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[REVIEW]: cerf: A Python package to evaluate the feasibility and costs of power plant siting for alternate futures #3601

Closed whedon closed 3 years ago

whedon commented 3 years ago

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

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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

@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

Code of Conduct

General checks

Functionality

Documentation

Software paper

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :tada:.

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fraukewiese commented 3 years ago

@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 commented 3 years ago

@whedon check repository

whedon commented 3 years ago

Wordcount for paper.md is 1163

whedon commented 3 years ago 
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 commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

crvernon commented 3 years ago

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

crvernon commented 3 years ago

@willu47 I believe I have incorporated all of your feedback (see PR chain above). I really appreciate you taking time to make suggestions and edits that were very beneficial to this software! Please let me know if you have any more questions and I'll be happy to address them.

crvernon commented 3 years ago

👋 @lisazeyen Don't hesitate to reach out if you have any questions. Thank you!

crvernon commented 3 years ago

@willu47 I have just merged functionality to incorporate your recent suggestion to separate the data (~200 MB) from the package. The package data can now be installed via a simple call which is all detailed in the docs via:

import cerf

# install package data
cerf.install_package_data()

or from the terminal after installing cerf via:

python -c 'import cerf; cerf.install_package_data()'

Thanks for the suggestion!

Please let me know if you have any more questions. 👍

willu47 commented 3 years ago

Hi @crvernon - looks good. One more broader issue linked above. Let's discuss in the issue. It would be good to get your feedback on my suggestion/question

whedon commented 3 years ago

:wave: @willu47 , please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @lisazeyen , please update us on how your review is going (this is an automated reminder).

crvernon commented 3 years ago

:wave: @willu47 and @lisazeyen - I have addressed all of your issues and comments. At this point we should be up-to-date. All changes have been incorporated on main and the docs and PyPi versions updated accordingly. Thanks so much for the great feedback!

crvernon commented 3 years ago

Just following up to see if you had any further questions @willu47 and @lisazeyen . Thanks for your feedback thus far!

crvernon commented 3 years ago

:wave: @lisazeyen I have addressed both of your recent issues. Thanks for the additional feedback!

fraukewiese commented 3 years ago

@lisazeyen @willu47 : I see you're nearly finished with your reviews - thanks a lot ! Please let me know when you are done and what your recommendation is.

crvernon commented 3 years ago

:wave: Hello @willu47 and @lisazeyen do you have any further comments for this review? I would love to try to wrap this up before the end of our fiscal year if possible. Thanks so much for your constructive and helpful review!

lisazeyen commented 3 years ago

@crvernon @fraukewiese : I am finished with my review. @crvernon has addressed all my comments.

fraukewiese commented 3 years ago

Thank you very much @lisazeyen for your thorough review!

willu47 commented 3 years ago

Apologies for the delay in following up, I have been on leave. @crvernon I am afraid I'm not fully happy with the data install yet as outlined in issue IMMM-SFA/cerf#71. Otherwise, I'm happy that my comments have been addressed.

crvernon commented 3 years ago

@willu47 I added in the option to download the illustrative test data to a user-defined location as described in https://github.com/IMMM-SFA/cerf/pull/72

🤝 Thanks for all of your input and the thoughtful review! I now have addressed all of your inquiries.

crvernon commented 3 years ago

:wave: @fraukewiese at this point I believe I have addressed all reviewer comments. Thanks!

fraukewiese commented 3 years ago

@willu47 Are you satisfied with the way crvernon has addressed your comment on the data install?

willu47 commented 3 years ago

@willu47 Are you satisfied with the way crvernon has addressed your comment on the data install?

Yes, @crvernon has addressed all my requests.

fraukewiese commented 3 years ago

@willu47 Thank you for that information. If you are satisfied with everything, could you then check the last checkbox in your review list? Thanks a lot for your thorough review that has improved the submission a lot.

fraukewiese commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

fraukewiese commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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 commented 3 years ago

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

fraukewiese commented 3 years ago

@crvernon At this point could you:

I can then move forward with accepting the submission.

crvernon commented 3 years ago

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

Thanks!

fraukewiese commented 3 years ago

@whedon set <v2.0.9> as version

whedon commented 3 years ago

OK. <v2.0.9> is the version.

fraukewiese commented 3 years ago

@whedon set v2.0.9 as version

whedon commented 3 years ago

OK. v2.0.9 is the version.

fraukewiese commented 3 years ago

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

fraukewiese commented 3 years ago

@whedon set 10.5281/zenodo.5527334 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5527334 is the archive.

fraukewiese commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
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 commented 3 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/2609

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 3 years ago

@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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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