[REVIEW]: GLUE Code: A framework handling communication and interfaces between scales

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@apachalieva@danielskatz<!--end-editor-- Reviewers: @govarguz, @keipertk Archive: 10.5281/zenodo.7469110

Status

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Markdown: [![status](https://joss.theoj.org/papers/a200507cb0091621b80baa85ee59186c/status.svg)](https://joss.theoj.org/papers/a200507cb0091621b80baa85ee59186c)

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

@govarguz & @keipertk, 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 @danielskatz 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 @keipertk

📝 Checklist for @govarguz

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (727.1 files/s, 113859.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            710           1106           2180
C/C++ Header                     4             87            482            577
JSON                             9              0              0            508
C                                5             68             61            474
Markdown                         5             62              0            267
C++                              2             45             25            256
TeX                              1             25              0            220
Fortran 90                       3             42             93            198
YAML                             2              5              6             70
CMake                            3             14              7             53
Bourne Shell                     2              0              0             32
-------------------------------------------------------------------------------
SUM:                            49           1058           1780           4835
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1783

editorialbot commented 2 years ago

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

OK DOIs

- 10.1103/physreve.102.023310 is OK
- 10.1063/1.1724389 is OK
- 10.1063/1.4921935 is OK
- 10.1103/physrevlett.112.135001 is OK
- 10.1103/PhysRevLett.118.185003 is OK
- 10.1063/1.872643 is OK
- 10.1145/1362622.1362700 is OK
- 10.2172/10176421 is OK
- 10.1007/10968987_3 is OK
- 10.48550/arXiv.1202.1056 is OK
- 10.1145/2834899.2834908 is OK
- 10.1177/1094342009106189 is OK
- 10.1063/1.5031206 is OK
- 10.1021/ct400566j is OK
- 10.48550/ARXIV.2209.09811 is OK
- 10.1038/s41598-020-69661-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

danielskatz commented 2 years ago

@govarguz and @keipertk - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4822 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 about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

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

danielskatz commented 2 years ago

👋 @govarguz and @keipertk - I'm just checking in after 2 weeks. Please do get started when you, by generating your checklists. To do this, use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

keipertk commented 2 years ago

Review checklist for @keipertk

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/lanl/GLUE?
[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 (@apachalieva) 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?

keipertk commented 2 years ago

Review is complete on my end. Great work by the LANL team!

danielskatz commented 2 years ago

thanks @keipertk - you found just the one issue that has been addressed, and are happy for this to be published?

danielskatz commented 2 years ago

👋 @govarguz - just checking in again after ~3 weeks. Please do get started when you can by generating your checklist. To do this, use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

If you have any issues or concerns about the process, please let me know.

keipertk commented 2 years ago

@danielskatz Yes I'm happy for this to be published.

danielskatz commented 2 years ago

👋 @govarguz - it's now been ~5 weeks. Please do get started when you can by generating your checklist. To do this, use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

If you have any issues or concerns about the process, please let me know.

govarguz commented 2 years ago

@danielskatz, I plan to send my comments in this week. thanks for the reminder!

govarguz commented 2 years ago

Review checklist for @govarguz

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/lanl/GLUE?
[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 (@apachalieva) 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?

danielskatz commented 2 years ago

thanks @govarguz - from all the items on your list being checked off, it looks like you are happy for this to be published?

govarguz commented 2 years ago

Dear @apachalieva, there is a new #PR with the general review of GLUE, and a couple of issues I raised also at GLUE's repo. Best, Horacio. cc: @danielskatz

danielskatz commented 2 years ago

@govarguz - sorry, I don't understand - can you link to any issues that you think need to be resolved before we accept? Ideally, if you mention openjournals/joss-reviews#4822 in any issues or PRs, a link is created to this thread and we can see their status here.

danielskatz commented 2 years ago

👋 @apachalieva - I see a bunch of issues above, and progress on some - can you say a little bit here about what else you think you need to do to resolve them and about how long this might take?

apachalieva commented 2 years ago

Hi @danielskatz, my colleagues and I are working on the open issues. We have divided the tasks among our team and requested additional information from the reviewer, wherever necessary. The open issues do not include any implementation work; therefore, we hope to resolve them by the end of next week.

apachalieva commented 1 year ago

Dear @danielskatz, my colleagues and I believe we have addressed all reviewer requests. Here are the links to all the issues:

https://github.com/lanl/GLUE/issues/7 https://github.com/lanl/GLUE/issues/8 https://github.com/lanl/GLUE/issues/9 https://github.com/lanl/GLUE/issues/11 https://github.com/lanl/GLUE/issues/14

We appreciate the reviewers' input which improved the content and readability of the manuscript/repository.

There is a small dispute about the wording of the title - we disagree with one of the reviewers, and we would like to ask you to give us guidance on how to proceed on this issue. You can see the issue and the discussion here: https://github.com/lanl/GLUE/issues/10

Thank you, GLUE Code development team

danielskatz commented 1 year ago

👋 @govarguz - are you ok with this being published now?

junghans commented 1 year ago

Last issue resolved, I think we are good now.

junghans commented 1 year ago

ping @danielskatz

danielskatz commented 1 year ago

Sorry to have missed the earlier note - I'll work on this shortly

danielskatz commented 1 year ago

@apachalieva and @junghans - At this point could you:

[ ] 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.

junghans commented 1 year ago

@apachalieva and @junghans - At this point could you:

[x] Make a tagged release of your software, and list the version tag of the archived version here.

[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

[x] 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.

[x] Please list the DOI of the archived version here.

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

4 x Done

junghans commented 1 year ago

@danielskatz I think we are done, do you need anything else?

danielskatz commented 1 year ago

no. Sorry, I missed that update for some reason, and I'll get this going now

danielskatz commented 1 year ago

@editorialbot set 1.1 as version

editorialbot commented 1 year ago

Done! version is now 1.1

danielskatz commented 1 year ago

@editorialbot set 10.5281/zenodo.7469110 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7469110

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1103/physreve.102.023310 is OK
- 10.1063/1.1724389 is OK
- 10.1063/1.4921935 is OK
- 10.1103/physrevlett.112.135001 is OK
- 10.1103/PhysRevLett.118.185003 is OK
- 10.1063/1.872643 is OK
- 10.1145/1362622.1362700 is OK
- 10.2172/10176421 is OK
- 10.1007/10968987_3 is OK
- 10.48550/arXiv.1202.1056 is OK
- 10.1145/2834899.2834908 is OK
- 10.1177/1094342009106189 is OK
- 10.1063/1.5031206 is OK
- 10.1021/ct400566j is OK
- 10.48550/ARXIV.2209.09811 is OK
- 10.1038/s41598-020-69661-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year 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/3843, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@junghans - After proofreading, I've suggested some minor changes in https://github.com/lanl/GLUE/pull/20 - please merge this, or let me know what you disagree with, and then we can proceed.

apachalieva commented 1 year ago

@danielskatz, looks great! I merged it already.

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "year" (NAME) [#<BibTeX::Bibliography data=[15]>, "@", #<BibTeX::Entry >, {:title=>["Using {C}harm++ to support multiscale multiphysics on the {T}rinity supercomputer"], :author=>["Pavel, Robert and Junghans, Christoph and Mniszewski, Susan M and Germann, Timothy C"], :booktitle=>["Proceedings of the Programming Models and Co-Design Meeting"]}]

editorialbot commented 1 year ago

:warning: Error preparing paper acceptance.

danielskatz commented 1 year ago

Sorry, I missed a comma - can you merge https://github.com/lanl/GLUE/pull/21 to fix it?

rspavel commented 1 year ago

Thanks, merged

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1103/physreve.102.023310 is OK
- 10.1063/1.1724389 is OK
- 10.1063/1.4921935 is OK
- 10.1103/physrevlett.112.135001 is OK
- 10.1103/PhysRevLett.118.185003 is OK
- 10.1063/1.872643 is OK
- 10.1145/1362622.1362700 is OK
- 10.2172/10176421 is OK
- 10.1007/10968987_3 is OK
- 10.48550/arXiv.1202.1056 is OK
- 10.1145/2834899.2834908 is OK
- 10.1177/1094342009106189 is OK
- 10.1063/1.5031206 is OK
- 10.1021/ct400566j is OK
- 10.48550/ARXIV.2209.09811 is OK
- 10.1038/s41598-020-69661-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year 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/3844, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

One more small change - https://github.com/lanl/GLUE/pull/22 - maybe I shouldn't be working today...

openjournals / joss-reviews