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

whedon · 2021-10-27T07:18:29Z

Submitting author: @mforets (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:

Status

Status badge code:

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:

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✨ 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

As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Authorship: Has the submitting author (@mforets) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

Paper format

Authors: Does the paper.tex file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
Page limit: Is the page limit for full papers respected by the submitted document?

Content

Context: is the scientific context motivating the work correctly presented?
Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
Results: are the results presented and compared to approaches with similar goals?

Review checklist for @blegat

Conflict of interest

As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Authorship: Has the submitting author (@mforets) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

Paper format

Authors: Does the paper.tex file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
Page limit: Is the page limit for full papers respected by the submitted document?

Content

Context: is the scientific context motivating the work correctly presented?
Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
Results: are the results presented and compared to approaches with similar goals?

The text was updated successfully, but these errors were encountered:

whedon · 2021-10-27T07:18:32Z

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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whedon · 2021-10-27T07:18:40Z

Failed to discover a Statement of need section in paper

whedon · 2021-10-27T07:18:41Z

Wordcount for paper.tex is 68

whedon · 2021-10-27T07:18:42Z

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 · 2021-10-27T07:18:44Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

whedon · 2021-10-27T07:19:04Z

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 · 2021-10-27T07:28:23Z

@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 · 2021-11-01T08:16:24Z

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

mforets · 2021-11-01T14:37:11Z

@whedon generate pdf

whedon · 2021-11-01T14:37:23Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

mforets · 2021-11-01T14:38:35Z

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 · 2021-11-01T14:39:54Z

@whedon check references

whedon · 2021-11-01T14:40:06Z

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 · 2021-11-02T19:16:16Z

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

Page 1 line 13 of right column: "comment" -> "comments"
"Optimization over a polyhedron corresponds to solving a linear program" -> this assumes that the objective function is linear
"parameters to represent" should probably be "parameters that represent" or "parameters needed to represent"
“common functionality” -> “common functionalities” or “a common functionality”
“fresh set” -> “new set” or “fresh new set”
In the LaTeX formula at the beginning of the last paragraph of page 3, none of the symbols are defined, I would say that CH is defined in Table 1, X0, E_+ are sets and Phi is a matrix (as defined later).
In the definition of the support function, “maximum” should be supremum unless necessary assumptions are met for X
“over polygon” -> “over the polygon” or “over a polygon”
“numeric queries”: what do you mean ? Do you mean “numerical queries” ?
Section 4.2, “Fig. 2 (left)” should be “Fig. 2 (right)”
In Section 5.1, the first equation does not render well. It should be either in LaTeX math or in monospace font (e.g. wth texttt)
In caption of Fig. 5, the first “(right)” should be “(left)”
In the second line of the right column of page 10, “d1” and “d2” are not define. Moreover, d should have length 2n in this equation while it is defined to have length n
The reference to MathOptInterface should be update: it is now published and contains a DOI (since a few days ago). “MathOptInterface” should be capitalized
In the reference of TaylorModels.jl, “Taylormodels.jl” -> M should be capitalized

schillic · 2021-11-03T13:09:23Z

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

schillic · 2021-11-03T14:17:37Z

@whedon generate pdf

whedon · 2021-11-03T14:17:55Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

gdalle · 2021-11-04T16:24:33Z

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

As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Authorship: Has the submitting author (@mforets) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

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

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

Paper format

Authors: Does the paper.tex file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
Page limit: Is the page limit for full papers respected by the submitted document?

Content

Context: is the scientific context motivating the work correctly presented?
Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
Results: are the results presented and compared to approaches with similar goals?

gdalle · 2021-11-04T16:27:51Z

I have put more detailed comments in this issue JuliaReach/LazySets-JuliaCon21#4

whedon · 2021-11-10T07:18:43Z

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

whedon · 2021-11-10T07:18:43Z

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

gdalle · 2021-11-10T09:52:45Z

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

matbesancon · 2021-11-10T10:15:16Z

no problem, sorry for the automatic whedon reminder

matbesancon · 2021-12-17T09:55:54Z

@whedon set 10.5281/zenodo.5761068 as archive

whedon · 2021-12-17T09:55:58Z

OK. 10.5281/zenodo.5761068 is the archive.

whedon · 2021-12-17T09:56:13Z

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 · 2021-12-17T09:56:20Z

@whedon set v1.53.4 as version

whedon · 2021-12-17T09:56:23Z

OK. v1.53.4 is the version.

matbesancon · 2021-12-17T09:56:50Z

Also: can you check the missing DOI and add it to the references?
#97 (comment)

whedon · 2021-12-17T09:56:51Z

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

schillic · 2021-12-17T16:17:09Z

@whedon generate pdf

whedon · 2021-12-17T16:17:23Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

schillic · 2021-12-17T16:17:43Z

@whedon check references

whedon · 2021-12-17T16:18:06Z

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

OK DOIs

- 10.1134/S0965542508060055 is OK
- 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

- None

INVALID DOIs

- None

schillic · 2021-12-17T16:19:30Z

@matbesancon

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

confirmed

can you check the missing DOI and add it to the references?

Yes, sorry, it's there now!

matbesancon · 2021-12-17T16:31:42Z

@whedon recommend-accept

whedon · 2021-12-17T16:31:45Z

Attempting dry run of processing paper acceptance...

whedon · 2021-12-17T16:32:00Z

👋 @JuliaCon/jcon-eics, this paper is ready to be accepted and published.

Check final proof 👉 JuliaCon/proceedings-papers#49

If the paper PDF and Crossref deposit XML look good in JuliaCon/proceedings-papers#49, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

matbesancon · 2021-12-17T16:32:13Z

@whedon accept deposit=true

whedon · 2021-12-17T16:32:16Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2021-12-17T16:32:18Z

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

OK DOIs

- 10.1134/S0965542508060055 is OK
- 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

- None

INVALID DOIs

- None

whedon · 2021-12-17T16:32:39Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jcon.00097 proceedings-papers#50
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jcon.00097
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

matbesancon · 2021-12-17T16:33:17Z

Thanks @gdalle and @blegat and congrats to the authors :)

mforets · 2021-12-17T22:32:49Z

Thank you @matbesancon for the editorial work and @gdalle and @blegat for your time reviewing our submission.

It was our first experience with an open review process. It went so smoothly! We would highly recommend it to our colleagues.

whedon · 2022-01-27T15:08:45Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

Markdown:
[![DOI](https://proceedings.juliacon.org/papers/10.21105/jcon.00097/status.svg)](https://doi.org/10.21105/jcon.00097)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jcon.00097">
  <img src="https://proceedings.juliacon.org/papers/10.21105/jcon.00097/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://proceedings.juliacon.org/papers/10.21105/jcon.00097/status.svg
   :target: https://doi.org/10.21105/jcon.00097

This is how it will look in your documentation:

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matbesancon · 2022-01-27T15:54:37Z

@mforets sorry there is a rendering error: https://proceedings.juliacon.org/papers/10.21105/jcon.00097
can you remove the $^*$ in the title and put the footnote in the text, we'll then update the paper page

schillic · 2022-01-28T11:28:35Z

@matbesancon we just merged JuliaReach/LazySets-JuliaCon21#7 to remove the star. What should we do now?

matbesancon · 2022-01-28T11:47:56Z

Thank you, the rest will be on our side to change the paper :)

schillic · 2022-01-28T12:16:09Z

Thanks, and sorry for the extra work.

whedon added Julia review Ruby TeX labels Oct 27, 2021

whedon assigned matbesancon Oct 27, 2021

whedon mentioned this issue Oct 27, 2021

[PRE REVIEW]: LazySets.jl: Scalable Symbolic-Numeric Set Computations #86

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schillic mentioned this issue Nov 3, 2021

Review 1 JuliaReach/LazySets-JuliaCon21#2

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whedon added the recommend-accept label Dec 17, 2021

whedon added accepted published labels Dec 17, 2021

matbesancon closed this as completed Jan 27, 2022

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

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

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whedon commented Oct 27, 2021 • edited by editorialbot

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gdalle commented Nov 4, 2021 • edited

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gdalle commented Nov 4, 2021

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whedon commented Oct 27, 2021 •

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