[REVIEW]: GBOML: Graph-Based Optimization Modeling Language

whedon commented 2 years ago

Submitting author: !--author-handle-->@MiftariB@fraukewiese<!--end-editor-- Reviewers: @odow, @leonardgoeke Archive: 10.5281/zenodo.6470268

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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

@odow & @leonardgoeke, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

✨ 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

[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 repository url?
[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 (@MiftariB) 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 and who the target audience is?
[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?

Review checklist for @leonardgoeke

✨ 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

[ ] 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

[ ] I confirm that I read and will adhere to the JOSS 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?
[ ] Contribution and authorship: Has the submitting author (@MiftariB) 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

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 and who the target audience is?
[ ] 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?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @odow, @leonardgoeke 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.

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whedon commented 2 years ago

Wordcount for paper.md is 1140

whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.24 s (376.7 files/s, 63682.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          42           2574           1795           6915
JSON                             8              0              0           1735
reStructuredText                29            537            640            424
TeX                              1             18              0            176
Markdown                         4             40              0             87
YAML                             2              8              2             36
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            89           3189           2445           9411
-------------------------------------------------------------------------------

Statistical information for the repository '0293c427244edeb7ca01327c' was
gathered on 2022/02/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
AdrienBolland                    1            21             22            0.12
Bardh                          140         17830          10443           80.85
Christophe Druet                 1             1              0            0.00
Hatim Djelassi                  20           690            471            3.32
Mathias Berger                   5          1449             23            4.21
MiftariB                        18          3163            855           11.49

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
Bardh                     10853           60.9          4.8                6.62
Hatim Djelassi              103           14.9         11.1                0.00
Mathias Berger               82            5.7          0.5               46.34
MiftariB                    246            7.8          4.7                5.28

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

- 10.1137/15M1020575 is OK
- 10.1007/s12532-011-0026-8 is OK
- 10.1007/s12532-012-0036-1 is OK
- 10.1287/mnsc.36.5.519 is OK
- 10.1007/s12532-009-0008-2 is OK
- 10.1007/978-1-4613-0215-5_8 is OK
- 10.5334/jors.188 is OK
- 10.23919/PSCC.2018.8442948 is OK
- 10.21105/joss.00825 is OK
- 10.1016/j.esr.2018.01.003 is OK
- 10.1016/j.enpol.2011.06.033 is OK
- 10.3389/fenrg.2021.671279 is OK

MISSING DOIs

- None

INVALID DOIs

- None

fraukewiese commented 2 years ago

@odow @leonardgoeke – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Both reviewers have checklists at the top of this thread (in that first comment) 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 https://github.com/openjournals/joss-reviews/issues/4158 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

odow commented 2 years ago

The repo is on a self-hosted GitLab instance, so linking won't work. Here's the start of a review issue: https://gitlab.uliege.be/smart_grids/public/gboml/-/issues/1

fraukewiese commented 2 years ago

Thanks @odow for opening the gitlab issue.

MiftariB commented 2 years ago

Dear Oscar and Frauke,

@odow : First and foremost, thank you for accepting to review this submission and providing valuable comments so quickly. We really appreciate the feedback and we are currently working to address it. We will provide a written answer shortly and make some adjustments in the paper as well.

@fraukewiese : @odow highlighted several points that should be updated in our paper, such as a more in-depth comparison with other tools and providing a short example of GBOML code. We would be happy to do so and wanted to check with you whether the original 1000 word limit could be exceeded?

Best Regards,

MIFTARI B

fraukewiese commented 2 years ago

@MiftariB : 1000 words is not a very strict limit. However please still be concise when doing the additions in the paper and maybe check if you can shorten at other parts.

fraukewiese commented 2 years ago

@leonardgoeke : Could you give us an update on how the review is going? Your review checklist can be found in this issue, the discussion/comments/feedback takes place here: https://gitlab.uliege.be/smart_grids/public/gboml/-/issues/1

fraukewiese commented 2 years ago

@ooo March 05 until March 16

leonardgoeke commented 2 years ago

I've added my comments to the review thread, but I don't manage to edit the checklist. My best guess is I'm missing the permission.

fraukewiese commented 2 years ago

@editorialbot add @leonardgoeke as reviewer

editorialbot commented 2 years ago

@leonardgoeke is already included in the reviewers list

fraukewiese commented 2 years ago

@leonardgoeke : Sorry for the late reply and inconvenience. I have tried to assign you again. Could you try if you can edit the checklist now?

kthyng commented 2 years ago

Hi @leonardgoeke! We had a tech change for JOSS and now you can make your own checklist with: @editorialbot generate my checklist

@fraukewiese this is the way to do this going forward.

leonardgoeke commented 2 years ago

Review checklist for @leonardgoeke

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://gitlab.uliege.be/smart_grids/public/gboml?
[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 (@MiftariB) 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 and who the target audience is?
[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?

MiftariB commented 2 years ago

Dear Oscar and Leonard,

We are pleased to let you know that the paper has now been updated. We tried to address your comments and implement the action items that we listed in the Gitlab issue as best we could. The only deviation from them was probably in the description of the SMS++ and Plasmo.jl frameworks. After putting some more thought into it, it seemed more appropriate and fair to us to focus on and concisely state the vision that underpins each tool, rather than getting into a detailed discussion of similarities, differences and limitations that may stem from their current development status.We would be happy to have your thoughts on the updated version of the paper.

Best,

GBOML Team

MiftariB 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:

MiftariB commented 2 years ago

Dear @fraukewiese,

Some elements are missing in the previewed pdf :

Co-authorship
Orcid of authors

Is this normal for a preview version ? Is it possible to add an email address ?

Best Regards,

Miftari Bardhyl

leonardgoeke commented 2 years ago

My objections are sufficiently addressed in the revised version and I’ve updated my checklist above accordingly.

fraukewiese commented 2 years ago

@MiftariB : Yes, that is normal for a preview version. You can have a look at already published papers, there you can see that the Orcid are not directly included in the paper pdf but still available. About the email address: They are usually not added in the paper.

fraukewiese commented 2 years ago

@leonardgoeke Thank you very much for your thorough review!

fraukewiese commented 2 years ago

@odow : Thank you very much for your fast and thorough review. Are you satisfied with the changes made by the authors?

odow commented 2 years ago

Yes, I'm happy with the latest revision.

MiftariB commented 2 years ago

Dear @fraukewiese,

Thanks for the precision concerning the paper. We are unsure of what is expected from us at this point. Could you clarify the next steps?

Best Regards,

Miftari B

fraukewiese commented 2 years ago

@odow Thank you very much for your thorough review!

fraukewiese commented 2 years ago

@MiftariB At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

MiftariB commented 2 years ago

Dear @fraukewiese,

Thanks for the instructions.

The version tag is "JOSS" : https://gitlab.uliege.be/smart_grids/public/gboml/-/tags/JOSS
The archival deposit is : https://zenodo.org/record/6470268#.Yl6-k_NByeA
The DOI is : 10.5281/zenodo.6470268

Regards,

MIFTARI B

fraukewiese commented 2 years ago

@editorialbot set 10.5281/zenodo.6470268 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6470268

fraukewiese commented 2 years ago

@editorialbot set JOSS as version

editorialbot commented 2 years ago

Done! version is now JOSS

fraukewiese commented 2 years ago

@MiftariB : Could you make a numbered version tag of the style vx.x.x ? Thank you.

MiftariB commented 2 years ago

@fraukewiese, the new tag is v0.1.1

fraukewiese commented 2 years ago

If there are special reasons for not having a numbered version tag, let me know, but usually the vx.x.x style is used.

MiftariB commented 2 years ago

No particular reason, it was just to make it clearer which version was related to the JOSS publication. v0.1.1 is just fine.

fraukewiese commented 2 years ago

@editorialbot set v0.1.1 as version

editorialbot commented 2 years ago

Done! version is now v0.1.1

fraukewiese commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1137/15M1020575 is OK
- 10.1007/s12532-011-0026-8 is OK
- 10.1007/s12532-012-0036-1 is OK
- 10.1287/mnsc.36.5.519 is OK
- 10.1007/s12532-009-0008-2 is OK
- 10.1007/978-1-4613-0215-5_8 is OK
- 10.5334/jors.188 is OK
- 10.23919/PSCC.2018.8442948 is OK
- 10.21105/joss.00825 is OK
- 10.1016/j.esr.2018.01.003 is OK
- 10.1016/j.enpol.2011.06.033 is OK
- 10.3389/fenrg.2021.671279 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3146

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3146, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

MiftariB commented 2 years ago

@fraukewiese there is still the co-first authorship missing in the PDF. What could we do to fix that ?

arfon commented 2 years ago

@fraukewiese there is still the co-first authorship missing in the PDF. What could we do to fix that ?

Please see this recent example on how to denote co-authorship: https://gitlab.com/culturalcartography/text2map/-/blob/master/paper/paper.md

MiftariB commented 2 years ago

@arfon Thanks for the reply. However, I am unsure of what needs to be done. In the above mentionned example, they wrote :

authors:
- name: Dustin S. Stoltz^[co-first author]
  orcid: 0000-0002-4774-0765
  affiliation: 1
- name: Marshall A. Taylor^[co-first author]
  orcid: 0000-0002-7440-0723
  affiliation: 2

We wrote :

- name: Bardhyl Miftari^[co-first author, corresponding author]
    orcid: 0000-0001-5334-0234
    affiliation: 1
- name: Mathias Berger^[co-first author, corresponding author]
    orcid: 0000-0003-3081-4833
    affiliation: 1

And when compiling our paper on https://whedon.theoj.org/ everything seems fine. I am no expert but It seems like the new editorialbot does not accept having both co-first author and corresponding author as footnote at once.

arfon commented 2 years ago

Ah OK, I see what's going on here. @tarleb – any chance you could take a look here? It looks like the footnotes here are breaking with both 'co-first author' and 'corresponding author'.

MiftariB commented 2 years ago

@editorialbot generate pdf

openjournals / joss-reviews