[REVIEW]: mpi4py-fft - Parallel Fast Fourier Transforms with MPI for Python

[whedon]

Submitting author: @mikaem (Mikael Mortensen)
Repository: https://bitbucket.org/mpi4py/mpi4py-fft
Version: 2.0.2
Editor: @VivianePons
Reviewer: @iljah, @rainwoodman
Archive: 10.5281/zenodo.2621442

Status

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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) 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

@iljah & @rainwoodman, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @VivianePons know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @iljah

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: 2.0.2
• Authorship: Has the submitting author (@mikaem) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @rainwoodman

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: 2.0.2
• Authorship: Has the submitting author (@mikaem) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @iljah, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[iljah]

@VivianePons bitbucket doesn't seem to have releases so this item isn't applicable "Does the release version given match the GitHub release (v2.0.0)". I'll mark it as completed...

[mikaem]

@iljah The most recent version released on pypi and conda-forge is now 2.0.1. I need to change the JOSS version number. The tags on bitbucket, used for these releases, are here.

[iljah]

@mikaem this condition might not hold for mpi4py-fft: "Does the repository contain a plain-text LICENSE file". Even though rst isn't a binary format it still doesn't look like plain text when viewed in a plain text editor.

[iljah]

I couldn't find examples on how to use mpi4py-fft as required by "Example usage: Do the authors include examples of how to use the software". At least one simple example would be informative.

[iljah]

Community guidelines as listed in our checklists also seem to be missing.

[iljah]

Functionality documentation also seems to be missing, unless using external websites is allowed, @VivianePons ?

[iljah]

Ah looks like most documentation is "hidden" in docs/source directory. Mentioning this directory in top level readme should be sufficient to cover doc requirements...

[dalcinl]

@iljah About LICENSE.rst: In general lines, reStructuredText, Markdown, etc can be considered plain-text, they were designed with very lightweight markup in mind. In the very particular case of our LICENSE.rst, we only deviate for extreme pure-text in the two fields :Author: and :Contact:, however this markup is extremely lightweight, IMHO it does not interfere at all with reading it in a text editor, and we get the bonus of nice rendering when viewed in Bitbucket or GitHub.

Of course, I'm not a lawyer. @VivianePons What should we do?

@mikaem Anyway, we need to update the license file to read 2017-2019.

[dalcinl]

@iljah The documentation is not "hidden" in docs/source. It is just the reStructuredText sources for what is available online in https://mpi4py-fft.readthedocs.io. BTW, our README file has the usual docs:passing badge at the top with the link to readthedocs.

[dalcinl]

@iljah About examples, did you take a look under the examples directory?

[arfon]

Of course, I'm not a lawyer. @VivianePons What should we do?

IANAL too but I think this is OK.

[iljah]

our README file has the usual docs:passing badge at the top with the link to readthedocs

As I understood my instructions, documentation should be in readme file so link to external website isn't sufficient, @VivianePons ? I think just cloning the repo should give everything my instructions are asking for, at least minimal versions of each item.

did you take a look under the examples directory?

No as it wasn't mentioned in readme. I guess examples dir is good enough but mentioning it would be nice.

[iljah]

I couldn't find separate API documentation (in git repo) but using dir and help commands on mpi4py_fft and its contents looks good enough.

[VivianePons]

@whedon set version 2.0.1

[VivianePons]

@whedon set 2.0.1 as version

[whedon]

OK. 2.0.1 is the version.

[VivianePons]

licence: I believe a .rst file is ok
documentation: the readthedoc version is ok, considering the source is in the repo. It would be good to have a link from the readme
Same for "examples", make it easy for a user to find everything from the readme file by just adding a few links.

[rainwoodman]

@VivianePons : Do I need to pay special attention to avoid biasing my review by seeing other reviewer's comments?

[VivianePons]

No don't worry about that, the idea is that the discussion is open between both reviewers and the authors. I trust your judgement anyway ;)

[rainwoodman]

The guideline calls for citations to existing software performing similar functionalities.
The submission contains citations that demonstrates the merit / usefulness of this software, but is missing a citations to existing software that also performs distributed parallel FFTs: fftw-mpi, p3dfft, pfft, accfft, to name a few.

[rainwoodman]

@VivianePons Is there a mechanism to submit comments in bulk and keep track of them?

[iljah]

This might work well: https://help.github.com/en/articles/about-task-lists

[mikaem]

The guideline calls for citations to existing software performing similar functionalities.
The submission contains citations that demonstrates the merit / usefulness of this software, but is missing a citations to existing software that also performs distributed parallel FFTs: fftw-mpi, p3dfft, pfft, accfft, to name a few.

@rainwoodman Thank you for the feedback. The guidelines (under What should my paper contain?) state that we should include key references and Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it. There seem to be no call for citations to existing software performing similar functionalities.

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[VivianePons]

Can you please:

• update the archive with the latest changes
• update the archive metainfo so that the title is the same than the paper title
• Add David Elliot Keyes to the list of authors in the archive

[mikaem]

@VivianePons Created a new release and there's a new doi: 10.5281/zenodo.2621442
This one has all three authors and the same title as the paper.

[mikaem]

@whedon set version 2.0.2

[mikaem]

@whedon set 2.0.2 as version

[whedon]

I'm sorry @mikaem, I'm afraid I can't do that. That's something only editors are allowed to do.

[mikaem]

@VivianePons Looks like you need to update the version to 2.0.2

[VivianePons]

@whedon set 2.0.2 as version

[whedon]

OK. 2.0.2 is the version.

[VivianePons]

@whedon set 10.5281/zenodo.2621442 as archive

[whedon]

OK. 10.5281/zenodo.2621442 is the archive.

[VivianePons]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[VivianePons]

Congratulations, this paper is good to go! Thank you @mikaem for this submission and @iljah and @rainwoodman for the reviews!

@openjournals/joss-eics it's up to you

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#598

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#598, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

OK DOIs

- 10.1016/j.jpdc.2019.02.006 is OK
- 10.21105/joss.01071 is OK
- 10.1016/j.jpdc.2007.09.005 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1109/JPROC.2004.840301 is OK
- 10.1016/j.cpc.2016.02.005 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🚨🚨🚨 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.01340 joss-papers#599
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01340
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...

[kyleniemeyer]

@mikaem congrats on your JOSS publication, and thanks to @iljah and @rainwoodman for reviewing and @VivianePons for editing!

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

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</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01340/status.svg
   :target: https://doi.org/10.21105/joss.01340

This is how it will look in your documentation:

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