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

editorialbot commented 3 weeks ago

Submitting author: !--author-handle-->@jbousquin<!--end-author-handle-- (Justin Bousquin) Repository: https://github.com/USEPA/harmonize-wq Branch with paper.md (empty if default branch): paper_JOSS Version: 0.5.0 Editor: Pending Reviewers: Pending Managing EiC: Kristen Thyng

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editorialbot commented 3 weeks ago

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editorialbot commented 3 weeks ago

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 commented 3 weeks ago

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 commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1086

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

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

editorialbot commented 3 weeks ago

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

editorialbot commented 3 weeks ago

Five most similar historical JOSS papers:

The fqar package: R tools for analyzing floristic quality assessment data Submitting author: @equitable-equations Handling editor: @mikemahoney218 (Active) Reviewers: @ifoxfoot, @mhesselbarth Similarity score: 0.7196

tidyhydat: Extract and Tidy Canadian Hydrometric Data Submitting author: @boshek Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.7089

tbeptools: An R package for synthesizing estuarine data for environmental research Submitting author: @fawda123 Handling editor: @kthyng (Active) Reviewers: @paleolimbot, @richardsc Similarity score: 0.6941

tidyqpcr: Quantitative PCR analysis in the tidyverse. Submitting author: @ewallace Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.6937

HyRiver: Hydroclimate Data Retriever Submitting author: @cheginit Handling editor: @kthyng (Active) Reviewers: @raoulcollenteur, @arbennett Similarity score: 0.6900

⚠️ 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 commented 3 weeks ago

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:

[x] OSI-approved license
[x] Installation instructions
[x] Documentation exists at all
[x] Tests of some sort
[ ] Check paper (make sure compiles, read through, check for length 250-1000 words)
[x] Substantial scholarly effort
[x] 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: https://github.com/pyOpenSci/software-submission/issues/157

jbousquin commented 3 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

@editorialbot set paper_JOSS as branch

editorialbot commented 2 weeks ago

Done! branch is now paper_JOSS

kthyng commented 2 weeks ago

@editorialbot generate pdf

editorialbot commented 2 weeks 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 weeks ago

Five most similar historical JOSS papers:

The fqar package: R tools for analyzing floristic quality assessment data Submitting author: @equitable-equations Handling editor: @mikemahoney218 (Active) Reviewers: @ifoxfoot, @mhesselbarth Similarity score: 0.7202

tidyhydat: Extract and Tidy Canadian Hydrometric Data Submitting author: @boshek Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.7092

tidyqpcr: Quantitative PCR analysis in the tidyverse. Submitting author: @ewallace Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.6947

tbeptools: An R package for synthesizing estuarine data for environmental research Submitting author: @fawda123 Handling editor: @kthyng (Active) Reviewers: @paleolimbot, @richardsc Similarity score: 0.6935

A Framework to Quality Control Oceanographic Data Submitting author: @castelao Handling editor: @kthyng (Active) Reviewers: @jessicaaustin, @evanleeturner Similarity score: 0.6934

⚠️ 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 commented 2 weeks ago

@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 commented 4 days ago

@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 commented 2 days ago

@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.

openjournals / joss-reviews

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

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