[REVIEW]: interflow: A Python package to organize, calculate, and visualize sectoral interdependency flow data

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@kmongird@fraukewiese<!--end-editor-- Reviewers: @wiljnich, @j3r3m1 Archive: 10.5281/zenodo.6620928

Status

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Markdown: [![status](https://joss.theoj.org/papers/ae736aa6e75758498cf79ab8ec3fa886/status.svg)](https://joss.theoj.org/papers/ae736aa6e75758498cf79ab8ec3fa886)

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

@wiljnich & @j3r3m1, 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 @wiljnich

📝 Checklist for @j3r3m1

editorialbot commented 2 years 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:

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

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.69 s (128.2 files/s, 60783.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      10           2406           2464           9227
HTML                            24           1059              0           8548
reStructuredText                23           3703             53           4440
Python                          16           1858           1717           4236
CSS                              5            338             52           1306
Markdown                         4             49              0            116
TeX                              1             22              0            104
YAML                             2             11              4             54
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0            347             15
make                             1              4              7              9
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            89           9458           4645          28082
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 901

editorialbot commented 2 years ago

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

OK DOIs

- 10.1021/acs.est.8b00139 is OK
- 10.1007/s11269-013-0331-2 is OK
- 10.1021/acs.est.6b01065 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

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:

wiljnich commented 2 years ago

Review checklist for @wiljnich

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/pnnl/interflow?
[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 (@kmongird) 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

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 and who the target audience is?
[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?

wiljnich commented 2 years ago

I am very pleased with this package and happily recommend interflow for publication in JOSS. I have one recommendation, which is not acceptance blocking. To conform with the review criteria (Documentation #5), I believe that a short explainer of the test cases and instructions for their use should be added to the documentation site.

This is a great package that solves a painful need - I have built Sankey energy flows in Python before, and this is a vast improvement. Excellent work by @kmongird and team.

kmongird commented 2 years ago

@wiljnich thank you very much for your review! We greatly appreciate your time and comments.

Just to get some clarification on the recommendation you’ve described and to make sure we’re on the same page, when you state “short explainer of the test cases and instructions for their use should be added” are you referring to the test suite for the package or the usage of the sample data in the quickstarter?

wiljnich commented 2 years ago

@kmongird I am referring to the test suite

kmongird commented 2 years ago

Great, thanks very much.

fraukewiese commented 2 years ago

@wiljnich Thank you very much for your review!

fraukewiese commented 2 years ago

@kmongird : Please let us know when you have updated the explainer and instructions for the test suite.

kmongird commented 2 years ago

Thanks @fraukewiese, will do

kmongird commented 2 years ago

@fraukewiese and @wiljnich, the documentation has been updated to include an explainer of the test suite which be found here: https://pnnl.github.io/interflow/api_docs.html#test-validation-suite

fraukewiese commented 2 years ago

Thanks @kmongird @wiljnich : Do you think that explainer is adequate?

wiljnich commented 2 years ago

@kmongird thank you for making this update! @fraukewiese, I am pleased. All elements of my review have been satisfied.

j3r3m1 commented 2 years ago

Review checklist for @j3r3m1

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/pnnl/interflow?
[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 (@kmongird) 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

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 and who the target audience is?
[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?

j3r3m1 commented 2 years ago

Hi @kmongird thank you for your contribution. I have started the review today. I will add new issues in your repo soon.

j3r3m1 commented 2 years ago

I have finished my review, I think when my comments will be answered this would be fine for me to accept the paper. Nice job @kmongird and coauthors.

kmongird commented 2 years ago

@j3r3m1 Thank you for your review! I will begin addressing your comments and comment again here when I'm done.

kmongird commented 2 years ago

@j3r3m1 and @fraukewiese, I have completed my changes and addressed the comments. Thank you again for your review, we appreciate your time and effort going through our submission.

fraukewiese commented 2 years ago

@j3r3m1 Are your comments adequately considered or are there any open points? Thank you very much for your review!

j3r3m1 commented 2 years ago

@editorialbot generate pdf

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:

fraukewiese commented 2 years ago

@j3r3m1 Are your comments adequately considered or are there any open points?

j3r3m1 commented 2 years ago

All points have been quite well adressed, thank you to authors. However, the added diagram (Figure 2) is quite complicated to understand and hardly fit with text description. I have added a comment in the initial related issue (https://github.com/pnnl/interflow/issues/8).

kmongird commented 2 years ago

@j3r3m1 thank you for the follow-up comments, we appreciate your thorough review. We have simplified the figure in the paper considerably and better aligned it with the text.

fraukewiese commented 2 years ago

@editorialbot generate pdf

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:

j3r3m1 commented 2 years ago

Thank you @kmongird and coauthor for responding my remarks. It is OK for me to publish the manuscript as it is. And thank to you for your contribution to the community.

kmongird commented 2 years ago

@fraukewiese at your earliest convenience, please let me know what steps I should take next. Thank you again to both reviewers!

fraukewiese commented 2 years ago

@kmongird , some minor point regarding the article, please check:

Line 21: I think there is something missing in the sentence, maybe "to" before pull?
Line 22: Should it be "help "to" investigate?" - Here I am absolutely not sure since I am not a native speaker, so please check and if you think it is correct without "to", then it is fine
Reference List: Greenberg et al 2017: Link not working
Reference List: Webber 2017: Please include the DOI. Then the title does not need to be linked

fraukewiese commented 2 years ago

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.

kmongird commented 2 years ago

@fraukewiese I have updated the link for the Greenberg et al. 2017 reference and provided the DOI for the Webber 2017 reference. Regarding the sentences in lines 21 and 22, both have been double checked in a grammar evaluation software and confirmed to be grammatically correct as is so no changes have been made to the text.

kmongird commented 2 years ago

version tag for tagged release: v1.0.3

Zenodo DOI: 10.5281/zenodo.6620928

fraukewiese commented 2 years ago

@editorialbot set 10.5281/zenodo.6620928 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6620928

fraukewiese commented 2 years ago

@editorialbot set v1.0.3 as version

editorialbot commented 2 years ago

Done! version is now v1.0.3

fraukewiese commented 2 years ago

@editorialbot generate pdf

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:

fraukewiese commented 2 years ago

@kmongird In the latest article proof I cannot see the changes made (Greenberg et al. 2017 link and Webber 2017 DOI) - could you please check where you made the changes? Thank you.

kmongird commented 2 years ago

Hi @fraukewiese,

On lines 103-104, the broken Greenberg et al. 2017 link has been removed and has been replaced with this working link: https://flowcharts.llnl.gov/report

For the Webber 2017 reference, I removed the title link and have included the doi that is now shown on line 129: https://doi.org/10.1016/B978-0-12-803237-4.00012-4

fraukewiese commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/B978-0-12-803237-4.00012-4 is OK
- 10.1021/acs.est.8b00139 is OK
- 10.1007/s11269-013-0331-2 is OK
- 10.1021/acs.est.6b01065 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 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/3274

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3274, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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