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

[editorialbot]

Submitting author: !--author-handle-->@rohanbabbar04<!--end-author-handle-- (Rohan Babbar) Repository: https://github.com/PyLops/pylops-mpi Branch with paper.md (empty if default branch): joss Version: v0.1.0 Editor: !--editor-->@gkthiruvathukal<!--end-editor-- Reviewers: @gonsie, @mikaem Managing EiC: Daniel S. Katz

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[editorialbot]

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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]

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
- 10.1109/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

- 10.1190/1.1444517 may be a valid DOI for title: Least-squares migration of incomplete reflection d...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1162.5 files/s, 152316.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           1140           2091           4702
reStructuredText                17            300            279            394
Markdown                         3             58              0            229
YAML                             7             13             12            182
TeX                              1              9              0            121
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           1574           2400           5853
-------------------------------------------------------------------------------

Commit count by author:

   183  rohanbabbar04
    44  mrava87
    23  Rohan Babbar
     4  Matteo Ravasi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1822

✅ 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]

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

[editorialbot]

Five most similar historical JOSS papers:

mpi4jax: Zero-copy MPI communication of JAX arrays Submitting author: @dionhaefner Handling editor: @kellyrowland (Active) Reviewers: @1313e, @Himscipy Similarity score: 0.6752

GridapDistributed: a massively parallel finite element toolbox in Julia Submitting author: @amartinhuertas Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown Similarity score: 0.6702

mpi4py-fft: Parallel Fast Fourier Transforms with MPI for Python Submitting author: @mikaem Handling editor: @VivianePons (Retired) Reviewers: @iljah, @rainwoodman Similarity score: 0.6702

pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems Submitting author: @nwu63 Handling editor: @poulson (Retired) Reviewers: @jgoldfar, @vissarion, @matbesancon Similarity score: 0.6689

shmem4py: OpenSHMEM for Python Submitting author: @mrogowski Handling editor: @danielskatz (Active) Reviewers: @greghbauer, @gonsie Similarity score: 0.6682

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[rohanbabbar04]

@editorialbot commands

[editorialbot]

Hello @rohanbabbar04, 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

[rohanbabbar04]

@editorialbot check references

[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

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

mpi4jax: Zero-copy MPI communication of JAX arrays Submitting author: @dionhaefner Handling editor: @kellyrowland (Active) Reviewers: @1313e, @Himscipy Similarity score: 0.6755

mpi4py-fft: Parallel Fast Fourier Transforms with MPI for Python Submitting author: @mikaem Handling editor: @VivianePons (Retired) Reviewers: @iljah, @rainwoodman Similarity score: 0.6702

GridapDistributed: a massively parallel finite element toolbox in Julia Submitting author: @amartinhuertas Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown Similarity score: 0.6701

pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems Submitting author: @nwu63 Handling editor: @poulson (Retired) Reviewers: @jgoldfar, @vissarion, @matbesancon Similarity score: 0.6689

shmem4py: OpenSHMEM for Python Submitting author: @mrogowski Handling editor: @danielskatz (Active) Reviewers: @greghbauer, @gonsie Similarity score: 0.6685

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

@rohanbabbar04 - thanks for your submission. I'll be the track editor, working on it until it gets assigned to an editor, and then coming back at the end to handle final processing.

At this point, can you

1. ensure that references have spaces before them in the .md file, so that we don't have things like where the space is missing in the PDF
2. Consider removing some of your paper in favor of pointing to documentation in the repo. Your paper is about 1800 words, and JOSS papers are recommended to be 250-1000 words.
3. Consider if you need an Acknowledgments section, to acknowledge any funding or other support or help

I'll mark this as paused - please ping me when you are ready to proceed or have questions.

[rohanbabbar04]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1195.3 files/s, 155625.0 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            171
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           5799
-------------------------------------------------------------------------------

Commit count by author:

   185  rohanbabbar04
    44  mrava87
    24  Rohan Babbar
     4  Matteo Ravasi

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1009

✅ 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)

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

shmem4py: OpenSHMEM for Python Submitting author: @mrogowski Handling editor: @danielskatz (Active) Reviewers: @greghbauer, @gonsie Similarity score: 0.7771

X-PSI: A Python package for neutron star X-ray pulse simulation and inference Submitting author: @drannawatts Handling editor: @adonath (Active) Reviewers: @JohannesBuchner, @matteobachetti Similarity score: 0.7575

mpi4jax: Zero-copy MPI communication of JAX arrays Submitting author: @dionhaefner Handling editor: @kellyrowland (Active) Reviewers: @1313e, @Himscipy Similarity score: 0.7410

parafields: A generator for distributed, stationary Gaussian processes Submitting author: @dokempf Handling editor: @diehlpk (Active) Reviewers: @shahmoradi, @gchure Similarity score: 0.7354

Micro Manager: a Python package for adaptive and flexible two-scale coupling Submitting author: @IshaanDesai Handling editor: @philipcardiff (Active) Reviewers: @mayrmt, @mrogowski, @mbkumar Similarity score: 0.7349

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[rohanbabbar04]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1185.9 files/s, 154388.3 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:

   186  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)

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

shmem4py: OpenSHMEM for Python Submitting author: @mrogowski Handling editor: @danielskatz (Active) Reviewers: @greghbauer, @gonsie Similarity score: 0.7748

X-PSI: A Python package for neutron star X-ray pulse simulation and inference Submitting author: @drannawatts Handling editor: @adonath (Active) Reviewers: @JohannesBuchner, @matteobachetti Similarity score: 0.7569

mpi4jax: Zero-copy MPI communication of JAX arrays Submitting author: @dionhaefner Handling editor: @kellyrowland (Active) Reviewers: @1313e, @Himscipy Similarity score: 0.7414

PyNumDiff: A Python package for numerical differentiation of noisy time-series data Submitting author: @florisvb Handling editor: @christinahedges (Retired) Reviewers: @pmli, @billtubbs Similarity score: 0.7398

Your: Your Unified Reader Submitting author: @KshitijAggarwal Handling editor: @dfm (Active) Reviewers: @pravirkr, @paulray Similarity score: 0.7360

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[rohanbabbar04]

@rohanbabbar04 - thanks for your submission. I'll be the track editor, working on it until it gets assigned to an editor, and then coming back at the end to handle final processing.

At this point, can you

1. ensure that references have spaces before them in the .md file, so that we don't have things like <img alt="Screenshot 2024-10-09 at 16 47 50" width="251" src="https://private-user-images.githubusercontent.com/2913845/375126758-aa82bb61-7849-488d-8be6-5a2896a26813.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3Mjg2MzI3MjksIm5iZiI6MTcyODYzMjQyOSwicGF0aCI6Ii8yOTEzODQ1LzM3NTEyNjc1OC1hYTgyYmI2MS03ODQ5LTQ4OGQtOGJlNi01YTI4OTZhMjY4MTMucG5nP1gtQW16LUFsZ29yaXRobT1BV1M0LUhNQUMtU0hBMjU2JlgtQW16LUNyZWRlbnRpYWw9QUtJQVZDT0RZTFNBNTNQUUs0WkElMkYyMDI0MTAxMSUyRnVzLWVhc3QtMSUyRnMzJTJGYXdzNF9yZXF1ZXN0JlgtQW16LURhdGU9MjAyNDEwMTFUMDc0MDI5WiZYLUFtei1FeHBpcmVzPTMwMCZYLUFtei1TaWduYXR1cmU9MzgxOTg2YTk1ZjdkZWExOWM0ZGQ5MDIyNzU5ODY0Njg0NTU1YmY2OTMxZmI4YTY2ZmQxNjJjNjU2MGY3NWFjNyZYLUFtei1TaWduZWRIZWFkZXJzPWhvc3QifQ.M9P3DR7Iq4_P3oXjdwPHKvZPK6wx5INo2IYwcGIRY7I"> where the space is missing in the PDF

2. Consider removing some of your paper in favor of pointing to documentation in the repo. Your paper is about 1800 words, and JOSS papers are recommended to be 250-1000 words.

3. Consider if you need an Acknowledgments section, to acknowledge any funding or other support or help

I'll mark this as paused - please ping me when you are ready to proceed or have questions.

Thanks @danielskatz for a quick review of the paper and providing your feedback. I have made the updates following your suggestions.

• Ensured that all references have spaces before them in the .md file to prevent any formatting issues in the PDF.
• The content is now within 250-1000 words to align the paper with JOSS's recommended length.
• Added an Acknowledgments section to acknowledge support.

Please let me know if there are any other changes required. I’m happy to proceed whenever you’re ready.

[rohanbabbar04]

@editorialbot check references

[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

[rohanbabbar04]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

shmem4py: OpenSHMEM for Python Submitting author: @mrogowski Handling editor: @danielskatz (Active) Reviewers: @greghbauer, @gonsie Similarity score: 0.7751

X-PSI: A Python package for neutron star X-ray pulse simulation and inference Submitting author: @drannawatts Handling editor: @adonath (Active) Reviewers: @JohannesBuchner, @matteobachetti Similarity score: 0.7579

mpi4jax: Zero-copy MPI communication of JAX arrays Submitting author: @dionhaefner Handling editor: @kellyrowland (Active) Reviewers: @1313e, @Himscipy Similarity score: 0.7415

PyNumDiff: A Python package for numerical differentiation of noisy time-series data Submitting author: @florisvb Handling editor: @christinahedges (Retired) Reviewers: @pmli, @billtubbs Similarity score: 0.7414

Your: Your Unified Reader Submitting author: @KshitijAggarwal Handling editor: @dfm (Active) Reviewers: @pravirkr, @paulray Similarity score: 0.7369

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[rohanbabbar04]

Hi @danielskatz, I have addressed your suggestions and made the necessary changes. Is it ready to be removed from the paused status?

[danielskatz]

Thanks @rohanbabbar04 - I'll get back to this by Monday...

[danielskatz]

@rohanbabbar04 - yes, this looks good. I'll "unpause" it now, but it will still need to wait a little until a relevant editor becomes free.

[danielskatz]

👋 @gkthiruvathukal - it looks like one of your edited submissions is just about done. Would you be able to take on this one?

[danielskatz]

@editorialbot invite @gkthiruvathukal as editor

[editorialbot]

Invitation to edit this submission sent!

[gkthiruvathukal]

@danielskatz Yes, as long as you can bear with slow progress over no progress!

[danielskatz]

@editorialbot assign @gkthiruvathukal as editor

Thanks @gkthiruvathukal

[editorialbot]

Assigned! @gkthiruvathukal is now the editor

[rohanbabbar04]

Thanks @gkthiruvathukal for taking this up

[gkthiruvathukal]

@rohanbabbar04 Can you let me know if you have any suggestions for potential reviewers? I am thinking of iljah and rainwoodman since they were involved in a similar JOSS submission where mpi4py was used.

[rohanbabbar04]

Hi @gkthiruvathukal, Sure, you can ask iljah and rainwoodman if they are available, as I can see they have worked with mpi4py before. I can also look into potential reviewers to find more people.

[gkthiruvathukal]

@rohanbabbar04 I was thinking of these two as well!

[gkthiruvathukal]

@iljah and @rainwoodman, are you willing to help review this JOSS submission? I think it would be of interest, based on your past review for JOSS.

[rohanbabbar04]

Hi @gkthiruvathukal , It looks as if iljah and rainwoodman are not available at the moment, do you suggest we should look for more reviewers?