[REVIEW]: The Spreadsheet Energy System Model Generator (SESMG): A tool for the optimization of urban energy systems

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@chrklemm@timtroendle<!--end-editor-- Reviewers: @nick-gorman, @willu47 Archive: 10.5281/zenodo.8344791

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/377ee4d8f3dfa756cdf6def4be55ab8b"><img src="https://joss.theoj.org/papers/377ee4d8f3dfa756cdf6def4be55ab8b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/377ee4d8f3dfa756cdf6def4be55ab8b/status.svg)](https://joss.theoj.org/papers/377ee4d8f3dfa756cdf6def4be55ab8b)

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

@nick-gorman & @willu47, 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 @timtroendle 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 @willu47

📝 Checklist for @nick-gorman

editorialbot commented 1 year 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 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.18 s (725.7 files/s, 135675.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           80           2454           7033          10053
reStructuredText                 23            942            565           2263
Markdown                         13            203              0            770
TeX                               1             20              0            152
JSON                              3              3              0            107
YAML                              5             20             28            107
Bourne Again Shell                2              8              0             37
DOS Batch                         2             12              0             37
Bourne Shell                      2             12              0             31
CSS                               1              1              0              6
TOML                              1              0              0              2
--------------------------------------------------------------------------------
SUM:                            133           3675           7626          13565
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 885

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.apenergy.2022.120574 is OK
- 10.1186/s13705-021-00323-3 is OK
- 10.1155/2018/6937505 is OK
- 10.1016/j.rser.2014.02.003 is OK
- 10.1109/PSCC.2016.7541031 is OK
- 10.1016/j.amc.2009.03.037 is OK
- 10.1016/j.apenergy.2018.09.041 is OK
- 10.1016/j.apenergy.2017.03.001 is OK
- 10.3390/en12244656 is OK
- 10.1016/j.apenergy.2019.113705 is OK

MISSING DOIs

- None

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:

willu47 commented 1 year ago

Review checklist for @willu47

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/SESMG/SESMG?
[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 (@chrklemm) 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?

nick-gorman commented 1 year ago

Review checklist for @nick-gorman

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/SESMG/SESMG?
[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 (@chrklemm) 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?

timtroendle commented 1 year ago

@willu47 , @nick-gorman can you please give us an update where you stand with your review? We are approaching the end of the review period.

willu47 commented 1 year ago

Hi @timtroendle - I should be able to complete the review by the end of the week. I've raised one issue regarding the installation and have a few more issues to ask of the authors.

nick-gorman commented 1 year ago

@timtroendle apologies, hopefully I'll finish it on Friday or the weekend

nick-gorman commented 1 year ago

@chrklemm SESMG looks like great software. I really like the idea of making the omeof capabilities available to users who don't use python by creating a standard spreadsheet input format.

Here is my review of the documentation and paper as per the checklist:

Functionality:

I haven't been able to run the file model_definition_example.xlsx to completion. I'll raise an issue about this separately. Just as an aside, examples that run quickly are more useful for helping new users learn about the tool.

Documentation:

I can't find a clear statement of need (please direct me in the right direction if one exists). Further to this, although not required by the JOSS review I think the read-the-docs pages lack a good introduction to orient the reader. At least a statement of need should be added, and the authors should consider adding an intro to the read-the-docs page.
Again, while technically the documentation includes an example as part of the application section this isn't broken out separately in a way that makes it easy to understand holistically, i.e. explain the energy system, explain the problem that is being solved in the example, walk the user through how this is done with the software. Not 100% necessary for the JOSS review but should be considered by the authors.
Also, the examples folder on GitHub appears empty? (https://github.com/SESMG/SESMG/tree/master/examples)
Functionality documentation, I don't think the descriptions of the various modelling capability are detailed/clear enough. This would probably be improved with an example that uses each type of functionality, i.e. an example that uses clustering that demonstrates how inputs affect the clustering (for example, it isn't clear to me what selecting hours for clustering will actually do).

Software paper:

Not sure that the statement of need addresses who the target audience is.
Other commonly used packages are not addressed in the paper.

chrklemm commented 1 year ago

Dear @nick-gorman, thank you for your helpful comments! I have moved the comments to a sepparate issue where we will answer them. I hope this is ok for you.

Best regards, @chrklemm

timtroendle commented 1 year ago

@openjournals/joss-eics, I will be out of office 7--25 August.

timtroendle commented 1 year ago

Hi @chrklemm, could you let us know where you stand with responding to the comments by the reviewers and how much more time you will need?

chrklemm commented 1 year ago

Hello @timtroendle,

thank you for getting back in touch with us. We have processed most of the reviewer comments. They are waiting for confirmation from the reviewers that the issues can be closed:

https://github.com/SESMG/SESMG/issues/190 (responsible reviewer: @nick-gorman) https://github.com/SESMG/SESMG/issues/193 (responsible reviewer: @willu47) https://github.com/SESMG/SESMG/issues/194 (responsible reviewer: @nick-gorman)

The last issue is quite challenging for us, but we expect to complete it by the end of the week:

https://github.com/SESMG/SESMG/issues/188 (responsible reviewer: @willu47)

Best regards, @chrklemm

Addendum: the following issue has already been closed by the responsible reviewer:

https://github.com/SESMG/SESMG/issues/189 (responsible reviewer: @nick-gorman)

nick-gorman commented 1 year ago

@timtroendle @chrklemm Apologies for the delay, I think everything is now in order from my perspective.

chrklemm commented 1 year ago

Dear @timtroendle, dear reviewers,

thank you again for your very helpful feedback and suggestions. We believe, that the SESMG already has improved by the changes we made based on your comments.

However, we are still facing https://github.com/SESMG/SESMG/issues/188 . Within this aspect we are developing an entirely new way to execute the SESMG. While in the current version the users have to install Python, the SESMG and single sub-packages one by one, the execution will be possible in the future by executing a single exe (windows), dmg (mac), respectively deb (linux)-file.

We are facing some challenges as we need to need to generate new knowledge in the field of application development and publication. Those are based on the creation of a standalone executable for different operating systems and the management of operating system processes, which is required because the web-based architecture of SESMG is not straightforwardly compatible with the executable system structure. Therefore, I am sorry to inform you that we need more time to develop this new feature. We are working at high pressure on this and will inform you here as soon as the development is completed. You can follow the current progress in the following branch: https://github.com/SESMG/SESMG/tree/issue-188

Thank you for your patience and best regards, SESMG-Dev-Team

chrklemm commented 1 year ago

Dear @timtroendle, Dear reviewers,

we were finally able to finish our development regarding https://github.com/SESMG/SESMG/tree/issue-188. As soon as @willu47 agrees with these changes, we have addressed all issues raised by the reviewers.

We would like to thank the editor and the reviewers for their help and patience during this review process. Best regards, SESMG-Dev-Team

chrklemm commented 1 year ago

Dear @timtroendle,

The proposed changes to the last open issue have been approved by the responsible reviewer @willu47. Thus, all suggested changes have been included in the SESMG and approved by the respective reviewers.

If further changes are needed, please let us know. However, for the case that no further changes are needed, we have already initiated the next steps:

We have released a new version of the SESMG: v1.0.0
The current version has been published on Zenodo (metadata identical to the Joss-paper) and can be found at the following DOI: .

Once again, we would like to thank all the editors and reviewers involved for their help and patience during this review process. Best regards, SESMG-Dev-Team

timtroendle commented 1 year ago

@editorialbot set v1.0.0 as version

editorialbot commented 1 year ago

Done! version is now v1.0.0

timtroendle commented 1 year ago

@editorialbot set 10.5281/zenodo.8344791 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8344791

timtroendle 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:

timtroendle 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

- 10.1016/j.apenergy.2022.120574 is OK
- 10.1186/s13705-021-00323-3 is OK
- 10.1155/2018/6937505 is OK
- 10.1016/j.rser.2014.02.003 is OK
- 10.1109/PSCC.2016.7541031 is OK
- 10.1016/j.amc.2009.03.037 is OK
- 10.1016/j.apenergy.2018.09.041 is OK
- 10.1016/j.apenergy.2017.03.001 is OK
- 10.3390/en12244656 is OK
- 10.1016/j.apenergy.2019.113705 is OK
- 10.5281/zenodo.596235 is OK
- 10.1016/j.rser.2020.110206 is OK

MISSING DOIs

- None

INVALID DOIs

- None

timtroendle commented 1 year ago

Thank you for the update @chrklemm . It all looks good to me and I will therefore move on and recommend acceptance.

timtroendle 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

- 10.1016/j.apenergy.2022.120574 is OK
- 10.1186/s13705-021-00323-3 is OK
- 10.1155/2018/6937505 is OK
- 10.1016/j.rser.2014.02.003 is OK
- 10.1109/PSCC.2016.7541031 is OK
- 10.1016/j.amc.2009.03.037 is OK
- 10.1016/j.apenergy.2018.09.041 is OK
- 10.1016/j.apenergy.2017.03.001 is OK
- 10.3390/en12244656 is OK
- 10.1016/j.apenergy.2019.113705 is OK
- 10.5281/zenodo.596235 is OK
- 10.1016/j.rser.2020.110206 is OK

MISSING DOIs

- None

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/4571, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Klemm given-names: Christian orcid: "https://orcid.org/0000-0003-0801-4178" - family-names: Becker given-names: Gregor orcid: "https://orcid.org/0000-0001-8803-6873" - family-names: Tockloth given-names: Jan N. orcid: "https://orcid.org/0000-0003-2582-1043" - family-names: Budde given-names: Janik orcid: "https://orcid.org/0000-0002-1617-5900" - family-names: Vennemann given-names: Peter orcid: "https://orcid.org/0000-0002-0767-5014" contact: - family-names: Klemm given-names: Christian orcid: "https://orcid.org/0000-0003-0801-4178" doi: 10.5281/zenodo.8344791 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Klemm given-names: Christian orcid: "https://orcid.org/0000-0003-0801-4178" - family-names: Becker given-names: Gregor orcid: "https://orcid.org/0000-0001-8803-6873" - family-names: Tockloth given-names: Jan N. orcid: "https://orcid.org/0000-0003-2582-1043" - family-names: Budde given-names: Janik orcid: "https://orcid.org/0000-0002-1617-5900" - family-names: Vennemann given-names: Peter orcid: "https://orcid.org/0000-0002-0767-5014" date-published: 2023-09-17 doi: 10.21105/joss.05519 issn: 2475-9066 issue: 89 journal: Journal of Open Source Software publisher: name: Open Journals start: 5519 title: "The Spreadsheet Energy System Model Generator (SESMG): A tool for the optimization of urban energy systems" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05519" volume: 8 title: "The Spreadsheet Energy System Model Generator (SESMG): A tool for the optimization of urban energy systems" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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/4583
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05519
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 @chrklemm on your article's publication in JOSS! Please consider signing up to review, if you haven't already.

Many thanks to @nick-gorman and @willu47 for reviewing this, and @timtroendle for editing.

editorialbot commented 1 year ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05519/status.svg)](https://doi.org/10.21105/joss.05519)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05519">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05519/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05519/status.svg
   :target: https://doi.org/10.21105/joss.05519

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews