search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
704 stars 37 forks source link

[REVIEW]: lattice-symmetries: A package for working with quantum many-body bases #3537

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @twesterhout (Tom Westerhout) Repository: https://github.com/twesterhout/lattice-symmetries Version: v0.8.2 Editor: @jedbrown Reviewer: @jeffhammond, @joselado Archive: 10.5281/zenodo.5235336

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/73ffd9e15be1c3de2de4faf976501960"><img src="https://joss.theoj.org/papers/73ffd9e15be1c3de2de4faf976501960/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/73ffd9e15be1c3de2de4faf976501960/status.svg)](https://joss.theoj.org/papers/73ffd9e15be1c3de2de4faf976501960)

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

@jeffhammond & @joselado, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jedbrown 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 ✨

Review checklist for @jeffhammond

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @joselado

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jeffhammond, @joselado it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

: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:

watching

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

notifications

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago

Wordcount for paper.md is 1191

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/physrevb.100.155142 is OK
- 10.1103/physreve.98.033309 is OK
- 10.1016/j.cpc.2017.04.006 is OK
- 10.21468/scipostphys.2.1.003 is OK
- 10.1063/1.3518900 is OK
- 10.1038/s41467-020-15402-w is OK
- 10.1145/1731022.1731031 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (734.8 files/s, 185004.9 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
C/C++ Header                            15            562           1991           6461
C++                                     16            409            374           3320
Python                                  10            254            240           1255
Markdown                                 5            245              0            826
C                                        5             64             90            511
CMake                                    5             52            101            344
TeX                                      3             15              2            266
YAML                                     7             25              7            234
Windows Module Definition                1              0              0            122
make                                     2              9              0             38
Pascal                                   1              0              0             30
Bourne Shell                             1              3              2             25
---------------------------------------------------------------------------------------
SUM:                                    71           1638           2807          13432
---------------------------------------------------------------------------------------

Statistical information for the repository '07ac28b38e3efd71abeecc79' was
gathered on 2021/07/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Tom Westerhout                 178         20829           5296          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Tom Westerhout            15533           74.6          8.9               19.02
whedon commented 3 years ago

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

jedbrown commented 3 years ago

@jeffhammond @joselado :wave: Welcome to JOSS and thanks for agreeing to review!

The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the lattice-symmetries repository). I'll be watching this thread if you have any questions.

JOSS reviews are different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention this issue (https://github.com/openjournals/joss-reviews/issues/3537) so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@jedbrown) if you have any questions/concerns.

jeffhammond commented 3 years ago

Summary

This paper describes a software package for exact diagonalization of lattice Hamiltonians. This is an important domain of computational science. The software for solving problems in this space is challenging to write and use. The author's contribution here is significant, and I have personal experience with how important it is to have efficient implementations of this capability.

This submission seems like an appropriate and useful contribution to JOSS and I recommend that it be accepted.

Shortcomings of this review

I did not attempt to verify the performance claims in the paper. I did not download or install QuSpin or SPINPACK. On the other hand, I downloaded and verified SpinED, in addition to lattice-symmetries, and was satisfied with their compliance with the documentation and reported behavior.

Potential improvements

whedon commented 3 years ago

:wave: @joselado, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @jeffhammond, please update us on how your review is going (this is an automated reminder).

jeffhammond commented 3 years ago

My verdict in https://github.com/openjournals/joss-reviews/issues/3537#issuecomment-886594757 still stands ("I recommend that it be accepted").

joselado commented 3 years ago

Summary

This software presents a high-performance implementation of spin operators in a quantum many-body context. High-performance solvers for quantum many-body Hamiltonians are a tool of critical importance in quantum physics and condensed matter physics, and as a result, the current implementation is of very high value for the computational quantum community. The code is well documented and easy to use, and the manuscript presents a comprehensive summary of the computational package. Given all the points above, I recommend the manuscript to be accepted in JOSS.

Suggestions

I would suggest that it can be interesting to write in the manuscript an example formula of the Hamiltonians that the code can solve. This is, of course, not necessary for experts, yet it can be informative to potential readers and users not familiar with the topic.

Recommendation

As noted above, I believe that this software is a highly valuable contribution to the community and fulfills all the acceptance criteria of JOSS. Therefore, I strongly recommend its publication in JOSS.

jedbrown commented 3 years ago

Thanks for your reviews, @jeffhammond and @joselado.

@jeffhammond Could you please tick the "performance" box in your review checklist if you feel it has reasonably been addressed. (I see your review adds some nuance that you didn't compare with every alternative, and that's entirely fine.)

@twesterhout Could you please revise based on reviewer suggestions and let me know when ready?

twesterhout commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

twesterhout commented 3 years ago

Thank you @jeffhammond and @joselado for your reviews! I have modified the manuscript according to your suggestions. Please, see twesterhout/lattice-symmetries@06838f62b2b9ece183dadb8dc007f6b71b903d0c and twesterhout/lattice-symmetries@ff35f4f8c54917678e536ec169522ec797cf426a commits.

Please, let me know if anything else needs to be corrected/improved.

joselado commented 3 years ago

Thank you @twesterhout for the updated manuscript. The current version looks perfect, I recommend publishing the work as it is in JOSS.

twesterhout commented 3 years ago

One final tiny correction: I've added a link to Github repo of the project which uses lattice-symmetries to simulate quantum circuits (twesterhout/lattice-symmetries@99254416b9edb2bbf973cac98fcc9d1063e87faf). I haven't done it earlier because the code only just became public.

@jedbrown are there any further steps I need to take?

twesterhout commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

twesterhout commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

jedbrown commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/physrevb.100.155142 is OK
- 10.1103/physreve.98.033309 is OK
- 10.1016/j.cpc.2017.04.006 is OK
- 10.21468/scipostphys.2.1.003 is OK
- 10.1063/1.3518900 is OK
- 10.1038/s41467-020-15402-w is OK
- 10.1145/1731022.1731031 is OK

MISSING DOIs

- None

INVALID DOIs

- None
jedbrown commented 3 years ago

@twesterhout Thanks for your revisions. To move forward, could you please:

I can then move forward with accepting the submission.

twesterhout commented 3 years ago

@jedbrown DOI of the archived version (0.8.2) is 10.5281/zenodo.5235336.

p.s.: I decided to go with 0.8.2 rather than 0.9.0 because the new features are not public yet (they are meant for internal testing / benchmarks).

jedbrown commented 3 years ago

@whedon set v0.8.2 as version

whedon commented 3 years ago

OK. v0.8.2 is the version.

jedbrown commented 3 years ago

@whedon set 10.5281/zenodo.5235336 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5235336 is the archive.

jedbrown commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/physrevb.100.155142 is OK
- 10.1103/physreve.98.033309 is OK
- 10.1016/j.cpc.2017.04.006 is OK
- 10.21468/scipostphys.2.1.003 is OK
- 10.1063/1.3518900 is OK
- 10.1038/s41467-020-15402-w is OK
- 10.1145/1731022.1731031 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2538

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2538, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
twesterhout commented 3 years ago

The paper PDF looks good.

danielskatz commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2539
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03537
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

Congratulations to @twesterhout (Tom Westerhout)!!

And thanks to @jedbrown for editing, and @jeffhammond and @joselado for reviewing! We couldn't do this without you!

whedon commented 3 years ago

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03537/status.svg)](https://doi.org/10.21105/joss.03537)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03537">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03537/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03537/status.svg
   :target: https://doi.org/10.21105/joss.03537

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

twesterhout commented 3 years ago

Thank you @jedbrown, @jeffhammond, and @joselado!