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[REVIEW]: LazySets.jl: Scalable Symbolic-Numeric Set Computations #97

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@mforets<!--end-author-handle-- (Marcelo Forets) Repository: https://github.com/JuliaReach/LazySets-JuliaCon21 Branch with paper.md (empty if default branch): Version: v1.53.4 Editor: Reviewers: @gdalle, @blegat Archive:

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HTML: <a href="https://proceedings.juliacon.org/papers/681437dbee39acec76df25669b3a3542"><img src="https://proceedings.juliacon.org/papers/681437dbee39acec76df25669b3a3542/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/681437dbee39acec76df25669b3a3542/status.svg)](https://proceedings.juliacon.org/papers/681437dbee39acec76df25669b3a3542)

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

@gdalle & @blegat, 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 @matbesancon 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 @gdalle

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

whedon commented 2 years ago

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

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whedon commented 2 years ago

Failed to discover a Statement of need section in paper

whedon commented 2 years ago

Wordcount for paper.tex is 68

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.02 s (996.3 files/s, 203793.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                             18            514            305           3251
Julia                            1             80             70            185
Ruby                             1              8              4             45
YAML                             1              0              0             22
Markdown                         1              7              0              9
-------------------------------------------------------------------------------
SUM:                            22            609            379           3512
-------------------------------------------------------------------------------

Statistical information for the repository 'f77981a21b75d0f7f8255858' was
gathered on 2021/10/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
mforets                          1            57              0          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
Marcelo Forets               57          100.0          0.0                7.02
whedon commented 2 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 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.29007/zkf6 is OK
- 10.29007/7dt2 is OK
- 10.5281/zenodo.4993670 is OK
- 10.1137/15M1020575 is OK
- 10.1145/3447928.3456704 is OK
- 10.1109/MEMOCODE51338.2020.9314994 is OK
- 10.1137/141000671 is OK
- 10.1146/annurev-control-071420-081941 is OK
- 10.1145/3178126.3178128 is OK
- 10.1007/978-3-319-57288-8_20 is OK
- 10.5281/zenodo.2613102 is OK
- 10.29007/zbkv is OK
- 10.1007/978-3-642-22110-1_30 is OK
- 10.1109/CDC.2006.377036 is OK
- 10.1145/3302504.3311804 is OK
- 10.1561/2400000035 is OK
- 10.1109/TCAD.2020.3012859 is OK

MISSING DOIs

- 10.1007/978-3-030-89716-1_6 may be a valid DOI for title: Reachability of weakly nonlinear systems using Carleman linearization

INVALID DOIs

- None
matbesancon commented 2 years ago

@mforets please note the issues reported by whedon above, namely the missing DOI and the section on a statement of need. This is fine if this doesn't have this name but there should be at least a paragraph in the paper stating it

matbesancon commented 2 years ago

when you do some modifications, you can rerun compilation yourself with @whedon generate pdf

mforets commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

mforets commented 2 years ago

the section on a statement of need. This is fine if this doesn't have this name but there should be at least a paragraph in the paper stating it

The statement of need can be found in paragraph 2 of the Introduction (Section 1). We just made a small change describing who the target audience is.

mforets commented 2 years ago

@whedon check references

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.29007/zkf6 is OK
- 10.29007/7dt2 is OK
- 10.5281/zenodo.4993670 is OK
- 10.1137/15M1020575 is OK
- 10.1145/3447928.3456704 is OK
- 10.1007/978-3-030-89716-1_6 is OK
- 10.1109/MEMOCODE51338.2020.9314994 is OK
- 10.1137/141000671 is OK
- 10.1146/annurev-control-071420-081941 is OK
- 10.1145/3178126.3178128 is OK
- 10.1007/978-3-319-57288-8_20 is OK
- 10.5281/zenodo.2613102 is OK
- 10.29007/zbkv is OK
- 10.1007/978-3-642-22110-1_30 is OK
- 10.1109/CDC.2006.377036 is OK
- 10.1145/3302504.3311804 is OK
- 10.1561/2400000035 is OK
- 10.1109/TCAD.2020.3012859 is OK

MISSING DOIs

- None

INVALID DOIs

- None
blegat commented 2 years ago

The paper is well written, I would recommend acceptance with minor revision. My comments are the following:

schillic commented 2 years ago

@blegat Thanks for the thorough reading! We added https://github.com/JuliaReach/LazySets-JuliaCon21/pull/2 to address the review. Feel free to comment there.

schillic commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

gdalle commented 2 years ago

General review

This paper introduces a very rich and thoughtfully-crafted package for set representation. The key features of LazySets.jl are clearly stated and illustrated with very visual examples. Its natural syntax, high performance, integration into the Julia ecosystem and extensive documentation are tremendous assets. I recommend acceptance with minor revision.

To make the paper even better, the authors could emphasize why the core functionalities of their package (like support function computations) are precisely the ones we need, especially in fields like convex analysis or reachability. A more thorough comparison with competing libraries would also be welcome. Provided these two points are addressed, I will be able to check the remaining boxes in the Context section below.

For some reason I am not able to edit the checklist, so I reproduce it below.

Reviewer checklist

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

gdalle commented 2 years ago

I have put more detailed comments in this issue https://github.com/JuliaReach/LazySets-JuliaCon21/issues/4

whedon commented 2 years ago

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

whedon commented 2 years ago

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

gdalle commented 2 years ago

I am waiting on a revised version by @mforets and @schillic to check the remaining boxes

matbesancon commented 2 years ago

no problem, sorry for the automatic whedon reminder

schillic commented 2 years ago

@gdalle: We have started with the revision but are not finished yet. We will let you know.

mforets commented 2 years ago

@gdalle: we have replied in https://github.com/JuliaReach/LazySets-JuliaCon21/pull/5

gdalle commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

schillic commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

schillic commented 2 years ago

@gdalle: We merged the PR so you can see the new version here.

gdalle commented 2 years ago

Lets try this again then

gdalle commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

matbesancon commented 2 years ago

@mforets let us know when everything is addressed from the reviews on your side

gdalle commented 2 years ago

I'm sorry I will do the second pass before next week

gdalle commented 2 years ago

My second review pass is available here: https://github.com/JuliaReach/LazySets-JuliaCon21/pull/5#issuecomment-986201407

The changes made by the authors significantly improve the clarity of the paper. I still have a handful of very minor formatting issues (see issue link) but I can now recommend acceptance

mforets commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

schillic commented 2 years ago

@matbesancon I believe we fixed all the items raised in the reviews. (Recall that @gdalle was not able to modify the OP checklist.) What is the next step?

matbesancon commented 2 years ago

@whedon check references

matbesancon commented 2 years ago

@whedon commands

whedon commented 2 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
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@whedon add @username as reviewer

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@whedon re-invite @username as reviewer

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@whedon remove @username as reviewer

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@whedon set 10.0000/zenodo.00000 as archive

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matbesancon commented 2 years ago

@whedon check references

matbesancon commented 2 years ago

@schillic can you confirm that 10.5281/zenodo.5761068 is the DOI of the latest version (which corresponds to the paper)?

matbesancon commented 2 years ago

@whedon set 10.5281/zenodo.5761068 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5761068 is the archive.

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.29007/zkf6 is OK
- 10.29007/7dt2 is OK
- 10.5281/zenodo.4993670 is OK
- 10.1137/15M1020575 is OK
- 10.1287/ijoc.2021.1067 is OK
- 10.1145/3447928.3456704 is OK
- 10.1007/978-3-030-89716-1_6 is OK
- 10.1016/j.compstruc.2021.106699 is OK
- 10.1109/MEMOCODE51338.2020.9314994 is OK
- 10.1137/141000671 is OK
- 10.1146/annurev-control-071420-081941 is OK
- 10.1145/3178126.3178128 is OK
- 10.1007/978-3-319-57288-8_20 is OK
- 10.5281/zenodo.2613102 is OK
- 10.29007/zbkv is OK
- 10.1007/978-3-642-22110-1_30 is OK
- 10.1109/CDC.2006.377036 is OK
- 10.1145/3302504.3311804 is OK
- 10.1561/2400000035 is OK
- 10.1109/TCAD.2020.3012859 is OK
- 10.1515/9781400884179 is OK

MISSING DOIs

- 10.1134/s0965542508060055 may be a valid DOI for title: The modified method of refined bounds for polyhedral approximation of convex polytopes

INVALID DOIs

- None
matbesancon commented 2 years ago

@whedon set v1.53.4 as version

whedon commented 2 years ago

OK. v1.53.4 is the version.

matbesancon commented 2 years ago

Also: can you check the missing DOI and add it to the references? https://github.com/JuliaCon/proceedings-review/issues/97#issuecomment-996584733