[REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats

[editorialbot]

Submitting author: @jbousquin (Justin Bousquin)
Repository: https://github.com/USEPA/harmonize-wq
Branch with paper.md (empty if default branch): paper_JOSS
Version: 0.5.0
Editor: @kthyng
Reviewers: @kthyng
Archive: 10.5281/zenodo.13356847

Status

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Markdown: [![status](https://joss.theoj.org/papers/cf3275a731d860635d261fb0388fa791/status.svg)](https://joss.theoj.org/papers/cf3275a731d860635d261fb0388fa791)

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

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✨ 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

@kthyng, please create your checklist typing: @editorialbot generate my checklist

[editorialbot]

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]

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

✅ OK DOIs

- 10.21105/joss.03485 is OK
- 10.1111/j.1752-1688.2011.00573.x is OK
- 10.1016/j.envsoft.2021.105210 is OK
- 10.21105/joss.03175 is OK
- 10.5066/P9X4L3GE is OK
- 10.1371/journal.pone.0239691 is OK
- 10.5066/P94I5TX3 is OK
- 10.5281/zenodo.5573592 is OK
- 10.1002/eap.2130 is OK
- 10.1002/2016WR019993 is OK
- 10.1029/2019WR024883 is OK
- 10.1021/acs.est.9b06406 is OK
- 10.1038/s41597-020-0478-7 is OK
- 10.1016/j.watres.2016.12.024 is OK
- 10.18637/jss.v059.i10 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Pint: Operate and manipulate physical quantities i...
- No DOI given, and none found for title: WQX Web API
- No DOI given, and none found for title: WQX Web User Guide

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (366.2 files/s, 375905.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          12            998           3491           2592
Jupyter Notebook                 7              0          37867            685
YAML                             9             52             59            321
TeX                              1             17              0            184
reStructuredText                 9            115            124            152
Markdown                         2             47              0            131
Rmd                              1             63            164             48
TOML                             1              7              0             39
DOS Batch                        1              8              1             26
make                             1              4              7              9
JSON                             2              0              0              8
-------------------------------------------------------------------------------
SUM:                            46           1311          41713           4195
-------------------------------------------------------------------------------

Commit count by author:

   334	Bousquin
   117	Justin Bousquin
     9	Cristina Mullin
     2	Romain Caneill
     2	cristinamullin
     1	Mullin
     1	Timothy Hodson

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1073

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kthyng]

This submission was already reviewed through pyOpenSci and the review issue is available here: pyOpenSci/software-submission#157

[kthyng]

@jbousquin Do you have a Zenodo or similar archive of your code?

[kthyng]

After these checks are complete, I will publish your submission!

• Check that version was updated and make sure the version from JOSS matches github and Zenodo.
• Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
• Check paper.

[jbousquin]

Current Zenodo DOI: 10.5281/zenodo.13356847

[kthyng]

@jbousquin

• is v0.5.0 still correct for this publication?
• Can you update the title and author list in Zenodo to match your JOSS publication?

[kthyng]

@editorialbot set 10.5281/zenodo.13356847 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13356847

[jbousquin]

@kthyng I'm new to using zenodo - would it better to do a 0.5.1 release that includes the paper_JOSS merged?

[kthyng]

How the paper file is arranged in the archive or if it is the most up to date isn't important since the words will be present in the paper itself, so no need from our perspective to do a new release for any changes in the paper.

[jbousquin]

I think I was able to edit the authors (moved other types of contributors from creators to contributors) and title, everything else about that zenodo archive is auto-populated from github. Please let me know if any other fields need to be updated or anything doesn't match as it should.

[jbousquin]

@kthyng - Just wanted to check in that the zenodo updates were what you were looking for and there isn't anything else you need from me.

[kthyng]

@jbousquin Looks good! Ready to wrap up.

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Bousquin
  given-names: Justin
  orcid: "https://orcid.org/0000-0001-5797-4322"
- family-names: Mullin
  given-names: Cristina A.
  orcid: "https://orcid.org/0000-0002-0615-6087"
doi: 10.5281/zenodo.13356847
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bousquin
    given-names: Justin
    orcid: "https://orcid.org/0000-0001-5797-4322"
  - family-names: Mullin
    given-names: Cristina A.
    orcid: "https://orcid.org/0000-0002-0615-6087"
  date-published: 2024-10-22
  doi: 10.21105/joss.07305
  issn: 2475-9066
  issue: 102
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7305
  title: "harmonize-wq: Standardize, clean and wrangle Water Quality
    Portal data into more analytic-ready formats"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07305"
  volume: 9
title: "harmonize-wq: Standardize, clean and wrangle Water Quality
  Portal data into more analytic-ready formats"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07305 joss-papers#6033
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07305
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congratulations on your new publication @jbousquin!

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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