[PRE REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats #7135

editorialbot · 2024-08-22T20:35:50Z

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
Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cf3275a731d860635d261fb0388fa791"><img src="https://joss.theoj.org/papers/cf3275a731d860635d261fb0388fa791/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cf3275a731d860635d261fb0388fa791/status.svg)](https://joss.theoj.org/papers/cf3275a731d860635d261fb0388fa791)

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editorialbot · 2024-08-22T20:35:52Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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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 · 2024-08-22T20:36:13Z

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

✅ OK DOIs

- 10.21105/joss.03485 is OK
- 10.1016/j.envsoft.2021.105210 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
- 10.1029/2019WR024883 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

🟡 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: Tidy data
- No DOI given, and none found for title: WQX Web Application Programming Interface (API)
- No DOI given, and none found for title: WQX Web User Guide

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1111/j.17521688.2011.00573.x is INVALID

editorialbot · 2024-08-22T20:36:14Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (339.6 files/s, 355960.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          12            998           3491           2592
Jupyter Notebook                 7              0          37867            685
YAML                             8             51             55            302
TeX                              1             15              0            160
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:                            45           1308          41709           4152
-------------------------------------------------------------------------------

Commit count by author:

   329	Bousquin
   112	Justin Bousquin
     9	Cristina Mullin
     2	Romain Caneill
     2	cristinamullin
     1	Mullin
     1	Timothy Hodson

editorialbot · 2024-08-22T20:36:18Z

Paper file info:

📄 Wordcount for paper.md is 1086

✅ The paper includes a Statement of need section

editorialbot · 2024-08-22T20:36:23Z

License info:

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

editorialbot · 2024-08-22T20:37:23Z

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

editorialbot · 2024-08-22T20:38:08Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

kthyng · 2024-08-22T21:13:06Z

Hi @jbousquin and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

OSI-approved license
Installation instructions
Documentation exists at all
Tests of some sort
Check paper (make sure compiles, read through, check for length 250-1000 words)
Substantial scholarly effort
Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any).

I see that this has already been reviewed in pyOpenSci here: pyOpenSci/software-submission#157

jbousquin · 2024-08-23T01:33:01Z

Hi @kthyng and thank you! From editorialbot that invalid doi was maybe missing a dash (DOI: 10.1111/j.1752‐1688.2011.00573.x link), and tidy data should be https://doi.org/10.18637/jss.v059.i10. I'll work on a PR for those.

jbousquin · 2024-08-26T17:09:21Z

Made some minor updates to paper/paper.bib on the branch paper_JOSS. The doi editorialbot identified as invalid did contain the '-' but it wasn't being encoded correctly. Confirmed the doi link works as it should now in the pdf generated by the workflow.

kthyng · 2024-08-28T20:24:52Z

@editorialbot set paper_JOSS as branch

editorialbot · 2024-08-28T20:24:55Z

Done! branch is now paper_JOSS

kthyng · 2024-08-28T20:25:01Z

@editorialbot generate pdf

editorialbot · 2024-08-28T20:26:54Z

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

editorialbot · 2024-08-28T20:27:42Z

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tidyhydat: Extract and Tidy Canadian Hydrometric Data
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kthyng · 2024-08-28T20:41:40Z

@jbousquin a few paper comments (still need to read through in detail)

the parenthetical references aren't in there correctly. You'll want to create a list of them rather than listed one, then another, each with parentheses. Here is an example paper: https://joss.readthedocs.io/en/latest/example_paper.html#example-paper
Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example, "r" is not capitalized, but please check others.
You and I are the only people that will be reading your paper so please check everything carefully! Usually reviewers and an editor would also be checking, but your repo was already reviewed so the paper will only be checked by us.

kthyng · 2024-09-10T22:13:28Z

@jbousquin Can you check through your paper? I can also wait and start the review issue before we go into these details if you prefer.

jbousquin · 2024-09-12T22:49:51Z

@kthyng have made those changes but have to wait to merge until I’m back in the office next week (should be Tuesday). I will give it another final read through then for any copy edits as well.

jbousquin · 2024-09-17T18:26:25Z

@editorialbot generate pdf

editorialbot · 2024-09-17T18:28:05Z

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

editorialbot · 2024-09-17T18:31:00Z

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

jbousquin · 2024-09-17T18:33:19Z

@kthyng those comments should be resolved in the latest version and ready for your detailed read-through.

kthyng · 2024-09-30T18:10:51Z

@editorialbot generate pdf

editorialbot · 2024-09-30T18:12:28Z

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

editorialbot · 2024-09-30T18:13:25Z

Five most similar historical JOSS papers:

tidyhydat: Extract and Tidy Canadian Hydrometric Data
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wdpar: Interface to the World Database on Protected Areas
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Similarity score: 0.7337

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kthyng · 2024-09-30T18:13:45Z

@editorialbot add me as editor

editorialbot · 2024-09-30T18:13:47Z

Assigned! @kthyng is now the editor

kthyng · 2024-09-30T18:14:07Z

@editorialbot add @kthyng as reviewer

editorialbot · 2024-09-30T18:14:10Z

@kthyng added to the reviewers list!

kthyng · 2024-09-30T18:14:21Z

@editorialbot start review

editorialbot · 2024-09-30T18:14:25Z

OK, I've started the review over in #7305.

editorialbot added pre-review Track: 6 (ESE) Earth Sciences and Ecology labels Aug 22, 2024

editorialbot added Python TeX labels Aug 22, 2024

kthyng added the pyOpenSci Submissions associated with pyOpenSci label Sep 30, 2024

editorialbot assigned kthyng Sep 30, 2024

editorialbot closed this as completed Sep 30, 2024

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[PRE REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats #7135

[PRE REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats #7135

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[PRE REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats #7135

[PRE REVIEW]: harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats #7135

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