[REVIEW]: shmem4py: OpenSHMEM for Python about joss-reviews HOT 19 OPEN

@mrogowski

Seems like the Community Guidelines stuff is missing (I couldn't find any guidance on the documentation site, nor in the repo itself).

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

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All I have left to do is test the functionality. I hope to get to that within the next week or so.

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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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (1120.0 files/s, 135661.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          36            981           1254           4297
C/C++ Header                    15            219             41           1316
Dockerfile                       8             44              6            204
TeX                              1             13              0            130
Markdown                         3             22              0             87
make                             5             19              7             81
INI                              2              8              0             70
Bourne Shell                     1             12              0             61
YAML                             2              6              1             60
reStructuredText                 2             85            284             41
C                                1             12             10             35
DOS Batch                        1              8              1             26
TOML                             1              0              0              7
-------------------------------------------------------------------------------
SUM:                            78           1429           1604           6415
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 706

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

OK DOIs

- 10.1145/2020373.2020375 is OK
- 10.25080/Majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.1109/TPDS.2022.3225481 is OK
- 10.1109/IPDPS.2015.35 is OK
- 10.1007/978-3-319-41321-1_15 is OK
- 10.1109/HiPC.2017.00037 is OK
- 10.1109/IPDPSW50202.2020.00104 is OK
- 10.1007/978-3-319-05215-1 is OK
- 10.1007/978-3-319-05215-1_2 is OK
- 10.1109/ICPP.2012.55 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/3291168.3291210 is INVALID

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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@greghbauer and @gonsie - 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#5444 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.

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Review checklist for @gonsie

Conflict of interest

• 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

• 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/mpi4py/shmem4py?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mrogowski) 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?

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👋 @greghbauer - Can you generate your checklist, and ideally check off the first two items, just to make sure all the permissions here are working right?

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👋 @gonsie - Are you doing ok on your review? Is anything blocking you?

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👋 @greghbauer - Can you generate your checklist, and ideally check off the first two items, just to make sure all the permissions here are working right?

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👋 @gonsie - Are you doing ok on your review? Is anything blocking you?

from joss-reviews.

👋 @gonsie - Are you doing ok on your review? Is anything blocking you?

from joss-reviews.

👋 @greghbauer - Can you generate your checklist, and ideally check off the first two items, just to make sure all the permissions here are working right?

from joss-reviews.

Review checklist for @greghbauer

Conflict of interest

• 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

• 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/mpi4py/shmem4py?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mrogowski) 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?

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After several false starts, I was able to complete the functionality testing, using Open MPI OpenSHMEM on NCSA Delta with anaconda, with SLURM srun replacing oshrun. I was able to do some of the tests across more than one node.

The install instructions at https://shmem4py.readthedocs.io/en/latest/installation.html state "Once a working OpenSHMEM implementation is installed" trivializes the task.

The install instructions at https://github.com/mpi4py/shmem4py/blob/master/INSTALL.rst are more complete but assume root level capabilities with the user of sudo apt-get.

I did not try to use the docker container docker build scripts. On HPC sites docker is typically not possible. Would sif build scripts be possible?

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@gonsie and @greghbauer - thanks for your comments and concerns. Once @mrogowski has addressed them, I hope we will see comments here from him.

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Thank you for your comments! I will make necessary changes and respond within a few days.

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