[REVIEW]: EllipticForest: A Direct Solver Library for Elliptic Partial Differential Equations on Adaptive Meshes

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@DamynChipman@vissarion<!--end-editor-- Reviewers: @sandeshkatakam, @lukeolson Archive: 10.5281/zenodo.11035127

Status

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Markdown: [![status](https://joss.theoj.org/papers/99b10d1d1b714cdccf6306eb6edfad2c/status.svg)](https://joss.theoj.org/papers/99b10d1d1b714cdccf6306eb6edfad2c)

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

@sandeshkatakam & @lukeolson, 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 @vissarion 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 @sandeshkatakam

📝 Checklist for @lukeolson

editorialbot commented 8 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 8 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (1266.2 files/s, 182868.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             60           1359           1322           5013
C/C++ Header                    31           1264           3496           3642
Markdown                        12            236              0            622
CMake                           13             72             31            316
TeX                              1             16              0            109
YAML                             2              1             12             69
Bourne Shell                     2              6              7             18
INI                              1              0              0              8
-------------------------------------------------------------------------------
SUM:                           122           2954           4868           9797
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 8 months ago

Wordcount for paper.md is 1784

editorialbot commented 8 months ago

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

OK DOIs

- 10.1137/130918988 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1007/978-94-009-1908-2_14 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

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

DamynChipman commented 7 months ago

@sandeshkatakam and @lukeolson, just pinging you again and checking if there's anything you need for this review. Thanks!

sandeshkatakam commented 7 months ago

Review checklist for @sandeshkatakam

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/DamynChipman/EllipticForest?
[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 (@DamynChipman) 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?

DamynChipman commented 6 months ago

Hey @vissarion, I'm following up on this review. Is there anything I can do to facilitate this better? @sandeshkatakam and @lukeolson, do you need anything from me to complete this review? Thanks all!

vissarion commented 6 months ago

@DamynChipman thanks for the follow up.

@sandeshkatakam, @lukeolson any news on this review?

sandeshkatakam commented 6 months ago

@DamynChipman thanks for the follow up.

@sandeshkatakam, @lukeolson any news on this review?

Hey I was travelling outside the country last week and couldn't respond

I'll finish the review by the end of this week

I'll let you know if i need something Thank you

DamynChipman commented 6 months ago

@vissarion, I've been working with @sandeshkatakam with question he has, and he appears to be done with his checklist. Thanks for working on that @sandeshkatakam!

I have not heard anything from @lukeolson.

We are past 6 weeks from when this was moved to review. Is it possible to find a new reviewer at this stage?

lukeolson commented 6 months ago

Review checklist for @lukeolson

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/DamynChipman/EllipticForest?
[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 (@DamynChipman) 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?

vissarion commented 6 months ago

@DamynChipman thanks for the update. It seems that @lukeolson has started working on his review.

@lukeolson please let us know when you finish your review.

lukeolson commented 6 months ago

@vissarion I've finished a pass at everything and left two comments in the form of issues for @DamynChipman . The first is a list of suggestions for revising the write up. The second is a reproducibility question -- I would like to see if it's possible to reproduce the figure in the paper. Other than that, everything check on my end.

DamynChipman commented 6 months ago

Thanks a ton! I commented on both of those issues; I'll incorporate your suggestions into the draft by the end of the week.

DamynChipman commented 5 months ago

The latest commit https://github.com/DamynChipman/EllipticForest/commit/d796f29d6f95873bcb615194ef33fe413030b4ee of the v1-joss-paper branch has the paper feedback from @lukeolson.

DamynChipman commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

DamynChipman commented 5 months ago

@lukeolson, I addressed both of the issues you raised in the paper repo:

https://github.com/DamynChipman/EllipticForest/issues/8 https://github.com/DamynChipman/EllipticForest/issues/9

DamynChipman commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

DamynChipman commented 5 months ago

Opps, I missed a couple formatting issues, now it's fixed.

DamynChipman commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

lukeolson commented 5 months ago

@DamynChipman the paper updates look great! thank you for the thorough updates to the .bib!

The updates to the examples look good too. I would encourage you to weave that polar star example into a separate example -- but for the paper everything looks good!

lukeolson commented 5 months ago

@DamynChipman thanks for the update. It seems that @lukeolson has started working on his review.

@lukeolson please let us know when you finish your review.

@vissarion all done here!

vissarion commented 5 months ago

@DamynChipman thanks for the follow up. @sandeshkatakam, @lukeolson any news on this review?

Hey I was travelling outside the country last week and couldn't respond

I'll finish the review by the end of this week

I'll let you know if i need something Thank you

Hi, @sandeshkatakam it seems that your checklist is complete. Are you waiting for some feedback from the author, or you are done?

sandeshkatakam commented 5 months ago

@DamynChipman thanks for the follow up. @sandeshkatakam, @lukeolson any news on this review?

Hey I was travelling outside the country last week and couldn't respond

I'll finish the review by the end of this week

I'll let you know if i need something Thank you

Hi, @sandeshkatakam it seems that your checklist is complete. Are you waiting for some feedback from the author, or you are done?

Yes I am done with my review. Good to go

vissarion commented 5 months ago

@lukeolson @sandeshkatakam thank you very much for your reviews!

@DamynChipman when a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (see this guide). Please do this and post the version number and archive DOI here.

DamynChipman commented 5 months ago

@vissarion, done!

v1.0.2: https://github.com/DamynChipman/EllipticForest/releases/tag/v1.0.2 DOI: 10.5281/zenodo.11035127

DamynChipman commented 5 months ago

Thanks a ton @sandeshkatakam and @lukeolson! I appreciate the feedback and the time to review this! 💥

vissarion commented 5 months ago

@editorialbot set 10.5281/zenodo.11035127 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.11035127

vissarion commented 5 months ago

@editorialbot set <v1.0.2> as version

editorialbot commented 5 months ago

Done! version is now <v1.0.2>

vissarion commented 5 months ago

@DamynChipman please use in zenodo the same title and author as in the JOSS submission

DamynChipman commented 5 months ago

@vissarion Done!

vissarion commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

vissarion commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 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/5274, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 5 months ago

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

OK DOIs

- 10.48550/arXiv.2402.14936 is OK
- 10.1137/130918988 is OK
- 10.1137/1.9781611976045 is OK
- 10.1145/800207.806417 is OK
- 10.1137/100791634 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.48550/arXiv.1506.01308 is OK
- 10.1007/978-94-009-1908-2_14 is OK
- 10.1201/b12985-29 is OK

MISSING DOIs

- No DOI given, and none found for title: MPI Implementation of the Quadtree-Adaptive Hierar...
- No DOI given, and none found for title: FISHPACK90: Efficient fortran subprograms for the ...
- No DOI given, and none found for title: MPI: A Message-Passing Interface Standard Version ...
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: ultraSEM: The ultraspherical spectral element meth...
- No DOI given, and none found for title: HPS_Demos: A collection of codes applying the HPS ...
- No DOI given, and none found for title: Streamer_HPS_DGSEM: Implementation of the spectral...

INVALID DOIs

- None

danielskatz commented 5 months ago

Thanks all - as AEiC, I'll be checking this in the next few hours and will let @DamynChipman know if anything else is needed.

danielskatz commented 5 months ago

@DamynChipman - I've suggested some small changes in https://github.com/DamynChipman/EllipticForest/pull/11 - please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication

DamynChipman commented 5 months ago

@danielskatz, I've merge your edits in, thanks!

https://github.com/DamynChipman/EllipticForest/pull/11

danielskatz commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

OK DOIs

- 10.48550/arXiv.2402.14936 is OK
- 10.1137/130918988 is OK
- 10.1137/1.9781611976045 is OK
- 10.1145/800207.806417 is OK
- 10.1137/100791634 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.48550/arXiv.1506.01308 is OK
- 10.1007/978-94-009-1908-2_14 is OK
- 10.1201/b12985-29 is OK

MISSING DOIs

- No DOI given, and none found for title: MPI Implementation of the Quadtree-Adaptive Hierar...
- No DOI given, and none found for title: FISHPACK90: Efficient Fortran subprograms for the ...
- No DOI given, and none found for title: MPI: A Message-Passing Interface Standard Version ...
- No DOI given, and none found for title: PETSc Web page
- No DOI given, and none found for title: ultraSEM: The ultraspherical spectral element meth...
- No DOI given, and none found for title: HPS_Demos: A collection of codes applying the HPS ...
- No DOI given, and none found for title: Streamer_HPS_DGSEM: Implementation of the spectral...

INVALID DOIs

- None

editorialbot commented 5 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/5280, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

openjournals / joss-reviews