[REVIEW]: Elephas: Distributed Deep Learning with Keras & Spark

whedon commented 2 years ago

Submitting author: !--author-handle-->@maxpumperla@diehlpk<!--end-editor-- Reviewers: @sepandhaghighi, @nmoran Archive: 10.5281/zenodo.7435012

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diehlpk commented 1 year ago

@sepandhaghighi moving forward this project will be maintained by Daniel Cahill. He decided to create this own fork. The important bit is that a) the info on the repo is still valid b) the project is considered feature-complete with the 3.0 release and c) the software will always be available as elephas package. Thanks for this question, though!

@maxpumperla I think it would be better if the repo url points to the new repo, since new updated will be pushed there. What do you think?

diehlpk commented 1 year ago

@editorialbot set mp_joss_paper as branch

editorialbot commented 1 year ago

Done! branch is now mp_joss_paper

diehlpk commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@maxpumperla It seems that

danielenricocahall 101 1855 2424 28.70

contributed to the code as well and is now the new maintainer. Would it make sense to add him as a second author?

maxpumperla commented 1 year ago

yes, thanks @diehlpk. In fact, I've invited @danielenricocahall a couple of times already to add his name to honour his contributions!

@danielenricocahall now would be a good time 👍

danielenricocahall commented 1 year ago

Hello @maxpumperla , sorry for the delay! Just added now :) Did I add myself correctly? https://github.com/maxpumperla/elephas/blob/mp_joss_paper/paper.md

danielenricocahall commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

danielenricocahall commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@sepandhaghighi moving forward this project will be maintained by Daniel Cahill. He decided to create this own fork. The important bit is that a) the info on the repo is still valid b) the project is considered feature-complete with the 3.0 release and c) the software will always be available as elephas package. Thanks for this question, though!

@maxpumperla I think it would be better if the repo url points to the new repo, since new updated will be pushed there. What do you think?

@danielenricocahall and @maxpumperla any comments?

diehlpk commented 1 year ago

@sepandhaghighi I think you can proceed with the review.

danielenricocahall commented 1 year ago

@sepandhaghighi moving forward this project will be maintained by Daniel Cahall. He decided to create this own fork. The important bit is that a) the info on the repo is still valid b) the project is considered feature-complete with the 3.0 release and c) the software will always be available as elephas package. Thanks for this question, though!
@maxpumperla I think it would be better if the repo url points to the new repo, since new updated will be pushed there. What do you think?

@danielenricocahall and @maxpumperla any comments?

I agree.

diehlpk commented 1 year ago

@danielenricocahall Could you please recommend some reviewers?

sepandhaghighi commented 1 year ago

@diehlpk @maxpumperla @danielenricocahall

Result:

A well-known and interesting tool from a prolific team 💯 But there are some concerns about documentation and community guidelines:

Documentation
- I didn't find any API level documentation (https://danielenricocahall.github.io/elephas/ is available but it only contains some examples, is it sufficient? I'm not sure!!)
- This link is broken
- Some functions don't have docstring
Community Guidelines
- No specific contribution guideline (without such a guideline, it's very hard to contribute to this project)
- No issue template
- No PR template

@danielenricocahall is one of the paper authors, so it would be better to remove his name from the Acknowledgments section
I suggest reporting your tests coverage (by something like codecov)

Best Regards SH

diehlpk commented 1 year ago

@maxpumperla @danielenricocahall Please have a look at these comments. All of them are important to finish the review.

diehlpk commented 1 year ago

Hi @urbanophile do you have time to review that paper?

diehlpk commented 1 year ago

Hi @nmoran do you have time to review that paper?

maxpumperla commented 1 year ago

@diehlpk happy to address the above comments, but given that we've submitted this ~10 months ago and not much happened in the meantime, I'd prefer to get a preliminary "go" from you first and only then put in more work.

diehlpk commented 1 year ago

@diehlpk happy to address the above comments, but given that we've submitted this ~10 months ago and not much happened in the meantime, I'd prefer to get a preliminary "go" from you first and only then put in more work.

I think you should address the comments. The software and paper is good and I think it deserves to be published. However, making the software user-friendly will take some effort.

maxpumperla commented 1 year ago

@diehlpk sure, like I said, we definitely intend to! After maintaining this for around 6 years now, I just lean towards being a little conservative when it comes to requests.

@danielenricocahall how does your November look like? Maybe we can discuss in private how to tackle these comments? I think this all very reasonable and should help the project a lot.

diehlpk commented 1 year ago

@maxpumperla Can you provide some timeline for the changes? So I can pause the review.

nmoran commented 1 year ago

Hi @diehlpk , apologies for delay, but was away for a bit. I can review in the coming week if not too late?

diehlpk commented 1 year ago

Hi @diehlpk , apologies for delay, but was away for a bit. I can review in the coming week if not too late?

Thank you.

diehlpk commented 1 year ago

@editorialbot add @nmoran as reviewer

editorialbot commented 1 year ago

@nmoran added to the reviewers list!

nmoran commented 1 year ago

Review checklist for @nmoran

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/danielenricocahall/elephas?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@maxpumperla) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

maxpumperla commented 1 year ago

@diehlpk sorry, currently down with Covid. Apologies for the delay on my part, I think I might get to this ~ mid December.

diehlpk commented 1 year ago

@diehlpk sorry, currently down with Covid. Apologies for the delay on my part, I think I might get to this ~ mid December.

Thanks for the heads-up. Sorry to hear and hope you are doing better soon.

danielenricocahall commented 1 year ago

Added some contribution guidelines here: https://github.com/danielenricocahall/elephas/blob/master/CONTRIBUTING.md
Added three issue templates: https://github.com/danielenricocahall/elephas/tree/master/.github/ISSUE_TEMPLATE
- Updated some function docstrings Will work on more in the todo list soon! I agree with the mid-December assessment.

danielenricocahall commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

arfon commented 1 year ago

@danielenricocahall it looks like the mp_joss_paper branch doesn't exist any longer? You can update the branch @editorialbot uses with the command:

@editorialbot set xxx as branch

danielenricocahall commented 1 year ago

Ah! I think because we're now pointing to my fork as the main repo. I can move the branch over there then retry the job later today. Apologies for that!

nmoran commented 1 year ago

I am running into some problems getting the software running while following the install instructions provided. I have opened the following two issues to track these.

https://github.com/danielenricocahall/elephas/issues/15

https://github.com/danielenricocahall/elephas/issues/16

diehlpk commented 1 year ago

@danielenricocahall @maxpumperla please have a look when ever you have time.

danielenricocahall commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

danielenricocahall commented 1 year ago

I believe I addressed the issues in the latest release (3.4.7), which required pinning the Tensorflow version to <=2.10. Also, PyPI now has the Github documentation: https://pypi.org/project/elephas/3.4.7/.

nmoran commented 1 year ago

The paper and software look good to me and is of use to many users as evidenced by the large number of monthly downloads 💯

I am happy to recommend this be published in JOSS.

In addition I think it could be useful to mention the versions of python that elephas was developed and tested with to save users time in case there are unforeseen incompatibilities with older or newer versions.

sepandhaghighi commented 1 year ago

@diehlpk LGTM 🚀

diehlpk commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1145/3357223.3362707 is OK

MISSING DOIs

- None

INVALID DOIs

- None

diehlpk commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

diehlpk commented 1 year ago

@maxpumperla or @danielenricocahall please add the city and country to the affiliations, and we can proceed with preparing the publication.

maxpumperla commented 1 year ago

affiliations:
  - name: IU Internationale Hochschule, Erfurt, Germany
    index: 1
  - name: Anyscale Inc, San Francisco, USA
    index: 2

@danielenricocahall I don't know which branch and repo we settled on for the PDF by now, but could you please update affiliation info for me like this when you update yours? thank you.

also, many thanks @diehlpk for finally moving this towards the finish line!!!

danielenricocahall commented 1 year ago

@editorialbot generate pdf

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