Joss-reviews: [REVIEW]: opt_einsum: A tensor contraction order optimizer for NumPy

[whedon]

Submitting author: @dgasmith (Daniel Smith)
Repository: https://github.com/dgasmith/opt_einsum
Version: v2.0.0
Editor: @pjotrp
Reviewer: @prasunanand
Archive: 10.5281/zenodo.1299981

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

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

1. Make sure you're logged in to your GitHub account
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 @pjotrp know.

Review checklist for @prasunanand

Conflict of interest

• [x] 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

• [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 repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: Does the release version given match the GitHub release (v2.0.0)?
• [x] Authorship: Has the submitting author (@dgasmith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @prasunanand it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

1. 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 :page_facing_up: <--

[pjotrp]

@dgasmith thanks for your submission! To expedite review, do you mind going through above check list to make sure we can tick all boxes? You can't tick them, just go through them.

[dgasmith]

@pjotrp Thanks, I believe I have them all except Community guidelines might be weak. Do you have examples of good repositories that do this? Would be interesting to do some sort of guidelines with URSSI or similar organizations.

[pjotrp]

Great @dgasmith. You can lift them from most papers in JOSS. It is not exactly a requirement, but a good to have. @prasunanand, we are ready for review!

[pjotrp]

Ping @prasunanand

[prasunanand]

Sorry for reviewing late. I am reviewing it today.

@dgasmith : I would suggest to add the link to ./.github/Contributing.md in ./README.md .

You also need to edit the Contributing.md. For example, in 1st paragraph project_name should be replaced with opt_einsum .

[dgasmith]

@prasunanand Great, thanks for the feedback. Patched up.

[pjotrp]

@prasunanand, are we ready to wrap this up?

[prasunanand]

@pjotrp : Review complete :)

@dgasmith : Cool software. Nice work :muscle:

%timeit contract('pi,qj,ijkl,rk,sl->pqrs', C, C, I, C, C)
The slowest run took 393.49 times longer than the fastest. This could mean that an intermediate result is being cached.
1000 loops, best of 3: 411 µs per loop

I am not sure if the message "regarding caching" could be suppressed.

[pjotrp]

@arfon YAPTBA (yet another paper to be accepted)

[pjotrp]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #753 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 11 0 11 0 0 113 0 --:--:-- --:--:-- --:--:-- 114
Error producing PDF.
! Missing $ inserted.

$
l.313

Looks like we failed to compile the PDF

[pjotrp]

@dgasmith can you fix the PDF generation? Just rerun using above whedon command.

[dgasmith]

@prasunanand I could not find this in our documentation, did we miss it? As a note %timeit is a Jupyter magic function that we do not have control over.

Thanks for the review and glad you like the work!

---

@pjotrp Could you give me a hint on what might be going wrong? This error looks a bit more vague than the previous failures and the article does not have a $ in it.

[arfon]

@pjotrp Could you give me a hint on what might be going wrong? This error looks a bit more vague than the previous failures and the article does not have a $ in it.

It seems like the underscore in the title is causing issues with Pandoc. I've fixed the issue in https://github.com/dgasmith/opt_einsum/pull/28

[dgasmith]

Thanks @arfon!

@whedon generate pdf

[prasunanand]

@dgasmith, You didn't miss anything. I was just wondering if it was possible to control %timeit to suppress the "caching" message.

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[dgasmith]

@prasunanand Unfortunately I do not see it in their options.

[pjotrp]

@arfon looks like we are good to go

[arfon]

@dgasmith - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[dgasmith]

@arfon Great: https://zenodo.org/record/1299981

As a note I made a minor typo fix to the paper here: https://github.com/dgasmith/opt_einsum/commit/b08d789873852074833b608b3ba665b2816d4eae

[arfon]

@whedon set 10.5281/zenodo.1299981 as archive

[whedon]

OK. 10.5281/zenodo.1299981 is the archive.

[arfon]

@prasunanand - many thanks for your review here and to @pjotrp for editing this submission ✨

@dgasmith - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00753 :zap: :rocket: :boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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This is how it will look in your documentation:

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[pjotrp]

Thanks @arfon!

[dgasmith]

Thanks everyone! Glad this is in.