[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.

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[rohanbabbar04]

Hi @mikaem ,

Thank you for your feedback!

Here are some points regarding the feedback:

• The installation procedure for developers is documented on the Installation page. We typically don't include this information in the README, but instead, document it in the installation guide. Additionally, we provide a Makefile that we ask developers to use for installation.
• DistributedArray and StackedDistributedArray have been updated to pylops_mpi.DistributedArray and pylops_mpi.StackedDistributedArray.
• I would like to retain the figure, as it illustrates the main architecture of the library and operators. However, I agree that it should be referenced appropriately. I've added a line referencing Fig 1.

[mikaem]

Hi @gkthiruvathukal @rohanbabbar04
This is ok by me.

[gkthiruvathukal]

@mikaem Thanks!
We will await input from @gonsie.