[REVIEW]: Singularity-EOS: Performance Portable Equations of State and Mixed Cell Closures

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@Yurlungur@kyleniemeyer<!--end-editor-- Reviewers: @parikshitbajpai, @snikolov3 Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/9d2ab99bcafa1421e2c9576899cd17bc/status.svg)](https://joss.theoj.org/papers/9d2ab99bcafa1421e2c9576899cd17bc)

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

@parikshitbajpai & @snikolov3, 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 @kyleniemeyer 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 @parikshitbajpai

📝 Checklist for @snikolov3

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (1457.9 files/s, 349182.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                    48           1517           2023          14855
C++                             49           1009           1488           9838
reStructuredText                12           1427           1352           2471
CMake                           28            256            470           1265
Python                          11            272            292           1180
Markdown                         7            235              0            980
Fortran 90                       2             79             62            633
YAML                            10             53             34            522
make                             3             57             55            178
TeX                              1             13              0            164
diff                             4             39            155            118
JSON                             1              0              0            111
Bourne Shell                     2              9             29             38
HTML                             2              0              1             36
DOS Batch                        1              8              1             26
-------------------------------------------------------------------------------
SUM:                           181           4974           5962          32415
-------------------------------------------------------------------------------

Commit count by author:

   296  Jonah Maxwell Miller
   286  Jeffrey H Peterson
   199  Jonah Miller
   180  Richard Berger
   174  Christopher Mauney
   148  Daniel Holladay
    54  Karen Chung-Yen Tsai
    40  Alexander Holas
    38  Jeff Peterson
    37  Josh Dolence
    34  Ann Elisabet Wills - 298385
    29  Gopinath Subramanian
    28  Benjamin Joel Musick
    25  Christopher Michael Mauney
    23  Anna Pietarila Graham
    15  AlexHls
    10  Ben R. Ryan
    10  Christoph Junghans
    10  mauneyc-LANL
     8  jdolence
     7  Karen C. Tsai
     5  Daniel Alphin Holladay
     5  github-actions[bot]
     4  Brandon Barker
     4  Patrick Mullen
     4  mari2895
     3  Shane Patrick Fogerty
     3  c0sm0-kramer
     2  Mariam Gogilashvili
     2  Peter Brady
     2  Shane Patrick Fogerty - 322405
     1  Ben Ryan
     1  Chad Meyer
     1  Matt Stack
     1  chadmeyer

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1812

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 1 month ago

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

OK DOIs

- 10.3847/1538-4365/ab007f is OK
- 10.3847/1538-4365/ab09fc is OK
- 10.3847/0004-637X/816/1/44 is OK
- 10.1109/TPDS.2021.3097283 is OK
- 10.1145/3388333.3388649 is OK
- 10.48550/arXiv.2206.08957 is OK
- 10.1145/2807591.2807623 is OK

MISSING DOIs

- No DOI given, and none found for title: Sesame: The Los Alamos National Laboratory Equatio...
- 10.1088/0264-9381/27/11/114103 may be a valid DOI for title: A new open-source code for spherically symmetric s...
- No DOI given, and none found for title: Stellar Collapse: Microphysics
- 10.2172/1765849 may be a valid DOI for title: EOSPAC User’s Manual: V.6.5
- No DOI given, and none found for title: Numerical Recipes with Source Code CD-ROM 3rd Edit...
- No DOI given, and none found for title: CUDA, release: 10.2.89
- No DOI given, and none found for title: Parallel programming in OpenMP

INVALID DOIs

- None

editorialbot commented 1 month ago

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

kyleniemeyer commented 1 month ago

👋 @Yurlungur @parikshitbajpai @snikolov3 the actual review will take place in here. Please take a look at the information at the top of the issue (especially the reviewers, since the instructions for creating your review checklists are given there). Thanks!

parikshitbajpai commented 1 month ago

Review checklist for @parikshitbajpai

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/singularity-eos?
[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 (@Yurlungur) 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

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] 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

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] 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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

snikolov3 commented 1 month ago

Review checklist for @snikolov3

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

[ ] Repository: Is the source code for this software available at the https://github.com/lanl/singularity-eos?
[ ] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@Yurlungur) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] 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.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[ ] 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

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] 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

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] 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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

Yurlungur commented 1 week ago

Hi @kyleniemeyer @parikshitbajpai @snikolov3 I just wanted to reach out and check on the status of review. Do you have a sense when you might be able to take a deeper look? Thanks!

parikshitbajpai commented 1 week ago

Hi @kyleniemeyer @parikshitbajpai @snikolov3 I just wanted to reach out and check on the status of review. Do you have a sense when you might be able to take a deeper look? Thanks!

Hi @Yurlungur, Sorry about the delay on this. I am half way through the review and should be able to finish it beginning of next week.

Yurlungur commented 1 week ago

Hi @kyleniemeyer @parikshitbajpai @snikolov3 I just wanted to reach out and check on the status of review. Do you have a sense when you might be able to take a deeper look? Thanks!

Hi @Yurlungur, Sorry about the delay on this. I am half way through the review and should be able to finish it beginning of next week.

:+1: thanks @parikshitbajpai .

openjournals / joss-reviews