[REVIEW]: cerf: A Python package to evaluate the feasibility and costs of power plant siting for alternate futures

[whedon]

Submitting author: @crvernon (Chris Vernon)
Repository: https://github.com/IMMM-SFA/cerf
Version: v2.0.9
Editor: @fraukewiese
Reviewer: @lisazeyen , @willu47
Archive: 10.5281/zenodo.5527334

⚠️ JOSS reduced service mode ⚠️

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/28fee3407bbbef020fb4bb19bd451407"><img src="https://joss.theoj.org/papers/28fee3407bbbef020fb4bb19bd451407/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/28fee3407bbbef020fb4bb19bd451407/status.svg)](https://joss.theoj.org/papers/28fee3407bbbef020fb4bb19bd451407)

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

@lisazeyen & @willu47 , please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 @lisazeyen

✨ 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 (@crvernon) 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?

Review checklist for @willu47

✨ 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 (@crvernon) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lisazeyen , @willu47 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[fraukewiese]

@lisazeyen , @willu47 – 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 #3601 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.

[fraukewiese]

@whedon check repository

[whedon]

Wordcount for paper.md is 1163

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (766.4 files/s, 157815.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                            10            157             24           5908
Python                          23           1004            902           1495
SVG                              4              4              4            298
CSS                              2             54             11            244
reStructuredText                 9            307            494            240
TeX                              1             11              0            133
Markdown                         2             29              0             78
XML                              3              0              0             50
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            221             15
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            57           1578           1664           8496
-------------------------------------------------------------------------------


Statistical information for the repository '35259e4da8023f93dbebfb4c' was
gathered on 2021/08/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chris Vernon                     3           490             14            0.63
Nino Zuljevic                    1          3276              2            4.10
Vernon                           7           437             62            0.62
Vernon, Chris R                  9           673            199            1.09
crvernon                       150         36822          38020           93.56

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
Vernon                        2            0.5         40.5                0.00
crvernon                   3399            9.2          4.4               15.77

[fraukewiese]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41560-020-00686-5 is OK
- 10.1016/j.rser.2018.09.022 is OK
- 10.1016/j.techfore.2013.08.025 is OK
- 10.1038/s41467-021-21785-1 is OK
- 10.1016/j.gloenvcha.2015.09.019 is OK
- 10.5334/jors.227 is OK
- 10.1007/s10584-012-0618-y is OK
- 10.1016/j.esr.2019.100411 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1038/s41467-018-08275-7 is OK
- 10.1016/j.apenergy.2019.114267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fraukewiese]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[crvernon]

@fraukewiese @lisazeyen @willu47 The following is a preemptive explanation of author contributions to this paper:

• Chris R. Vernon. Lead author and developer.
• Jennie S. Rice. Original product conception, algorithm development, and documentation.
• Nino Zuljevic. Algorithm, supporting data, and code development.
• Kendall Mongird. Algorithm, supporting data, and documentation development.
• Kristian Nelson. Supporting data and documentation development.
• Gokul Iyer. Supporting data and documentation development.
• Nathalie Voisin. Supporting data and documentation development.
• Matthew Binsted. Supporting data and documentation development.

[fraukewiese]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41560-020-00686-5 is OK
- 10.1016/j.rser.2018.09.022 is OK
- 10.1016/j.techfore.2013.08.025 is OK
- 10.1038/s41467-021-21785-1 is OK
- 10.1016/j.gloenvcha.2015.09.019 is OK
- 10.5334/jors.227 is OK
- 10.1007/s10584-012-0618-y is OK
- 10.1016/j.esr.2019.100411 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1038/s41467-018-08275-7 is OK
- 10.1016/j.apenergy.2019.114267 is OK
- 10.5194/gmd-12-677-2019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fraukewiese]

Both reviewers have stated that @crvernon has addressed all of their comments. We thus proceed to the final steps.

[fraukewiese]

@crvernon
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.

[crvernon]

@fraukewiese My release version is v2.0.9 and my DOI is 10.5281/zenodo.5527334

Thanks!

[fraukewiese]

@whedon set <v2.0.9> as version

[whedon]

OK. <v2.0.9> is the version.

[fraukewiese]

@whedon set v2.0.9 as version

[whedon]

OK. v2.0.9 is the version.

[fraukewiese]

@crvernon The title in the archive does not exactly match the paper title: alternative instead of alternate.

[fraukewiese]

@whedon set 10.5281/zenodo.5527334 as archive

[whedon]

OK. 10.5281/zenodo.5527334 is the archive.

[fraukewiese]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41560-020-00686-5 is OK
- 10.1016/j.rser.2018.09.022 is OK
- 10.1016/j.techfore.2013.08.025 is OK
- 10.1038/s41467-021-21785-1 is OK
- 10.1016/j.gloenvcha.2015.09.019 is OK
- 10.5334/jors.227 is OK
- 10.1007/s10584-012-0618-y is OK
- 10.1016/j.esr.2019.100411 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.1038/s41467-018-08275-7 is OK
- 10.1016/j.apenergy.2019.114267 is OK
- 10.5194/gmd-12-677-2019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2609

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2609, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[crvernon]

@crvernon The title in the archive does not exactly match the paper title: alternative instead of alternate.

@fraukewiese yes, I changed the name in the paper as well. The original should have used "alternative" instead. The current is correct. Thank you!

[crvernon]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03601 joss-papers#2610
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03601
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @crvernon (Chris Vernon) and co-authors!!

And thanks to @lisazeyen and @willu47 for reviewing, and @fraukewiese for editing!
We couldn't do this without you

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.03601/status.svg)](https://doi.org/10.21105/joss.03601)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03601">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03601/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03601/status.svg
   :target: https://doi.org/10.21105/joss.03601

This is how it will look in your documentation:

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