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[REVIEW]: CL-PFU: A suite of R packages for energy conversion chain analysis #6057

Closed editorialbot closed 8 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@MatthewHeun<!--end-author-handle-- (Matthew Heun) Repository: https://github.com/EnergyEconomyDecoupling/CL-PFU-JOSS-Paper Branch with paper.md (empty if default branch): Version: v0.1.9 Editor: !--editor-->@timtroendle<!--end-editor-- Reviewers: @abhishektiwari, @nmstreethran Archive: 10.5281/zenodo.10458774

Status

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Markdown: [![status](https://joss.theoj.org/papers/bbe9eff46386919972f242307c4cdc70/status.svg)](https://joss.theoj.org/papers/bbe9eff46386919972f242307c4cdc70)

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

@abhishektiwari & @nmstreethran, 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 @abhishektiwari

📝 Checklist for @nmstreethran

editorialbot commented 10 months 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 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (572.0 files/s, 110468.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             66              0            508
TeX                              1             60              4            242
R                                3             35             54            103
Rmd                              1             50            370             30
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                             8            212            432            901
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 2970

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.apenergy.2021.118413 is OK
- 10.1016/s0360-5442(02)00089-0 is OK
- 10.1021/es501217t is OK
- 10.1016/j.apenergy.2015.05.082 is OK
- 10.1016/0301-4215(76)90008-2 is OK
- 10.1016/s0360-5442(00)00070-0 is OK
- 10.1016/j.eneco.2016.11.020 is OK
- 10.1016/j.apenergy.2018.05.109 is OK
- 10.5281/zenodo.5228359 is OK
- 10.21105/joss.02959 is OK
- 10.1016/j.energy.2014.08.068 is OK
- 10.1007/s41247-022-00096-z is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5518/1199 is INVALID
editorialbot commented 10 months ago

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

abhishektiwari commented 10 months ago

Review checklist for @abhishektiwari

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

nmstreethran commented 10 months ago

Review checklist for @nmstreethran

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

MatthewHeun commented 10 months ago

@abhishektiwari and @nmstreethran

Thanks for your willingness to review!

timtroendle commented 9 months ago

@abhishektiwari could you please let us know about the status of your review?

abhishektiwari commented 9 months ago

@timtroendle currently going through functionality varificaiton - feedback to be shared mid next week.

abhishektiwari commented 9 months ago

@MatthewHeun Please see initial feedback.

General checks

Repository

Is the source code for this software available at the https://github.com/EnergyEconomyDecoupling/CL-PFU-JOSS-Paper? No.

Source code for packages in CL-PFU suite is available on different GitHub repositories, but there is no direct way to browse them from the GitHub repo used in this submission. Given this repo will be linked to digital version of paper, I strongly recommend authors to add a README.md to repo pointing to following 10 packages covered by the paper and under the scope of review.

Licence

Repositories seems to have dual licences (LICENSE vs, LICENSE.md). Given JOSS only accepts OSI approved software licence, please fix licence for following packages.

Documentation

Please add A statement of need and/or Community guidelines for following packages.

Paper

Summary

Given the large number of packages (10) covered under paper and CL-PFU suite, paper summary can be updated to reflect two different types of packages included in the suite

— Utility packages in support of PSUT framework (3) — Utility package in support of CL-PFU database (7)

MatthewHeun commented 9 months ago

@abhishektiwari: Thank you for your comments! I moved these comments to individual issues in the paper's repository to allow easier tracking.

timtroendle commented 9 months ago

Hi @MatthewHeun could you let us know by when you'll be able to implement the recommended changes?

MatthewHeun commented 9 months ago

Hi @MatthewHeun could you let us know by when you'll be able to implement the recommended changes?

@timtroendle Thanks for your query. You can see https://github.com/EnergyEconomyDecoupling/CL-PFU-JOSS-Paper/issues to see my progress. 10 of 13 issues are completed, so I am very close. My goal is to finish everything by end of this week, 22 Dec 2023. Please let me know if you have any further questions.

timtroendle commented 9 months ago

@MatthewHeun , thanks for letting us know! It would be great if you could ping me and the reviewers here once done. Personally, I will be off the next week without access to my mails.

MatthewHeun commented 9 months ago

Happy to do so. Stay tuned!

MatthewHeun commented 9 months ago

@timtroendle:

I believe I have addressed all of the issues raised by the reviewers at https://github.com/EnergyEconomyDecoupling/CL-PFU-JOSS-Paper/issues. The review process can proceed at your convenience.

@nmstreethran, @abhishektiwari:

Thank you for your constructive and helpful comments! They have improved both the paper and the software.

Happy holidays, everyone!

timtroendle commented 8 months ago

Thanks for the update, @MatthewHeun!

@abhishektiwari, can you please confirm that all your issues have been resolved by ticking the remaining boxes in your checklist?

abhishektiwari commented 8 months ago

Thanks for resolving all open issues @MatthewHeun.

@timtroendle Updated review checklist. Review is now complete from my side.

timtroendle commented 8 months ago

@editorialbot check references

timtroendle commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.apenergy.2021.118413 is OK
- 10.1016/s0360-5442(02)00089-0 is OK
- 10.1021/es501217t is OK
- 10.1016/j.apenergy.2015.05.082 is OK
- 10.1016/0301-4215(76)90008-2 is OK
- 10.1016/s0360-5442(00)00070-0 is OK
- 10.1016/j.eneco.2016.11.020 is OK
- 10.1016/j.apenergy.2018.05.109 is OK
- 10.5281/zenodo.5228359 is OK
- 10.21105/joss.02959 is OK
- 10.1016/j.energy.2014.08.068 is OK
- 10.1007/s41247-022-00096-z is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5518/1199 is INVALID
editorialbot commented 8 months ago

:warning: An error happened when generating the pdf. Problem with affiliations for Matthew Heun, perhaps the affiliations index need quoting?.

timtroendle commented 8 months ago

@MatthewHeun, could you have a look at the two problems above? First, there is an invalid DOI in your reference list. Second, your new affiliations are causing a technical issue. I suppose quoting them should resolve the issue.

Once that's done, I will have a final look at the manuscript and we can move forward.

In addition, I believe you have not yet archived the meta-package anywhere, correct? Could you please

MatthewHeun commented 8 months ago

@timtroendle, I'm happy to dig into those three problems. I'll add them as separate issues to the paper's repository at https://github.com/EnergyEconomyDecoupling/CL-PFU-JOSS-Paper/issues, so you can track progress. I'll also ping you again here when everything is done.

MatthewHeun commented 8 months ago

@timtroendle: I just made a tagged release of the metapackage. See https://github.com/EnergyEconomyDecoupling/CL-PFU-JOSS-Paper/issues/19 for details. The version is v0.1.8. The DOI is 10.5281/zenodo.10456048 (https://doi.org/10.5281/zenodo.10456048)

Please let me know if you have any questions.

timtroendle commented 8 months ago

@editorialbot set 10.5281/zenodo.10456048 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10456048

timtroendle commented 8 months ago

@editorialbot set v0.1.8 as version

editorialbot commented 8 months ago

Done! version is now v0.1.8

timtroendle commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

timtroendle commented 8 months ago

@MatthewHeun it looks all good to me. Apart from the invalid DOI, there is one more tiny issue to fix: the author list on Zenodo and in the paper differ. Can you please make sure both lists have the same order?

MatthewHeun commented 8 months ago

@timtroendle Thanks for your eagle-eyed spot of the different author order. That problem has now been fixed. Unfortunately, that meant I needed to generate a new release of the CLPFUDatabase package. I hope that doesn't mess up your system.

We're working on the invalid DOI, which is the input data repository for the database. We hope to have that done by early next week. So please stay tuned.

MatthewHeun commented 8 months ago

@timtroendle Thanks for your patience as we sorted out the un-minted DOI. The un-minted DOI contains output products from the database and is intended for a paper in review at the journal Environmental Research: Energy. We decided to remove the references to the un-minted DOI from the JOSS paper. The JOSS paper points to the Environmental Research: Energy paper which contains a references to the un-minted DOI. The un-minted DOI will go live at a later date coinciding with the publication of the Environmental Research: Energy paper.

I think this means we can move forward with the publication of the JOSS paper now.

Thanks for your deft guidance of this paper through the review process at JOSS. Also, my sincere thanks to @nmstreethran and @abhishektiwari for their reviews!

timtroendle commented 8 months ago

Thanks for letting us know @MatthewHeun. That'll allow us to move forward.

timtroendle commented 8 months ago

@editorialbot set v0.1.9 as version

editorialbot commented 8 months ago

Done! version is now v0.1.9

timtroendle commented 8 months ago

@editorialbot set 10.5281/zenodo.10458774 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10458774

timtroendle commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.apenergy.2021.118413 is OK
- 10.1016/s0360-5442(02)00089-0 is OK
- 10.1021/es501217t is OK
- 10.1016/j.apenergy.2015.05.082 is OK
- 10.1016/0301-4215(76)90008-2 is OK
- 10.1016/s0360-5442(00)00070-0 is OK
- 10.1016/j.eneco.2016.11.020 is OK
- 10.1016/j.apenergy.2018.05.109 is OK
- 10.5281/zenodo.5228359 is OK
- 10.21105/joss.02959 is OK
- 10.1016/j.energy.2014.08.068 is OK
- 10.1007/s41247-022-00096-z is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5518/1199 is INVALID
timtroendle commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

timtroendle commented 8 months ago

Hm the invalid DOI still appears in the reference check, but it's not included in the paper and so this looks good to me.

timtroendle commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.apenergy.2021.118413 is OK
- 10.1016/s0360-5442(02)00089-0 is OK
- 10.1021/es501217t is OK
- 10.1016/j.apenergy.2015.05.082 is OK
- 10.1016/0301-4215(76)90008-2 is OK
- 10.1016/s0360-5442(00)00070-0 is OK
- 10.1016/j.eneco.2016.11.020 is OK
- 10.1016/j.apenergy.2018.05.109 is OK
- 10.5281/zenodo.5228359 is OK
- 10.21105/joss.02959 is OK
- 10.1016/j.energy.2014.08.068 is OK
- 10.1007/s41247-022-00096-z is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5518/1199 is INVALID
editorialbot commented 8 months 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/4888, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

MatthewHeun commented 8 months ago

Hm the invalid DOI still appears in the reference check, but it's not included in the paper and so this looks good to me.

@timtroendle The invalid DOI was still in the .bib file but not referenced in the paper. I just removed the invalid DOI from the .bib file and pushed. So if you run another check, it should look OK.

We will look at the paper and get back to you with a final word by end of day tomorrow.

Thanks again for your good work!