[REVIEW]: CLOVER: A modelling framework for sustainable community-scale energy systems

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@phil-sandwell@fraukewiese<!--end-editor-- Reviewers: @EwaGomez, @fneum Archive: 10.5281/zenodo.7575877

Status

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Markdown: [![status](https://joss.theoj.org/papers/be3c026bd50dd9b53fd3c181cf6e8528/status.svg)](https://joss.theoj.org/papers/be3c026bd50dd9b53fd3c181cf6e8528)

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

@EwaGomez & @fneum, 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 @EwaGomez

📝 Checklist for @fneum

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.50 s (410.9 files/s, 179188.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          80           3920           7577          18171
JavaScript                      17           4510           4494          17123
HTML                            11           1369             33           8098
TeX                             25            885           1158           7321
reStructuredText                11            911           3729           2783
SVG                              1              0              0           2671
YAML                            32             95            845           1151
CSS                              6            294             52           1106
Markdown                         8            199              0            554
Bourne Shell                     5             11             53             60
JSON                             2              0              0             60
make                             2             22             11             50
DOS Batch                        2             17              2             47
INI                              2              0              0              8
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                           205          12233          17954          59209
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1344

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.6925534 is OK
- 10.1016/j.energy.2016.08.060 is OK
- 10.1016/j.esd.2016.09.002 is OK
- 10.1016/j.renene.2020.03.002 is OK
- 10.1016/j.egypro.2017.09.416 is OK
- 10.1016/j.rset.2021.100003 is OK
- 10.1016/j.seta.2021.101095 is OK
- 10.1016/j.esd.2021.11.008 is OK
- 10.1016/j.erss.2022.102636 is OK

MISSING DOIs

- 10.1891/9780826190123.ap02 may be a valid DOI for title: Transforming our world: the 2030 Agenda for Sustainable Development

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:

EwaGomez commented 1 year ago

Review checklist for @EwaGomez

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/CLOVER-energy/CLOVER?
[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 (@phil-sandwell) 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?

fraukewiese commented 1 year ago

@phil-sandwell : Please update us about the open issues

fraukewiese commented 1 year ago

@fneum : Any updates on how the review is going would be great :)

EwaGomez commented 1 year ago

@fraukewiese : I am waiting with my further review on the already opened issues.

phil-sandwell commented 1 year ago

Thank you very much for your support with this! We've responded to the issues raised by @EwaGomez here and here and edited the submission accordingly. Please let us know if you have any more questions, comments or suggestions.

EwaGomez commented 1 year ago

@fraukewiese My review is complete. The library CLOVER meets all criteria for me and I can recommend a publication in JOSS.

fraukewiese commented 1 year ago

Thank you very much @EwaGomez for your thorough review!

fraukewiese commented 1 year ago

@fneum : Could you give us a brief update on how the review is going or when you would be able to do it. Thank you very much :)

fneum commented 1 year ago

Review checklist for @fneum

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/CLOVER-energy/CLOVER?
[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 (@phil-sandwell) 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?

fneum commented 1 year ago

Sorry for not getting to this earlier. I have two main comments regarding the documentation and README. Otherwise, everything looks good or has already been addressed through @EwaGomez comments.

[x] README: The instructions and usage examples assume that the commands are run from the root of the git repository. However, they are not applicable if you follow the pip route. Here, I think python -m src.clover .... should be replaced with python -m clover. .....
[x] Documentation: The README is very good for getting started, but the general documentation is hidden in a PDF in the repository. A better option would be to move the documentation to a website like e.g. Readthedocs. Maybe pandoc can help you convert large chunks of the .tex to .rst format. Is this still up-to-date since it contains a 2020 date on the title page?

fraukewiese commented 1 year ago

Thank you very much @fneum ! @phil-sandwell : Please give us an update as soon as you have addressed the comments by @fneum

phil-sandwell commented 1 year ago

Thanks very much! We're currently addressing these comments here and here and will report back once complete.

BenWinchester commented 1 year ago

Thank you very much for your review @fneum An issue was raised here which was merged here with updates to address how to run the clover-energy package if installed via pip and with directions to the wiki pages which recently replaced the .pdf userguide. Please let me know if there's anything else that you need!

fneum commented 1 year ago

Great @BenWinchester! Sorry that I didn't suspect the documentation to be placed on the Wiki Pages.

I have one mini suggestion remaining, then good to go!

In the README, it would be good to hit the keyword "documentation" somehow, in case someone is Ctrl + Fing for it. Either as a header or just in-text where you incorporated the reference to the wiki.

fraukewiese commented 1 year ago

@EwaGomez and @fneum : Thank you very much for your effort, your thorough review and your support in improving the submission!

fraukewiese commented 1 year ago

@editorialbot generate pdf

fraukewiese commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.5281/zenodo.6925534 is OK
- 10.21105/joss.00884 is OK
- 10.20900/jsr20200009 is OK
- 10.5334/jors.188 is OK
- 10.1016/j.energy.2016.08.060 is OK
- 10.1016/j.esd.2016.09.002 is OK
- 10.1016/j.renene.2020.03.002 is OK
- 10.1016/j.egypro.2017.09.416 is OK
- 10.1016/j.rset.2021.100003 is OK
- 10.1016/j.seta.2021.101095 is OK
- 10.1016/j.esd.2021.11.008 is OK
- 10.1016/j.erss.2022.102636 is OK
- 10.1088/2515-7655/ac9dc0 is OK
- 10.25561/77296 is OK

MISSING DOIs

- 10.1891/9780826190123.ap02 may be a valid DOI for title: Transforming our world: the 2030 Agenda for Sustainable Development

INVALID DOIs

- None

editorialbot commented 1 year ago

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

fraukewiese commented 1 year ago

@BenWinchester and @phil-sandwell Two minor points: As raised by fneum: "In the README, it would be good to hit the keyword "documentation" somehow, in case someone is Ctrl + Fing for it. Either as a header or just in-text where you incorporated the reference to the wiki." Please add the DOI for Howells et al 2011: https://doi.org/10.1016/j.enpol.2011.06.033

fraukewiese commented 1 year ago

@phil-sandwell : Could you then please:

[ ] 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.

BenWinchester commented 1 year ago

@fraukewiese , the two points raised above were addressed in this issue and then merged into our master branch here and published on pypi here.

[x] Make a tagged release of your software, and list the version tag of the archived version here. A tagged release, v5.0.6, was made of the archived software, The tag is available here;
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) The archived software is available on Zenodo, with v5.0.6 available at 10.5281/zenodo.7575877 and the latest doi at 10.5281/zenodo.6925534;
[x] 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. The title of the Zenodo deposit, "CLOVER: A modelling framework for sustainable community-scale energy systems," matches that of the paper and the author list includes links to ORCID indentifiers;
[x] Please list the DOI of the archived version here. The latest DOI is 10.5281/zenodo.7575877:

Please let me know if there's anything else needed!

fraukewiese commented 1 year ago

@editorialbot set v5.0.6 as version

editorialbot commented 1 year ago

Done! version is now v5.0.6

fraukewiese commented 1 year ago

@BenWinchester and @phil-sandwell The author list in the paper should exactly match the one in the archival deposit. Could you please adjust this?

BenWinchester commented 1 year ago

Hi @fraukewiese ,

This has now been fixed here with the archive updated to match the paper.

We also spotted that bullet-point lists within the paper, which were compiling in our markdown editors, weren't being displayed properly by the action, so fixed this here . The paper.md is now up-to-date on both our publish (stand-alone) and master branches. (Annoyingly, black and pylint, used for automated checking and master-branch protection, were updated in the last two days, which resulted in our automated checks failing, so there have been formatting changes to the code to pass these but no functional changes. If need be, we can trigger a new tagged release?)

Let me know if there's anything else that needs doing :smile:

fraukewiese commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fraukewiese commented 1 year ago

@editorialbot set 10.5281/zenodo.7575877 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7575877

fraukewiese commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.5281/zenodo.6925534 is OK
- 10.21105/joss.00884 is OK
- 10.20900/jsr20200009 is OK
- 10.1016/j.enpol.2011.06.033 is OK
- 10.5334/jors.188 is OK
- 10.1016/j.energy.2016.08.060 is OK
- 10.1016/j.esd.2016.09.002 is OK
- 10.1016/j.renene.2020.03.002 is OK
- 10.1016/j.egypro.2017.09.416 is OK
- 10.1016/j.rset.2021.100003 is OK
- 10.1016/j.seta.2021.101095 is OK
- 10.1016/j.esd.2021.11.008 is OK
- 10.1016/j.erss.2022.102636 is OK
- 10.1088/2515-7655/ac9dc0 is OK
- 10.25561/77296 is OK

MISSING DOIs

- 10.1891/9780826190123.ap02 may be a valid DOI for title: Transforming our world: the 2030 Agenda for Sustainable Development

INVALID DOIs

- None

editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3950, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 year ago

I'm sorry @phil-sandwell, I'm afraid I can't do that. That's something only eics are allowed to do.

kyleniemeyer commented 1 year ago

Hi @phil-sandwell, just a final check to do: is 10.5281/zenodo.7612815 the correct DOI for the reviewed version? I followed the link for the DOI reported above and Zenodo said a newer one was available.

BenWinchester commented 1 year ago

Hi @kyleniemeyer , the DOI 10.5281/zenodo.7575877 is correct for the reviewed version (v5.0.6). 10.5281/zenodo.7612815 is a "beta" (pre-release) version, v5.0.7b1 released to deal with an issue that a researcher raised with respect to their modelling, merged here and released here :smiley:

kyleniemeyer commented 1 year ago

@BenWinchester got it, thanks

kyleniemeyer commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3951
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04799
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 1 year ago

Congratulations @phil-sandwell & @BenWinchester et al. on your article's publication in JOSS!

Many thanks to @EwaGomez and @fneum for reviewing this, and @fraukewiese for editing.

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04799/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04799/status.svg
   :target: https://doi.org/10.21105/joss.04799

This is how it will look in your documentation:

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