[REVIEW]: shmem4py: OpenSHMEM for Python

[editorialbot]

Submitting author: @mrogowski (Marcin Rogowski)
Repository: https://github.com/mpi4py/shmem4py
Branch with paper.md (empty if default branch): joss
Version: 1.0.0
Editor: @danielskatz
Reviewers: @greghbauer, @gonsie
Archive: 10.5281/zenodo.8143862

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c066080454299c383f8716af268fb2bb/status.svg)](https://joss.theoj.org/papers/c066080454299c383f8716af268fb2bb)

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

@greghbauer & @gonsie, 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 @gonsie

📝 Checklist for @greghbauer

[editorialbot]

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]

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

[editorialbot]

Wordcount for paper.md is 706

[editorialbot]

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

[editorialbot]

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

[danielskatz]

@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.

[gonsie]

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?

[danielskatz]

👋 @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?

[danielskatz]

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

[danielskatz]

👋 @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?

[danielskatz]

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

[danielskatz]

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

[danielskatz]

👋 @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?

[greghbauer]

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?

[gonsie]

@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

[gonsie]

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

[greghbauer]

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?

[danielskatz]

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

[mrogowski]

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

[mrogowski]

We have added a CONTRIBUTING.md file in the root directory of the repository. We hope it clarifies how to seek support, report issues and contribute to the software. We used a template recommended by other JOSS reviewers and tailored it to our application. Thanks for pointing it out, @gonsie @greghbauer!

[danielskatz]

@gonsie & @greghbauer - is the contributing part now ok?

@gonsie - I note you haven't checked off any of the functionality part of your list - Is something blocking this part for you?

@greghbauer - Re your comments above, are any of these issues that you think should block acceptance of this work? Or are they more suggestions for the future?

[greghbauer]

Hi. I am ok with the changes. Greg

…

On Mon, Jul 3, 2023 at 10:31 AM Daniel S. Katz ***@***.***> wrote: @gonsie <https://github.com/gonsie> & @greghbauer <https://github.com/greghbauer> - is the contributing part now ok? @gonsie <https://github.com/gonsie> - I note you haven't checked off any of the functionality part of your list - Is something blocking this part for you? @greghbauer <https://github.com/greghbauer> - Re your comments above <#5444 (comment)>, are any of these issues that you think should block acceptance of this work? Or are they more suggestions for the future? — Reply to this email directly, view it on GitHub <#5444 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQES7IYBRGCWXOZWSDNUESDXOLQTLANCNFSM6AAAAAAXWDBLOM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[danielskatz]

@greghbauer - can you check off your remaining item then?

[danielskatz]

@editorialbot set 1.0.0 as version

[editorialbot]

Done! version is now 1.0.0

[danielskatz]

@editorialbot recommend-accept

I will proofread this, and then talk about next steps

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4407, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

I'm trying to figure out what's going on with the bad DOI before we move forward - I've contacted Crossref and ACM about it.

[danielskatz]

The paper otherwise looks good, and we can proceed and acceptance and publication once the DOI issue is fixed, and I'll let you know what I find out about it.

[mrogowski]

Thank you. I also reported it using the form on https://doi.org, but I did not hear back yet.

[danielskatz]

Slight DOI progress - it turns out that the paper is a USENIX paper that was published through the ACM DL, so ACM is contacting USENIX now to see if they can fix this, as they are supposed to own the DOI.

[danielskatz]

It's not clear to me where the DOI for this came from, as the original from USENIX (https://www.usenix.org/conference/osdi18/presentation/alquraan) doesn't list a DOI. If this isn't resolve fairly quickly, the best option would probably be to remove the DOI from the bibtex entry and to add this URL instead, but let's see what USENIX says first.

[danielskatz]

@mrogowski - Let's go ahead and proceed as above. Can you remove the DOI that doesn't work and add the URL?

[mrogowski]

I just updated the bibtex entry to that listed on https://www.usenix.org/conference/osdi18/presentation/moritz, including the URL. Thanks for following up on that.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

- None

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4418, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Rogowski
  given-names: Marcin
  orcid: "https://orcid.org/0000-0002-5662-2082"
- family-names: Dalcin
  given-names: Lisandro
  orcid: "https://orcid.org/0000-0001-8086-0155"
- family-names: Hammond
  given-names: Jeff R.
  orcid: "https://orcid.org/0000-0003-3181-8190"
- family-names: Keyes
  given-names: David E.
  orcid: "https://orcid.org/0000-0002-4052-7224"
contact:
- family-names: Rogowski
  given-names: Marcin
  orcid: "https://orcid.org/0000-0002-5662-2082"
doi: 10.5281/zenodo.8143862
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Rogowski
    given-names: Marcin
    orcid: "https://orcid.org/0000-0002-5662-2082"
  - family-names: Dalcin
    given-names: Lisandro
    orcid: "https://orcid.org/0000-0001-8086-0155"
  - family-names: Hammond
    given-names: Jeff R.
    orcid: "https://orcid.org/0000-0003-3181-8190"
  - family-names: Keyes
    given-names: David E.
    orcid: "https://orcid.org/0000-0002-4052-7224"
  date-published: 2023-07-19
  doi: 10.21105/joss.05444
  issn: 2475-9066
  issue: 87
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5444
  title: "shmem4py: OpenSHMEM for Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05444"
  volume: 8
title: "shmem4py: OpenSHMEM for Python"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05444 joss-papers#4419
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05444
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @mrogowski (Marcin Rogowski) and co-authors on your publication!!

And thanks to @greghbauer and @gonsie for reviewing!
We couldn't do this without your voluntary efforts

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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</a>

reStructuredText:
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[mrogowski]

Thank you @danielskatz, @gonsie and @greghbauer!