[REVIEW]: ProMCDA: A Python package for Probabilistic Multi-Criteria Decision Analysis

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@Flaminietta@galessiorob<!--end-editor-- Reviewers: @limengbinggz, @B3J4y Archive: 10.5281/zenodo.13694286

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/cd66aa1ed9ff89b5519d977f4a16379d/status.svg)](https://joss.theoj.org/papers/cd66aa1ed9ff89b5519d977f4a16379d)

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

@limengbinggz & @B3J4y, 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 @galessiorob 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 @limengbinggz

📝 Checklist for @B3J4y

📝 Checklist for @paulrougieux

editorialbot commented 8 months 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:

@editorialbot generate pdf

editorialbot commented 8 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (541.8 files/s, 87446.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            493            306           2030
HTML                             1             84              5            620
Markdown                         2             75              0            256
TeX                              1             16              0            220
YAML                             3              8              2             58
JSON                             1              4              0             19
-------------------------------------------------------------------------------
SUM:                            26            680            313           3203
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 8 months ago

Wordcount for paper.md is 1415

editorialbot commented 8 months ago

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

OK DOIs

- 10.1007/s10669-020-09784-x is OK
- 10.1016/j.envsoft.2021.105208 is OK
- 10.1016/S0377-2217(97)00163-X is OK
- 10.1016/j.dss.2022.113848 is OK
- 10.21105/joss.04567 is OK
- 10.1016/j.envsoft.2020.104890 is OK
- 10.1016/j.omega.2017.04.007 is OK
- 10.1007/978-1-4757-2500-1_2 is OK
- 10.1007/0-387-31099-1_2 is OK
- 10.1007/s11205-017-1832-9 is OK
- 10.1016/j.ecolind.2018.06.009 is OK
- 10.1016/j.ecolind.2019.105731 is OK
- 10.1016/j.ijggc.2016.08.023 is OK
- 10.1007/978-1-4939-3094-4_12 is OK
- 10.1016/j.ecolind.2014.05.014 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

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

galessiorob commented 8 months ago

🚀 @limengbinggz, @B3J4y thank you so much for volunteering to review this paper! Please comment @editorialbot generate my checklist and start your review at your earliest convenience. Let me know if you have any questions.

galessiorob commented 8 months ago

👋 Hi @paulrougieux! @Flaminietta suggested you'd be a good reviewer for this paper - do you have the bandwidth to help us out? Thanks!

B3J4y commented 8 months ago

Review checklist for @B3J4y

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/wetransform-os/ProMCDA?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Flaminietta) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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?

B3J4y commented 8 months ago

Opened Issue:

[x] https://github.com/wetransform-os/ProMCDA/issues/18

paulrougieux commented 8 months ago

I accept this review.

👋 Hi @paulrougieux! @Flaminietta suggested you'd be a good reviewer for this paper - do you have the bandwidth to help us out? Thanks!

Dear @galessiorob I can do the review within a bit more than 2 weeks.

Flaminietta commented 8 months ago

@editorialbot generate preprint

editorialbot commented 8 months ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

Flaminietta commented 8 months ago

@editorialbot generate preprint

editorialbot commented 8 months ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

Flaminietta commented 8 months ago

@editorialbot generate preprint

editorialbot commented 8 months ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

limengbinggz commented 8 months ago

Review checklist for @limengbinggz

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/wetransform-os/ProMCDA?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Flaminietta) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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?

galessiorob commented 7 months ago

👋 Hi everyone! Checking in to see if anyone has questions on the review process or the paper itself, thanks!

B3J4y commented 7 months ago

Hi, thank you for checking in. I have no questions from my side so far.

B3J4y commented 7 months ago

[x] https://github.com/wetransform-os/ProMCDA/issues/19

paulrougieux commented 7 months ago

@editorialbot generate my checklist

editorialbot commented 7 months ago

@paulrougieux I can't do that because you are not a reviewer

paulrougieux commented 7 months ago

@galessiorob sorry, I was travelling at the beginning of this month and didn't manage to start this on time. The editorial bot tells me I'm not a reviewer, is it too late now to provide comments?

B3J4y commented 7 months ago

galessiorob commented 7 months ago

@editorialbot add @paulrougieux as reviewer

editorialbot commented 7 months ago

@paulrougieux added to the reviewers list!

galessiorob commented 7 months ago

Hey @paulrougieux 👋 I just added you as a reviewer, if you can get to this soon that'd be great and helpful for the paper. Thanks so much!

galessiorob commented 7 months ago

👋 @limengbinggz checking in, is there anything I can help with so you can get going with your review? Thanks!

limengbinggz commented 6 months ago

👋 @limengbinggz checking in, is there anything I can help with so you can get going with your review? Thanks!

Thank you for checking in. I have no questions on my side so far and am actively reviewing the code in the package.

galessiorob commented 6 months ago

Hey @limengbinggz looks like you've been taking action on all the feedback - please let me know if I can help in any way, and whenever you're ready for us to wrap up the review. Thanks.

limengbinggz commented 6 months ago

Hey @limengbinggz looks like you've been taking action on all the feedback - please let me know if I can help in any way, and whenever you're ready for us to wrap up the review. Thanks.

Thank you for checking in. Should I complete the checklist after the authors have closed the open issues in the repo?

galessiorob commented 6 months ago

Apologies! That ping was meant for @Flaminietta, please disregard.

@Flaminietta please let me know when you're ready for a final review, thanks.

Flaminietta commented 6 months ago

Good morning @galessiorob!

We have already addressed many of the valuable suggestions of the reviewers and still working on a couple of them. I'll let you know as soon as we are ready for the final review. I think we need a few more days, in particular, to take care of the editing of the text and figures, and to eliminate the input configuration file by transforming the package into a library.

I hope this is still OK with the schedule of the journal.

Looking forward to the final version. Best regards,

@Flaminietta and @mspada

galessiorob commented 6 months ago

👋 @Flaminietta and @mspada absolutely! Take the time you need and let me know.

paulrougieux commented 4 months ago

Review checklist for @paulrougieux

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/wetransform-os/ProMCDA?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Flaminietta) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] 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?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] 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?

paulrougieux commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

galessiorob commented 4 months ago

👋 it's been quite some time! 👋 @Flaminietta and @mspada, how is it going? Any updates on your side?

@paulrougieux, thanks for starting on your review, Is there anything I can help with and/or any feedback for the authors?

mspada commented 4 months ago

@galessiorob thank you for checking. I’ll work on the comments we already have next week.

mspada commented 2 months ago

Hi @galessiorob,

@Flaminietta and I closed some of the open issues so far, the question is how does all the process proceed? I saw that, for example, @paulrougieux generated the PDF for review on the 22.04 before the updated version of the paper, which included some of the issues raised by @limengbinggz and @B3J4y.

galessiorob commented 2 months ago

Hi @mspada

Thanks for the updates! @limengbinggz @B3J4y @paulrougieux could you please review the latest version of the paper and the changes implemented based on your feedback? If you are satisfied and can check your review list, it will be greatly appreciated 🙏

galessiorob commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

limengbinggz commented 2 months ago

Hi @mspada

Thanks for the updates! @limengbinggz @B3J4y @paulrougieux could you please review the latest version of the paper and the changes implemented based on your feedback? If you are satisfied and can check your review list, it will be greatly appreciated 🙏

Thank you for all the hard work! I have checked off my review list and am good with all the changes. 😄

paulrougieux commented 2 months ago

Review checklist for @paulrougieux

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/wetransform-os/ProMCDA?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@Flaminietta) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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

[x] 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 functionality 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

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)?
[ ] 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?

galessiorob commented 1 month ago

@paulrougieux mind posting some annotations about the checklist items you haven't checked as completed please? Thanks!

Flaminietta commented 1 month ago

Dear all, dear @galessiorob,

with the last PR, which solves the potential problem for some Windows users by dockerizing ProMCDA, I think that we have now addressed all issues related to this review.

Best regards, Flaminia

B3J4y commented 1 month ago

On my end, everything has been checked, the software works out of the box, and this lengthy process is now complete.

Thank you, @Flaminietta, for your effort and for pushing the development forward.

Thank you, @galessiorob, for consistently organizing and reminding everyone about their tasks throughout this long period.

mspada commented 1 week ago

@galessiorob I'm writing you since it is quite some time that we didn't hear anything anymore about the status of the paper. I guess the problem is that @paulrougieux didn't finalise his review yet, or? Looking forward for your update. Best, @mspada and @Flaminietta

galessiorob commented 6 days ago

@editorialbot generate pdf

openjournals / joss-reviews