editorialbot commented 7 months ago

Submitting author: !--author-handle-->@rg727@cheginit<!--end-editor-- Reviewers: @barneydobson, @ekblad Archive: 10.5281/zenodo.11061890

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/2eaeba28b1b6cd389bee36db7826af78/status.svg)](https://joss.theoj.org/papers/2eaeba28b1b6cd389bee36db7826af78)

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

@barneydobson & @ekblad, 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 @cheginit 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 @barneydobson

📝 Checklist for @ekblad

editorialbot commented 7 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 7 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (688.0 files/s, 165840.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          25           1375           1735           2346
Jupyter Notebook                 6              0           4845            680
YAML                            10             90             55            650
reStructuredText                 6            270            125            239
TeX                              1             19              0            185
Markdown                         3             29              0             78
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            53           1795           6768           4213
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 7 months ago

Wordcount for paper.md is 1467

editorialbot commented 7 months ago

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

OK DOIs

- 10.1023/B:CLIM.0000013684.13621.1f is OK
- 10.1029/2022WR033454 is OK
- 10.4211/hs.d3efcf0c930646fd9ef4f17c56436d20 is OK
- 10.1029/2020EF001503 is OK
- 10.1016/j.ejrh.2015.02.014 is OK
- 10.1126/science.aay9187 is OK
- 10.1029/2021GL095085 is OK
- 10.1029/2020WR028079 is OK
- 10.1073/pnas.082081699 is OK
- 10.1061/(ASCE)WR.1943-5452.0000626 is OK
- 10.1076/iaij.4.1.1.16462 is OK
- 10.1007/978-3-030-05252-2 is OK
- 10.1287/opre.41.3.435 is OK
- 10.1061/(ASCE)0733-9496(2004)130:6(480) is OK
- 10.1016/j.envsoft.2021.105052 is OK
- 10.1080/02508060508691893 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 7 months ago

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

cheginit commented 7 months ago

@barneydobson, @ekblad, thanks again for accepting to review this submission. This is the review thread for the submission. All of our communications will happen here from now on.

First, please follow the instructions in the first comment of this thread to create your review checklists.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied by editing your checklist comment that our EditorBot will create for you.

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 openjournals/joss-reviews#REVIEW_NUMBER 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 reviews to be completed within about 2–4 weeks. Please reach out to me if you need more time. We can also use EditorialBot to set automatic reminders if you know you'll be away for a known period of time.

Please don't hesitate to ping me (@cheginit) with any questions or concerns.

rg727 commented 7 months ago

@barneydobson, @ekblad thanks so much for agreeing to review our package. We are super excited to get some outside feedback. In case it's not clear, if you follow the links in the GitHub repo to the 5 tutorial Jupyter Notebooks, that's the easiest way to start testing out functionality.

cheginit commented 7 months ago

Just a friendly review reminder @barneydobson @ekblad

barneydobson commented 7 months ago

will be doing this either today or early this week - had a sick baby and then sick myself so everything is a bit delayed!

barneydobson commented 7 months ago

Review checklist for @barneydobson

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/IMMM-SFA/statemodify?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@rg727) 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?

ekblad commented 7 months ago

Review checklist for @ekblad

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/IMMM-SFA/statemodify?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@rg727) 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?

ekblad commented 6 months ago

hi all, i have finished with my comments for this version. in general, the library works as advertised, and documentation is nearing completion. some additional notes at IMMM-SFA/statemodify#54 can improve the user experience. a suggestion for two additional tests at IMMM-SFA/statemodify#55 provides some methodological confidence when using this library in applications other than the CRB. docs from SALib or elsewhere can be adapted for this purpose. neither issue is blocking, they are suggestions to improve uptake. thanks for the invite!

rg727 commented 6 months ago

@ekblad thanks for the thorough review! We are in the midst of tackling all the suggestions and will keep closing out issues as we get to them. Hopefully will have these done in about 2 weeks time.

cheginit commented 6 months ago

@ekblad Thanks for your time and effort for your timely review. Can you please check the remaining boxes in your review comment if they're addressed?

cheginit commented 6 months ago

Hi @@rg727, just checking in on the review progress here.

rg727 commented 6 months ago

Hi @cheginit thanks for checking in! Chris and I are in process of addressing the reviews and hope to finish within about 2 weeks. Is there a deadline?

cheginit commented 6 months ago

@rg727 Great! Two weeks sounds good.

cheginit commented 5 months ago

Hi @@rg727, please update us on your progress in addressing the outstanding issues.

rg727 commented 5 months ago

Hi @cheginit, thank you for the ping. @crvernon and I have addressed the comments and made changes to our code and introductory notebooks. All responses are linked back to this thread and each comment is addressed in the closed issues (see here: https://github.com/IMMM-SFA/statemodify/issues?q=is%3Aissue+is%3Aclosed)

cheginit commented 5 months ago

@rg727 Thanks for working on addressing the issues and updating me on the progress!

@ekblad and @barneydobson Can you please check if all your concerns have been addressed and if so check all the remaining boxes in your review?

barneydobson commented 5 months ago

@cheginit Happy with these revisions and all checkboxes ticked above.

@rg727 and @crvernon - in particular great job revising the notebooks, I think these changes will be a big QoL improvement for users!

cheginit commented 5 months ago

@barneydobson Thank you for your time and effort in reviewing this submission and helping to improve it.

cheginit commented 5 months ago

@rg727 I reached out to @ekblad via email. Once, they check the four remaining boxes in their review comment, I will proceed with the final check and publication process.

rg727 commented 5 months ago

Thank you @cheginit, @ekblad, and @barneydobson!

ekblad commented 5 months ago

all boxes checked above

cheginit commented 5 months ago

@ekblad Thanks for spending your time on reviewing this submission.

@rg727 Now, I will do my final check and start the acceptance process.

cheginit commented 5 months ago

@editorialbot check references

cheginit commented 5 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[ ] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[ ] Check that the archive title, author list, version tag, and the license are correct
[ ] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

editorialbot commented 5 months ago

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

OK DOIs

- 10.1023/B:CLIM.0000013684.13621.1f is OK
- 10.1029/2022WR033454 is OK
- 10.4211/hs.d3efcf0c930646fd9ef4f17c56436d20 is OK
- 10.1029/2020EF001503 is OK
- 10.1016/j.ejrh.2015.02.014 is OK
- 10.1126/science.aay9187 is OK
- 10.1029/2021GL095085 is OK
- 10.1029/2020WR028079 is OK
- 10.1073/pnas.082081699 is OK
- 10.1061/(ASCE)WR.1943-5452.0000626 is OK
- 10.1076/iaij.4.1.1.16462 is OK
- 10.1007/978-3-030-05252-2 is OK
- 10.1287/opre.41.3.435 is OK
- 10.1061/(ASCE)0733-9496(2004)130:6(480) is OK
- 10.1016/j.envsoft.2021.105052 is OK
- 10.1080/02508060508691893 is OK

MISSING DOIs

- No DOI given, and none found for title: The Colorado Water Plan
- No DOI given, and none found for title: A Breakthrough Deal to Keep the Colorado River Fro...
- No DOI given, and none found for title: MODSIM: decision support system for integrated riv...

INVALID DOIs

- None

cheginit commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

cheginit commented 5 months ago

@ekblad and @barneydobson, thanks so much again for your thoughtful reviews here.

@rg727, please address the following, so I can then move forward with recommending acceptance of the submission:

[ ] Go through the missing DOIs listed above and add them.
[ ] 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). Make sure that the license listed for the archive is the same as the software license!
[ ] 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.

rg727 commented 5 months ago

Hi @cheginit thanks for overseeing this process! Quick question: the publications missing DOIs are ones that don't have any DOIs associated with them. One is a state water plan, another is an older paper, and the final one is a New York Times article. Do you have any recommendations? Thanks!

rg727 commented 5 months ago

In response to the checklist

Version: 0.2.1 DOI for archive: 10.5281/zenodo.11061890

[ ] Go through the missing DOIs listed above and add them.

[x] Make a tagged release of your software, and list the version tag of the archived version here.

[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository). Make sure that the license listed for the archive is the same as the software license!

[x] 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.

[x] Please list the DOI of the archived version here.

cheginit commented 5 months ago

@editorialbot set 10.5281/zenodo.11061890 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.11061890

cheginit commented 5 months ago

@editorialbot set 0.2.1 as version

editorialbot commented 5 months ago

Done! version is now 0.2.1

cheginit commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

cheginit commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

OK DOIs

- 10.1023/B:CLIM.0000013684.13621.1f is OK
- 10.1029/2022WR033454 is OK
- 10.4211/hs.d3efcf0c930646fd9ef4f17c56436d20 is OK
- 10.1029/2020EF001503 is OK
- 10.1016/j.ejrh.2015.02.014 is OK
- 10.1126/science.aay9187 is OK
- 10.1029/2021GL095085 is OK
- 10.1029/2020WR028079 is OK
- 10.1073/pnas.082081699 is OK
- 10.1061/(ASCE)WR.1943-5452.0000626 is OK
- 10.1076/iaij.4.1.1.16462 is OK
- 10.1007/978-3-030-05252-2 is OK
- 10.1287/opre.41.3.435 is OK
- 10.1061/(ASCE)0733-9496(2004)130:6(480) is OK
- 10.1016/j.envsoft.2021.105052 is OK
- 10.1080/02508060508691893 is OK

MISSING DOIs

- No DOI given, and none found for title: The Colorado Water Plan
- No DOI given, and none found for title: A Breakthrough Deal to Keep the Colorado River Fro...
- No DOI given, and none found for title: MODSIM: decision support system for integrated riv...

INVALID DOIs

- None

editorialbot commented 5 months ago

:wave: @openjournals/ese-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/5272, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

cheginit commented 5 months ago

@rg727 Congratulations on your publication at JOSS!

While EiC/AEiC works on the final publication, please double-check the final PDF in the previous comment to ensure everything is correct, e.g., authors names and affiliations.

rg727 commented 5 months ago

@cheginit the pdf looks great, thanks!

kthyng commented 5 months ago

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

[x] Are checklists all checked off?
[x] Check that version was updated and make sure the version from JOSS matches github and Zenodo.
[x] Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
[x] Check paper.

kthyng commented 5 months ago

@rg727 We prefer to have the title and author list of the Zenodo archive associated with your JOSS submission exactly match the JOSS paper for consistency. Would you update the Zenodo metadata to do so?

kthyng commented 5 months ago

@rg727 Also your paper looks good but please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

crvernon commented 5 months ago

@editorialbot generate pdf

openjournals / joss-reviews

[REVIEW]: statemodify: a Python framework to facilitate accessible exploratory modeling for discovering drought vulnerabilities #6325

Status

Reviewer instructions & questions

Checklists

Review checklist for @barneydobson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @ekblad

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance