson removed from the reviewers list!

mrava87 commented 6 months ago

@sappelhoff thanks a lot for the feedback, this is a great news :)

Anything needed from me at this point?

sappelhoff commented 6 months ago

@mrava87 yes! In particular, we will now need a tagged release of your software, and an archive of that tagged version (for example on Zenodo, using the GitHub integration). I am going to let the bot create a checklist for us in the next comment.

sappelhoff commented 6 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

sappelhoff commented 6 months ago

And before I forget: A big thank you already at this point to @nirum and @ewu63 for completing your reviews. 👏

@mrava87 I could not find you in our reviewer database - we'd be very grateful if you considered signing up to pay it forward 🙂 you can do that here: https://reviewers.joss.theoj.org/join

@ewu63 I also did not find you in that reviewer database. If you enjoyed being a reviewer for JOSS and would consider doing so again in the future, please sign up, too!

sappelhoff commented 6 months ago

@mrava87 please let me know once you finished your items from the list above: https://github.com/openjournals/joss-reviews/issues/6326#issuecomment-1988377528

I will then work on my final items, and then it's (hopefully) finally time to ship it!

mrava87 commented 6 months ago

@sappelhoff thanks, I'll get on to this tomorrow and let you know when I am done.

And, I just signed up to the Joss database, so you should see me now :)

mrava87 commented 6 months ago

New version number: v8.0.0 (release notes: https://github.com/PyLops/pyproximal/releases/tag/v0.8.0

Zenodo DOI: DOI: 10.5281/zenodo.10805997 (https://zenodo.org/records/10805997)

mrava87 commented 6 months ago

@sappelhoff I followed your checklist. I don't see to be able to tick the boxes but the first one, but I think I have taken care of all the points.

Let me know if anything is missing :)

sappelhoff 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:

sappelhoff commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago

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

OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1561/2200000016 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1093/gji/ggab388 is OK
- 10.1109/GlobalSIP.2013.6737048 is OK
- 10.1190/tle42070457.1 is OK
- 10.3997/2214-4609.2022616015 is OK
- 10.1109/tci.2024.3359178 is OK
- 10.3997/2214-4609.2021612003 is OK

MISSING DOIs

- Entry without DOI or title found
- No DOI given, and none found for title: Proximal splitting methods in signal processing
- No DOI given, and none found for title: proxalgs
- No DOI given, and none found for title: proxmin
- No DOI given, and none found for title: The Proximity Operator Repository
- No DOI given, and none found for title: pyxu
- No DOI given, and none found for title: ProxImaL

INVALID DOIs

- None

sappelhoff commented 6 months ago

@mrava87 thanks for your checks! I did some digging into the references and found some DOIs that we should add to your bib entries. Please see below and check/add accordingly:

ProxImaL --> https://doi.org/10.1145/2897824.2925875 ... could cite this paper
Combettes, P., & Pesquet, J.-C. (2011) --> https://doi.org/10.1007/978-1-4419-9569-8_10 ... the chapter does seem to have a DOI
pyxu --> https://github.com/pyxu-org/pyxu/?tab=readme-ov-file#cite-us ... the way they want to be cited includes a DOI
proxmin --> https://doi.org/10.1007/s11081-018-9380-y ... could cite this paper
parikh (proximal algorithms) --> https://doi.org/10.1561/2400000003 ... this seems to be the right DOI

Please tag me once you have completed this work. Feel free to also type @editorialbot check references in a separate comment, once you are done.

mrava87 commented 6 months ago

@sappelhoff, done! Thanks for digging into DOIs for me :D

There are still 2 reference of GitHub packages without DOIs, but I can't really find any paper connected to it that we could cite instead. Initially I tried to cite repositories, but I agree with you that if a related paper exists it is better to cite a paper even if it is not 1-1 match with the software package.

mrava87 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago

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

OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1007/978-1-4419-9569-8_10 is OK
- 10.1561/2200000016 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1093/gji/ggab388 is OK
- 10.1109/GlobalSIP.2013.6737048 is OK
- 10.1190/tle42070457.1 is OK
- 10.3997/2214-4609.2022616015 is OK
- 10.1109/tci.2024.3359178 is OK
- 10.3997/2214-4609.2021612003 is OK
- 10.1007/s11081-018-9380-y is OK
- 10.5281/zenodo.4486431 is OK
- 10.1145/2897824.2925875 is OK

MISSING DOIs

- No DOI given, and none found for title: proxalgs
- No DOI given, and none found for title: The Proximity Operator Repository

INVALID DOIs

- doi.org/10.1561/2400000003 is INVALID because of 'doi.org/' prefix

mrava87 commented 6 months ago

Ops, I made a mistake… will fix the broken DOI soon :)

mrava87 commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago

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

OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1561/2400000003 is OK
- 10.1007/978-1-4419-9569-8_10 is OK
- 10.1561/2200000016 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1093/gji/ggab388 is OK
- 10.1109/GlobalSIP.2013.6737048 is OK
- 10.1190/tle42070457.1 is OK
- 10.3997/2214-4609.2022616015 is OK
- 10.1109/tci.2024.3359178 is OK
- 10.3997/2214-4609.2021612003 is OK
- 10.1007/s11081-018-9380-y is OK
- 10.5281/zenodo.4486431 is OK
- 10.1145/2897824.2925875 is OK

MISSING DOIs

- No DOI given, and none found for title: proxalgs
- No DOI given, and none found for title: The Proximity Operator Repository

INVALID DOIs

- None

mrava87 commented 6 months ago

@sappelhoff done :)

sappelhoff commented 6 months ago

@editorialbot set 10.5281/zenodo.10805997 as archive

editorialbot commented 6 months ago

Done! archive is now 10.5281/zenodo.10805997

sappelhoff commented 6 months ago

@editorialbot set v0.8.0 as version

editorialbot commented 6 months ago

Done! version is now v0.8.0

sappelhoff commented 6 months ago

@editorialbot generate pdf

openjournals / joss-reviews

[REVIEW]: PyProximal - scalable convex optimization in Python #6326

Status

Reviewer instructions & questions

Checklists

Review checklist for @ewu63

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @nirum

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance