[REVIEW]: fars_cleaner: A Python package for downloading and pre-processing vehicle fatality data in the US

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@mzabrams@majensen<!--end-editor-- Reviewers: @ethanwhite, @svburke Archive: 10.5281/zenodo.7249980

Status

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Markdown: [![status](https://joss.theoj.org/papers/2ca54c6935611fe3cb0303c49a354c51/status.svg)](https://joss.theoj.org/papers/2ca54c6935611fe3cb0303c49a354c51)

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

@ethanwhite & @svburke, 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 @majensen 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 @svburke

📝 Checklist for @ethanwhite

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (363.7 files/s, 45068.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          11            319            293           1417
Markdown                         2             46              0            183
YAML                             5             11              9             91
TeX                              1              7              0             53
TOML                             1              5              1             43
-------------------------------------------------------------------------------
SUM:                            20            388            303           1787
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 807

editorialbot commented 2 years ago

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

OK DOIs

- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 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:

svburke commented 2 years ago

Review checklist for @svburke

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/mzabrams/fars-cleaner?
[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 (@mzabrams) 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, 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?

svburke commented 2 years ago

I have left the following two issues on the main repository:

https://github.com/mzabrams/fars-cleaner/issues/1 https://github.com/mzabrams/fars-cleaner/issues/2

majensen commented 2 years ago

Hi @ethanwhite - how is your review coming along? Thanks.

mzabrams commented 2 years ago

@svburke I've addressed one of those two issues, and I am examining the other (mzabrams/fars-cleaner#1) -- I'm not sure why this is the behavior on windows and not on macOS, but I am trying to assess ways of importing the full dataset without running into the out-of-memory error on a 16GB setup. Further thoughts/progress will be addressed in the issue on the project repository as I work through it.

ethanwhite commented 2 years ago

Review checklist for @ethanwhite

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/mzabrams/fars-cleaner?
[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 (@mzabrams) 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

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] 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).
[ ] 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?
[ ] 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?

ethanwhite commented 2 years ago

Overall things look good. I've opened 4 issues in the fars-cleaner repo related to installation, documentation, functionality, and community guidelines, all of which are linked above.

majensen commented 2 years ago

Hi @mzabrams - how is the work progressing on the reviewer comments?

mzabrams commented 2 years ago

@majensen I've made some progress on these -- two issues remain open, one may need to be closed with a note made to system requirements to run the package (there seems to be a Windows-based issue that I've been unable to resolve to this point, potentially based on the way Windows handles memory usage compared to macOS and Linux systems), and I'm working on fixing the packaging for download from conda/conda-forge. Hopefully by the end of the week I'll have all this sorted!

mzabrams commented 2 years ago

@majensen All but one of the relevant issues have been closed -- regarding issue mzabrams/fars-cleaner#3, the package is available for download via conda and pip, but is awaiting review by the conda-forge team to be accessed through that channel. Not sure what the timeline is for that team to move things on, but I think I've addressed everything else raised by @svburke and @ethanwhite

majensen commented 2 years ago

Thanks @mzabrams - I'll do my editorial review of the paper itself (usu. pretty minor comments)- hope I can do it this weekend. Then the final steps to prep for the recommendation to the EIC are pretty rapid.

majensen 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:

majensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK

MISSING DOIs

- None

INVALID DOIs

- None

majensen commented 2 years ago

@mzabrams - I like this software a lot, it is the kind of work that increases the usability of siloed data; I hope it goes viral and energizes your field. 2 very minor items: 1) Can you put the Statement of Need section just after the Summary; 2) can you add links to your proceedings in the refs. I see, for example, this link is available: http://www.ircobi.org/wordpress/downloads/irc22/pdf-files/2212.pdf.

majensen commented 2 years ago

After doing the above, can you create an open archive of your code repo, using Zenodo, FigShare or similiar? A short tutorial using Zenodo is here. When this is done, please post the DOI you receive back in this thread. Thanks!

mzabrams commented 2 years ago

@majensen Thanks! I think I'd already set it up with Zenodo -- DOI for the most recent release version (1.3.3) is 10.5281/zenodo.7221282. I've made those additions to the references (there isn't a publicly available repository of World Congress of Biomechanics Proceedings, unfortunately), and moved the statement of need as well. Let me know if there's anything else! I appreciate the kind words about this project!!

majensen commented 2 years ago

@editorialbot check references

majensen 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:

editorialbot commented 2 years ago

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

OK DOIs

- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK

MISSING DOIs

- None

INVALID DOIs

- None

majensen commented 2 years ago

Thanks @mzabrams - on the archive, JOSS prefers the archive name to be the name of the paper verbatim, and the archive authors to include all the paper authors. Would you be willing to change the title and author metadata on your current archive? Or alternatively, create a one-off archive that meets those desirables?

mzabrams commented 2 years ago

@majensen I'll get the archive renamed with the underscore'd name this afternoon (may take a bit, as it will require a rename on PyPi as well, which is for the best as the conda and pip package names apparently differ -- I seem to have made a mistake there somewhere as pip is fars-cleaner and conda is fars_cleaner). Re: author metadata, currently Dr. Bass is an author on the paper (he is my PhD advisor), but not in the code metadata as he will not be a maintainer or responsible for correspondence/support/maintenance of the package in the future. Happy to make that change if it is the preference of the JOSS team, though

majensen commented 2 years ago

Thanks @mzabrams - yeah, I've seen several pip packages where the dash is used in the name, but the package comes in with an underscore in code. Not sure that's a big problem, might be automatically translated even. If you're ok putting your supervisor's name in the archive, then let's go ahead - might save a little editor-in-chief overhead.

mzabrams commented 2 years ago

Sounds good -- I'll go ahead and do that! You're right it's not the biggest deal, just personally I think I'd like the pip/conda packages to have the same name to avoid future confusion with installation (although I'll look into whether that gets automatically translated).

Just need to add the name to pyproject.toml? Or any other locations?

ethanwhite commented 2 years ago

Dr. Bass is an author on the paper (he is my PhD advisor), but not in the code metadata as he will not be a maintainer or responsible for correspondence/support/maintenance of the package in the future. Happy to make that change if it is the preference of the JOSS team, though

@mzabrams - in cases like this we have included them as authors in the Zenodo archive (via a .zenodo.json file; which is what JOSS wants) but not listed them in setup.py, pypi, etc. I think this both allows the software paper and repo to match the author line while not implying direct code contributions (or ability to serve as a maintainer).

mzabrams commented 2 years ago

I'll look into whether that gets automatically translated

For the record, it appears pip automatically gets the same package whether I run pip install fars_cleaner or pip install fars-cleaner

mzabrams commented 2 years ago

Should be solved now -- the Zenodo DOI for the most recent version is 10.5281/zenodo.7249980

The DOI for all versions is 10.5281/zenodo.3735486

majensen commented 2 years ago

@editorialbot set 10.5281/zenodo.7249980 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7249980

majensen commented 2 years ago

@editorialbot set v1.3.5 as version

editorialbot commented 2 years ago

Done! version is now v1.3.5

majensen 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

- 10.21105/joss.01181 is OK
- 10.21105/joss.01943 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/sbcs-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/3649, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

majensen commented 2 years ago

@mzabrams - fyi, we're waiting for the @openjournals/sbcs-eics (the editors-in-chief for this JOSS track, whom I just there cleverly pinged again) to do their final review.

mzabrams commented 1 year ago

@majensen Thanks for that update -- let me know if theres anything else you all need from me at this point!

majensen commented 1 year ago

:wave: @openjournals/sbcs-eics and maybe @arfon ...

arfon commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3687
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04678
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 1 year ago

Apologies it took a little while to get this one wrapped up.

@ethanwhite, @svburke – many thanks for your reviews here and to @majensen for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@mzabrams – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 1 year ago

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