[REVIEW]: PyLops-MPI - MPI Powered PyLops with mpi4py

[editorialbot]

Submitting author: @rohanbabbar04 (Rohan Babbar)
Repository: https://github.com/PyLops/pylops-mpi
Branch with paper.md (empty if default branch): joss
Version: v0.1.0
Editor: @gkthiruvathukal
Reviewers: @gonsie, @mikaem
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/be7da46cc87d0c182b26862b77a6e608/status.svg)](https://joss.theoj.org/papers/be7da46cc87d0c182b26862b77a6e608)

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

@gonsie & @mikaem, 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 @gkthiruvathukal 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 @mikaem

[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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1154.4 files/s, 150289.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           1140           2091           4702
reStructuredText                17            300            279            394
YAML                             7             13             12            182
Markdown                         3             50              0            170
TeX                              1              9              0            125
CSS                              2             24              7             91
make                             2             18              9             49
TOML                             1              3              0             41
HTML                             1              6              0             32
Bourne Shell                     1              3              2             12
-------------------------------------------------------------------------------
SUM:                            75           1566           2400           5798
-------------------------------------------------------------------------------

Commit count by author:

   187	rohanbabbar04
    44	mrava87
    24	Rohan Babbar
     4	Matteo Ravasi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 993

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Lesser General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.softx.2019.100361 is OK
- 10.1109/MCSE.2021.3083216 is OK
- 10.21105/joss.01340 is OK
- 10.21105/joss.06415 is OK
- 10.21105/joss.03419 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1093/gji/ggab388 is OK
- 10.1190/1.1444517 is OK
- 10.1109/tgrs.2022.3179626 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CuPy: A NumPy-Compatible Library for NVIDIA GPU Ca...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

[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/PyLops/pylops-mpi?
• 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 (@rohanbabbar04) 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?

[mikaem]

Review checklist for @mikaem

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/PyLops/pylops-mpi?
• 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 (@rohanbabbar04) 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?

[mikaem]

@editorialbot commands

[editorialbot]

Hello @mikaem, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[mikaem]

@gkthiruvathukal I have gone through the checklist and I have very few issues. The software installs immediately on my mac and the tests run with just a few fails that could simply be due to roundoff on my computer. The tests all pass on github actions and I see no need to follow this up further here. The documentation is good. One minor thing, you need to install the dev-environment.yml in order to run tests. That is not really what the README says and it should probably be fixed.

I have just a few issue with the written paper. The figure contains very small text and I don't think it is referenced in running text? I think it can safely be removed or else it needs to be introduced properly. Also, at the bottom of page 2 DistributedArray and StackedDistributedArray are formatted in bold, but I think they should be formatted like the other code objects, like pylops_mpi.MPIVstack.

[gkthiruvathukal]

@mikaem Thanks for this feedback. @rohanbabbar04, please respond and continue to engage here and address these issues.

We will give @gonsie time to enter a review and proceed from there!

[rohanbabbar04]

@gkthiruvathukal I have gone through the checklist and I have very few issues. The software installs immediately on my mac and the tests run with just a few fails that could simply be due to roundoff on my computer. The tests all pass on github actions and I see no need to follow this up further here. The documentation is good. One minor thing, you need to install the dev-environment.yml in order to run tests. That is not really what the README says and it should probably be fixed.

I have just a few issue with the written paper. The figure contains very small text and I don't think it is referenced in running text? I think it can safely be removed or else it needs to be introduced properly. Also, at the bottom of page 2 DistributedArray and StackedDistributedArray are formatted in bold, but I think they should be formatted like the other code objects, like pylops_mpi.MPIVstack.

Hi @mikaem ,
Thanks for the feedback, let me look into these and get back to you ASAP.