[REVIEW]: REMix: A GAMS-based framework for energy system optimization models

[editorialbot]

Submitting author: !--author-handle-->@mwetz<!--end-author-handle-- (Manuel Wetzel) Repository: https://gitlab.com/dlr-ve/esy/remix/framework Branch with paper.md (empty if default branch): joss Version: v0.10.1 Editor: !--editor-->@fraukewiese<!--end-editor-- Reviewers: @loeffko, @david-huck Archive: 10.5281/zenodo.5566694

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2aea6e13a5f7d48f9ebaf166f1a24aca"><img src="https://joss.theoj.org/papers/2aea6e13a5f7d48f9ebaf166f1a24aca/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2aea6e13a5f7d48f9ebaf166f1a24aca/status.svg)](https://joss.theoj.org/papers/2aea6e13a5f7d48f9ebaf166f1a24aca)

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

@loeffko & @david-huck, 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 @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 ✨

Checklists

📝 Checklist for @loeffko

📝 Checklist for @david-huck

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.67 s (95.6 files/s, 462550.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            44              1              0        1136515
SVG                             42             44            125          76640
Python                          53           1490           2952           7481
Markdown                        61           1650              1           4600
YAML                            49            123            181            902
TeX                              2             39              0            392
TOML                             1              8              0            140
make                             1             12              0             28
CSS                              1              3              0             13
HTML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                           255           3370           3259        1226717
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1233

[editorialbot]

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

OK DOIs

- 10.5334/jors.188 is OK
- 10.1016/j.eneco.2016.06.021 is OK
- 10.1016/j.renene.2021.08.016 is OK
- 10.1016/j.egyr.2021.07.005 is OK
- 10.1016/j.renene.2023.04.015 is OK
- 10.1016/j.apenergy.2016.12.023 is OK
- 10.1016/j.energy.2017.01.115 is OK
- 10.1016/j.renene.2016.12.043 is OK
- 10.3389/fenrg.2020.541495 is OK
- 10.1016/j.rser.2014.02.003 is OK
- 10.1016/j.enpol.2011.06.033 is OK
- 10.18419/opus-2015 is OK
- 10.3390/en12244656 is OK
- 10.1016/j.esr.2018.07.001 is OK
- 10.1016/j.simpa.2020.100028 is OK
- 10.3390/su10061916 is OK
- 10.1002/ese3.891 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[loeffko]

Review checklist for @loeffko

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.com/dlr-ve/esy/remix/framework?
• [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 (@mwetz) 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?

[david-huck]

Review checklist for @david-huck

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.com/dlr-ve/esy/remix/framework?
• [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 (@mwetz) 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?

[david-huck]

Is there anything else that is needed, besides going through the checklist items?

[fraukewiese]

@david-huck : Thank you for you review and sorry for not answering earlier. Probably during going through the checklist questions to the authors have appeared? You are very welcome to ask them here in this thread and also to make suggestions to further improve the submission. You might put these questions and suggestions here or, especially if it is difficulties in installation or required improvements etc., create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below.

[fraukewiese]

Then @david-huck , if all questions are clarified, it would be great if you could write here if all questions have been clarified and if you would recommend this submission for publication.

[fraukewiese]

@loeffko : Thanks for the review so far. Are there any suggestions, feedback from your side?

[fraukewiese]

@loeffko : Thanks for the review so far. Are there any suggestions, feedback from your side? Do you know when you will be able to take a further look at it? Thanks a lot :)

[loeffko]

@loeffko : Thanks for the review so far. Are there any suggestions, feedback from your side? Do you know when you will be able to take a further look at it? Thanks a lot :)

Hi, sorry that I did not respond on here yet! I have been in contact with some of the developers and have added a few issues in the respective repositories. I still have to get everything working properly for me, but it should mostly be minor issues. I will likely get to try again towards the end of the week.

[fraukewiese]

@loeffko : Great, thanks a lot for your review work and the update.

[david-huck]

@fraukewiese All of my questions have been clarified, issues that i opened have been resolved and if I recommend this submission for publication.

[fraukewiese]

@david-huck : Thank you very much for the review!

[loeffko]

@fraukewiese I have just added two more issues in the REMix repositories, but they are of minor nature. I would therefore conclude my review and would also recommend this for publication.

[fraukewiese]

@loeffko : Thank you very much for your thorough review!

[fraukewiese]

@mwetz : Please notify me when the issue raised by @loeffko is solved :)

[mwetz]

@fraukewiese All of the issues have been solved now!

@david-huck @loeffko Thanks to both of you for the thorough review from my side as well!

[fraukewiese]

@editorialbot generate pdf

[fraukewiese]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

No paper file path

[editorialbot]

:warning: An error happened when generating the pdf. Paper file not found.

[fraukewiese]

@mwetz : Thanks for the update :) Could you check why generating the pdf fails?

[fraukewiese]

Additionally, 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.

[mwetz]

@editorialbot generate pdf

[editorialbot]

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

[mwetz]

Hi @fraukewiese, building the pdf failed since the merge from dev for a bugfix removed the paper folder. Everything should now be working again. We are starting the release and zenodo upload now, will let you know when we finish.

[mwetz]

We created a new release joss-paper with the corresponding tag joss-paper, see https://gitlab.com/dlr-ve/esy/remix/framework/-/releases/joss-paper In addition there is a mirrored release of version 0.10.1 should semantic versioning be required.

[mwetz]

Hi @fraukewiese, we uploaded the release to zenodo here: https://doi.org/10.5281/zenodo.11653916

That should be everything, correct?

[hcgils]

@editorialbot Some of the references in the paper proof miss their corresponding web links provided in the bib file (ReMoDigital, UNSEEN, SESAME SEED, MARKAL-EFOM). Furthermore, another paper relying on REMix (https://doi.org/10.1016/j.est.2024.110959) was recently published and may be additionally be cited in the last sentence of the "Statement of Need" section. Can these adjustments be implemented?

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[fraukewiese]

@editorialbot generate pdf

[fraukewiese]

@editorialbot set v0.10.1 as version

[editorialbot]

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

[editorialbot]

Done! version is now v0.10.1

[fraukewiese]

@editorialbot set 10.5281/zenodo.5566694 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.5566694

[fraukewiese]

@mwetz Thank you very much for version number and Zenodo DOI, I have updated it in the submission accordingly

[fraukewiese]

@hcgils : You are very welcome to add the links in the reference list. I guess this would be the following ones, for which I would recommend to provide more information, at least a link (doi would be best), and if available r more information about author or institution and year

• ReMoDigital project description. (n.d.)
• SESAME SEEED project description. (n.d.)
• he integrated MARKAL-EFOM system (TIMES) - a bottom-up optimization model for151 energy-environment systems. (n.d.
• UNSEEN project description. (n.d.)

You are welcome to add an additional paper.

Please also add a free space in front of the () brackets on the first page.

[fraukewiese]

@hcgils : Please notify me as soon as these changes are made.

Is it correct that you are marked as corresponding author although @mwetz has submitted it?

[hcgils]

@hcgils : Please notify me as soon as these changes are made.

Is it correct that you are marked as corresponding author although @mwetz has submitted it?

@fraukewiese : yes, this is correct

[mwetz]

@editorialbot generate pdf

[editorialbot]

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

[mwetz]

@hcgils : Please notify me as soon as these changes are made.

@fraukewiese The changes are now in! Thanks for waiting

[fraukewiese]

Thanks @mwetz and @hcgils : Could you, in line 28 and 29 put spaces in front of the brackets, e.g. OSeMOSYS(Howells et al., 2011) -> OSeMOSYS (Howells et al., 2011) It is just a minor thing, but it would be great if you can correct it before the paper is published.

[mwetz]

@editorialbot generate pdf

[editorialbot]

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

[mwetz]

@editorialbot generate pdf