search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
722 stars 38 forks source link

[REVIEW]: SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations #3743

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: !--author-handle-->@EgorOrachyov<!--end-author-handle-- (Egor Orachev) Repository: https://github.com/JetBrains-Research/spbla Branch with paper.md (empty if default branch): joss-paper Version: v1.0.0 Editor: !--editor-->@Nikoleta-v3<!--end-editor-- Reviewers: @mlxd, @bencardoen Archive: 10.5281/zenodo.7009938

: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/1da10be51ab03b0f574f2fda4aabc3f9"><img src="https://joss.theoj.org/papers/1da10be51ab03b0f574f2fda4aabc3f9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1da10be51ab03b0f574f2fda4aabc3f9/status.svg)](https://joss.theoj.org/papers/1da10be51ab03b0f574f2fda4aabc3f9)

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

@abb58 & @mlxd, 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 @Nikoleta-v3 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 @abb58

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mlxd

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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. @abb58, @mlxd 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 394

whedon commented 3 years ago

PDF failed to compile for issue #3743 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:155:in `block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Egor Orachev^[co-first author] (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1186/1471-2105-14-149 is OK
- 10.1145/2499370.2462159 is OK
- 10.1145/3210259.3210264 is OK
- 10.1007/978-3-030-54832-2_6 is OK

MISSING DOIs

- 10.1007/978-3-319-46523-4_38 may be a valid DOI for title: Context-Free Path Queries on RDF Graphs

INVALID DOIs

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

github.com/AlDanial/cloc v 1.88  T=0.57 s (526.7 files/s, 94282.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                    96           4745           6380          22648
C++                             98           1677           1552           5539
OpenCL                          31            961            215           3345
CUDA                            29            602            605           1850
Python                          20            505            546           1128
Markdown                         8            204              0            708
CMake                            9             85             31            382
Bourne Shell                     6             17             21            109
YAML                             2             14              2            107
TeX                              1              5              0             70
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                           302           8815           9352          35888
-------------------------------------------------------------------------------

Statistical information for the repository '686d7eec9413c01fa1158df8' was
gathered on 2021/09/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Egor19035                       11          7145            913           11.05
EgorOrachev                      3            11           8250           11.33
Maria Karpenko                  15         45080          11508           77.62

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
EgorOrachev               11123       101118.2          2.7               25.60
Maria Karpenko            33597           74.5          2.5               15.90
Nikoleta-v3 commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
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:

Nikoleta-v3 commented 3 years ago

👋🏼 @EgorOrachyov @abb58, @mlxd this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements 🔝 As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is 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 #3743 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 about 2-4 weeks. Please let me know if any of 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 (@Nikoleta-v3 ) if you have any questions/concerns 👍🏻 😄

Nikoleta-v3 commented 3 years ago

@EgorOrachyov please fix the missing DOI: https://github.com/openjournals/joss-reviews/issues/3743#issuecomment-923893328 :)

EgorOrachyov commented 3 years ago

Missing doi fixed! :)

EgorOrachyov commented 3 years ago

@whedon generate pdf from branch joss-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch joss-paper. Reticulating splines etc...
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:

whedon commented 3 years ago

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

whedon commented 3 years ago

:wave: @abb58, please update us on how your review is going (this is an automated reminder).

EgorOrachyov commented 3 years ago

@mlxd Hi, thank you for your issue feedback. I hope, we've fixed it! Check out the latest source code version.

mlxd commented 3 years ago

@mlxd Hi, thank you for your issue feedback. I hope, we've fixed it! Check out the latest source code version.

Thanks @EgorOrachyov ! I'll try to get around to reviewing these in the coming days.

mlxd commented 3 years ago

HI @EgorOrachyov just a quick update. I am having GPU issues at the moment, expect it to be resolved in the coming days and will finish review once done.

Nikoleta-v3 commented 3 years ago

Thank you for the update! @abb58, please let us know how your review is going 😄

mlxd commented 2 years ago

Apologies for the delays. I have added a new issue for compiling the library at https://github.com/JetBrains-Research/spbla/issues/13

mlxd commented 2 years ago

Issue added for adding additional examples: https://github.com/JetBrains-Research/spbla/issues/14

mlxd commented 2 years ago

Issue added for community guidelines https://github.com/JetBrains-Research/spbla/issues/16

mlxd commented 2 years ago

Issue added for API functionality documentation https://github.com/JetBrains-Research/spbla/issues/15

Nikoleta-v3 commented 2 years ago

Hey @EgorOrachyov! Any update on your progress? 😄 and @abb58, please let us know how your review is going 😄

EgorOrachyov commented 2 years ago

@Nikoleta-v3 Hi! Thank you for your gentle reminder :) mlxd left a number of not critical but very important issues to our project, so we are going to fix it in a couple of upcoming days!

Nikoleta-v3 commented 2 years ago

Great, thank you @EgorOrachyov 😃

Nikoleta-v3 commented 2 years ago

Hey @EgorOrachyov 👋🏻 I hope everything is well with you!

The submission has been still for a while now. I was wondering if you had an update for us?

EgorOrachyov commented 2 years ago

@mlxd Hello, we apologize for such a long delay. I hope we have fixed all issues you've added to the project, so checkout the latest source code version! Also, we highlight additionally all changes and fixes here:

New project description with all useful links in one place:

image

mlxd commented 2 years ago

Hi @EgorOrachyov apologies for the delay. I'll get to this before the end-of-week.

EgorOrachyov commented 2 years ago

@mlxd Hello, thank you. We will be waiting for a response from you.

mlxd commented 2 years ago

Apologies for the delay. I am happy to report that I am done with my review, and all boxes are now ticked. Nice work @EgorOrachyov

EgorOrachyov commented 2 years ago

@mlxd It is great! Thank you so much for your review.

We apologize once more for such a delay from our side.

EgorOrachyov commented 2 years ago

@Nikoleta-v3 Hello, we hope it is not too late now :)

We wondering, what is the next step of the review process. If I understand correctly, we have to get the responses from other reviewer?

Nikoleta-v3 commented 2 years ago

Hey @EgorOrachyov that's correct. The second reviewer has been inactive for a while! I emailed them and I am waiting to hear back from them. If they do not reply I am going to find a new reviewer for the submission 👍🏻

EgorOrachyov commented 2 years ago

@Nikoleta-v3 Cool, thanks! We will be waiting for updates on this question.

Nikoleta-v3 commented 2 years ago

Just to let you know @EgorOrachyov - I have been emailing people every week but I haven't managed to find a new reviewer for the submission. I will keep you updated. In the meantime if you or @mlxd have any suggestions please let me know!

EgorOrachyov commented 2 years ago

@Nikoleta-v3 Hi, thank you for your message. Is it possible to assign as a reviewer someone who I have suggested in previous (pre-review) discussion?

EgorOrachyov commented 2 years ago

hausen arghdos pszi1ard JaroslavHron sarats camillescott wrathematics

Nikoleta-v3 commented 2 years ago

Yes I have been emailing people from this list 😄

EgorOrachyov commented 2 years ago

@Nikoleta-v3 Okay, I see :) So, is it possible to try to email others, if we have another look into excel table and try to find new possible reviewers?

Nikoleta-v3 commented 2 years ago

There only two reviewers from the above list I haven't reach out because I couldn't find their emails. I will ping them here 😄

Nikoleta-v3 commented 2 years ago

👋 @hausen & @arghdos would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

Nikoleta-v3 commented 2 years ago

I was corresponding with a few potential reviewers but unfortunately no one was able to commit at the end. I am going back into the excel spreadsheet.

Nikoleta-v3 commented 2 years ago

👋 @bencardoen & @chaypaterson & @alejandrogallo & @mkareshk would any of you be willing to review this submission for JOSS? One reviewer has already reviewed the submission, and I am looking for a second pair of 👀

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

bencardoen commented 2 years ago

@Nikoleta-v3 Sure, I'd be happy to review.

bencardoen commented 2 years ago

@Nikoleta-v3 the invite / confirm link at the top of the issue seems no longer valid, how do I start the review? (this is my first JOSS review)

EgorOrachyov commented 2 years ago

@Nikoleta-v3 Sure, I'd be happy to review.

@bencardoen Hi, thank you! 🎉

We will be waiting for your review/comments. If there are some issues, we will fix it as soon as possible.

Nikoleta-v3 commented 2 years ago

@editorialbot remove @abb58 from reviewers

editorialbot commented 2 years ago

@abb58 removed from the reviewers list!