[REVIEW]: GlobalSensitivity.jl: julia package for performant global sensitivity analysis

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@Vaibhavdixit02@jbytecode<!--end-editor-- Reviewers: @zhenwu0728, @storyetfall Archive: 10.5281/zenodo.6993162

Status

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Markdown: [![status](https://joss.theoj.org/papers/aaa43a640c8764640c2a8cc30b7d9dec/status.svg)](https://joss.theoj.org/papers/aaa43a640c8764640c2a8cc30b7d9dec)

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

@zhenwu0728 & @storyetfall, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode 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 ✨

Checklists

📝 Checklist for @zhenwu0728

📝 Checklist for @storyetfall

editorialbot commented 2 years ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1595.7 files/s, 134596.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           22            280            118           1563
Markdown                        14            290              0            939
TeX                              1             28              0            450
YAML                             6              8              7            152
TOML                             3              5              0             40
-------------------------------------------------------------------------------
SUM:                            46            611            125           3144
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1912

editorialbot commented 2 years ago

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1080/00949659708811825 is OK
- 10.1016/j.ress.2006.04.015 is OK
- 10.1016/j.envsoft.2006.10.004 is OK
- 10.2307/1269043 is OK
- 10.1016/j.ejor.2012.11.047 is OK
- 10.1016/S0010-4655(02)00280-1 is OK
- 10.1016/0167-9473(95)92843-M is OK
- 10.1080/00401706.1999.10485594 is OK
- 10.1016/j.envsoft.2010.04.012 is OK
- 10.1016/j.cpc.2009.09.018 is OK
- 10.1016/S0167-9473(97)00043-1 is OK
- 10.1021/cr040659d is OK
- 10.1002/9780470725184.ch4 is OK
- 10.1198/016214502388618447 is OK
- 10.1016/j.chemolab.2011.10.006 is OK
- 10.1016/j.matcom.2009.01.023 is OK
- 10.1016/S0378-4754(00)00270-6 is OK
- 10.1016/j.ress.2005.06.003 is OK
- 10.1016/j.cageo.2013.06.006 is OK
- 10.1016/j.ress.2009.11.005 is OK
- 10.1016/j.envsoft.2012.03.004 is OK
- 10.1007/978-3-319-41508-6_12 is OK
- 10.1137/141000671 is OK
- 10.1016/j.envsoft.2006.01.004 is OK
- 10.1007/s11538-021-00982-5 is OK
- 10.1002/psp4.6 is OK
- 10.21105/joss.03349 is OK
- 10.48550/ARXIV.2204.08775 is OK
- 10.48550/ARXIV.2001.04385 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot 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:

jbytecode commented 2 years ago

Dear reviewers @zhenwu0728 and @storyetfall,

This is the review thread. Please type

@editorialbot generate my checklist

to generate your task list. In this list, there are 20 review items. Whenever you complete a task, you can check off the corresponding check box.

You can always interact with the author(s), other reviewers, and the editor during the reviewing process. You can also open issues in the target repo and send pull request. Please mention the review page in those issues, so we can keep tracking outside of our world.

Thank you in advance.

zhenwu0728 commented 2 years ago

Review checklist for @zhenwu0728

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/SciML/GlobalSensitivity.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Vaibhavdixit02) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

ggdna commented 2 years ago

Review checklist for @storyetfall

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/SciML/GlobalSensitivity.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Vaibhavdixit02) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

jbytecode commented 2 years ago

Dear @zhenwu0728 and @storyetfall

Could you please update us on how is your review going?

Thank you in advance.

zhenwu0728 commented 2 years ago

Hi @jbytecode, I'm trying out the tutorials in the documentation and I plan to submit my review by the end of this week.

ggdna commented 2 years ago

I'm in a similar position! (Though more likely to submit after the weekend.)

zhenwu0728 commented 2 years ago

Hi @jbytecode, I would like to submit my review.

Overall, the package looks good to me, but I still have some comments:

I suggest removing the Example section in the paper.
Multiple citations in one place should be in the same bracket.
I suggest removing some of the citations in Summary - one per method should be enough.
Lack of docstring for gas function (Issue#68)
Tutorial doesn't work (Issue#69)

All of these remarks should be easy to fix.

jbytecode commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

Vaibhavdixit02 commented 2 years ago

Thanks for the review and also opening the issues @zhenwu0728, that was very helpful.

I suggest removing the Example section in the paper.

I think it makes sense, I will describe the experiment/example in text and add a link to the docs' section that has this example.

I suggest removing some of the citations in Summary - one per method should be enough.

They are there because of subsequent modifications offered by those papers and also the package contains multiple implementations for those papers.

Let me know what you think?

jbytecode commented 2 years ago

citations are okay but they can be refactored using semicolons to combine them in a single parenthesis.

zhenwu0728 commented 2 years ago

Thanks for the review and also opening the issues @zhenwu0728, that was very helpful.

I suggest removing the Example section in the paper.

I think it makes sense, I will describe the experiment/example in text and add a link to the docs' section that has this example.

I suggest removing some of the citations in Summary - one per method should be enough.

They are there because of subsequent modifications offered by those papers and also the package contains multiple implementations for those papers.

Let me know what you think?

Both sound good to me.

Vaibhavdixit02 commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

jbytecode commented 2 years ago

citations look good now.

one more issue: giving mutable links in pdf is a little bit problematic if you decide to change folder structure and the content in future. The links 1 and 2 route to changeable addresses by time.

The solution: can you provide a short example that presents the basic functionality of the software rather than a three-pages long one in manuscript?

@zhenwu0728 - how do you think about that?

Vaibhavdixit02 commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

ggdna commented 2 years ago

Review done! Everything looks good. Only a few very minor comments:

several formatting issues in the method docs, including but not limited to:
- in Regression Method "R^n -> R^m" appears as plain text and not LaTeX.
- in Regression Method there are newline issues in the first bullet points
- in eFAST "samples" should be LaTeX'd as \text{samples} or replaced with a variable like N_{s} ?
- in eFAST "num_harmonics" isn't described using the bullet point format of the other methods
- in Fractional Factorial there is no footprint line at the top
could be useful to explicitly define the Lotka-Volterra model in the text of the tutorials. it's clear by looking at the code and also many will be familiar, but there's no harm in being extra clear :)

jbytecode commented 2 years ago

@Vaibhavdixit02 - it seems we are close to the end, please take all of the latest suggestions into consideration and make your final edits. When you have done with them, please ping me here.

jbytecode commented 2 years ago

@editorialbot generate pdf

Vaibhavdixit02 commented 2 years ago

Yes, I'll get to it tomorrow, didn't get time for it today unfortunately!

editorialbot 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:

Vaibhavdixit02 commented 2 years ago

@jbytecode it should all be done now

jbytecode commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1080/00949659708811825 is OK
- 10.1016/j.ress.2006.04.015 is OK
- 10.1016/j.envsoft.2006.10.004 is OK
- 10.2307/1269043 is OK
- 10.1016/j.ejor.2012.11.047 is OK
- 10.1016/S0010-4655(02)00280-1 is OK
- 10.1016/0167-9473(95)92843-M is OK
- 10.1080/00401706.1999.10485594 is OK
- 10.1016/j.envsoft.2010.04.012 is OK
- 10.1016/j.cpc.2009.09.018 is OK
- 10.1016/S0167-9473(97)00043-1 is OK
- 10.1021/cr040659d is OK
- 10.1002/9780470725184.ch4 is OK
- 10.1198/016214502388618447 is OK
- 10.1016/j.chemolab.2011.10.006 is OK
- 10.1016/j.matcom.2009.01.023 is OK
- 10.1016/S0378-4754(00)00270-6 is OK
- 10.1016/j.ress.2005.06.003 is OK
- 10.1016/j.cageo.2013.06.006 is OK
- 10.1016/j.ress.2009.11.005 is OK
- 10.1016/j.envsoft.2012.03.004 is OK
- 10.1007/978-3-319-41508-6_12 is OK
- 10.1137/141000671 is OK
- 10.1016/j.envsoft.2006.01.004 is OK
- 10.1007/s11538-021-00982-5 is OK
- 10.1002/psp4.6 is OK
- 10.21105/joss.03349 is OK
- 10.48550/ARXIV.2204.08775 is OK
- 10.48550/ARXIV.2001.04385 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

jbytecode commented 2 years ago

@Vaibhavdixit02 - I have just sent a pull request in the submission repository:

https://github.com/SciML/GlobalSensitivity.jl/pull/74

Please review the changes carefully and If you are agreed with them, please apply.

jbytecode commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.21105/joss.00097 is OK
- 10.1080/00949659708811825 is OK
- 10.1016/j.ress.2006.04.015 is OK
- 10.1016/j.envsoft.2006.10.004 is OK
- 10.2307/1269043 is OK
- 10.1016/j.ejor.2012.11.047 is OK
- 10.1016/S0010-4655(02)00280-1 is OK
- 10.1016/0167-9473(95)92843-M is OK
- 10.1080/00401706.1999.10485594 is OK
- 10.1016/j.envsoft.2010.04.012 is OK
- 10.1016/j.cpc.2009.09.018 is OK
- 10.1016/S0167-9473(97)00043-1 is OK
- 10.1021/cr040659d is OK
- 10.1002/9780470725184.ch4 is OK
- 10.1198/016214502388618447 is OK
- 10.1016/j.chemolab.2011.10.006 is OK
- 10.1016/j.matcom.2009.01.023 is OK
- 10.1016/S0378-4754(00)00270-6 is OK
- 10.1016/j.ress.2005.06.003 is OK
- 10.1016/j.cageo.2013.06.006 is OK
- 10.1016/j.ress.2009.11.005 is OK
- 10.1016/j.envsoft.2012.03.004 is OK
- 10.1007/978-3-319-41508-6_12 is OK
- 10.1137/141000671 is OK
- 10.1016/j.envsoft.2006.01.004 is OK
- 10.1007/s11538-021-00982-5 is OK
- 10.1002/psp4.6 is OK
- 10.21105/joss.03349 is OK
- 10.48550/ARXIV.2204.08775 is OK
- 10.48550/ARXIV.2001.04385 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

jbytecode commented 2 years ago

@Vaibhavdixit02 - ORCID of the second author is missing, could you please provide it in the paper?

Thank you in advance.

Vaibhavdixit02 commented 2 years ago

Done

Vaibhavdixit02 commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

jbytecode commented 2 years ago

Dear @Vaibhavdixit02

[x] Please read the paper pdf carefully, one more time, correct any issue if exists. Please perform a full grammar check.
[x] Create a tagged release in the software repository. Report the version here. The version should be in form of vx.y.z, e.g. v1.2.3.
[x] Create a Zenodo archive in https://zenodo.org/
[x] The Zenodo archive (with the same name/title with the JOSS paper) should have the correct metadata, e.g. author names, ORCIDs, the title of the archive. Please set the archive title as the paper title.
[x] Please provide the tagged release id, zenodo archive DOI, and Zenodo archive URL here.

Thank you in advance.

Vaibhavdixit02 commented 2 years ago

Create a tagged release in the software repository. Report the version here. The version should be in form of vx.y.z, e.g. v1.2.3.

v2.1.1

Vaibhavdixit02 commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

Vaibhavdixit02 commented 2 years ago

tagged release id

Not sure what this is?

zenodo archive DOI

10.5281/zenodo.6992984

Zenodo archive URL

https://zenodo.org/record/6992984#.Yvpb6exBy3I

jbytecode commented 2 years ago

@editorialbot set v2.1.1 as version

editorialbot commented 2 years ago

Done! version is now v2.1.1

jbytecode commented 2 years ago

@Vaibhavdixit02 - the zenodo archive should include the full repo but not only the paper pdf.

Vaibhavdixit02 commented 2 years ago

Oh sorry! Updated now

doi - 10.5281/zenodo.6993162 url - https://zenodo.org/record/6993162#.Yvpk2uxBy3I

openjournals / joss-reviews