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[REVIEW]: weatherOz: An API Client for Australian Weather and Climate Data Resources in R #6717

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editorialbot opened this issue May 2, 2024 · 41 comments
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accepted published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review rOpenSci Submissions associated with rOpenSci TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented May 2, 2024

Submitting author: @bozaah (Rodrigo Pires)
Repository: https://github.com/ropensci/weatherOz
Branch with paper.md (empty if default branch): paper
Version: v0.0.1
Editor: @arfon
Reviewers: @JanLauGe, @rogerssam
Archive: 10.5281/zenodo.8191283

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/44a93e6baee10f5212735041123d400b"><img src="https://joss.theoj.org/papers/44a93e6baee10f5212735041123d400b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/44a93e6baee10f5212735041123d400b/status.svg)](https://joss.theoj.org/papers/44a93e6baee10f5212735041123d400b)

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

@JanLauGe & @rogerssam, 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 @arfon 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 @JanLauGe

@editorialbot editorialbot added R review rOpenSci Submissions associated with rOpenSci TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels May 2, 2024
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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

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Software report:

github.com/AlDanial/cloc v 1.90  T=1.08 s (100.5 files/s, 13630.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               55            708           2759           6106
Markdown                         7            206              0            789
JSON                            34              0              0            589
TeX                              2             23              0            212
YAML                             4             31             10            145
SVG                              1              1              1            117
Rmd                              6            412           2637             35
-------------------------------------------------------------------------------
SUM:                           109           1381           5407           7993
-------------------------------------------------------------------------------

Commit count by author:

   646	Adam H. Sparks
   460	Adam Sparks
    81	Rodrigo Pires
    55	Anna Hepworth
     1	Dean Marchiori
     1	Hepworth, Anna
     1	Maëlle Salmon
     1	Rebecca O'Leary
     1	mark padgham

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

OK DOIs

- 10.21105/joss.00411 is OK
- 10.1016/s1364-8152(01)00008-1 is OK
- 10.1016/S1474-7065(02)00140-7 is OK
- 10.1016/j.rser.2005.12.002 is OK
- 10.1016/j.landurbplan.2008.10.006 is OK
- 10.1016/S0169-2046(02)00076-2 is OK
- 10.1094/PHYTO.2003.93.4.428 is OK
- 10.1201/9780429459016 is OK

MISSING DOIs

- No DOI given, and none found for title: Weather Data Services
- No DOI given, and none found for title: apsimx: Inspect, Read, Edit and Run ’APSIM’ "Next ...
- No DOI given, and none found for title: WINS: Crop Stress Weather Information Delivery Sys...
- No DOI given, and none found for title: terra: Spatial Data Analysis
- No DOI given, and none found for title: data.table: Extension of ‘data.frame‘
- No DOI given, and none found for title: magick: Advanced Graphics and Image-Processing in ...
- No DOI given, and none found for title: SILO - Australian climate data from 1898 to yester...

INVALID DOIs

- None

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Paper file info:

📄 Wordcount for paper.md is 1090

✅ The paper includes a Statement of need section

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License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

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

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bozaah commented May 3, 2024

Thank you @arfon for moving our submission to review. Also, much appreciated @JanLauGe & @rogerssam for your time to 'continue' the review process here.

I am linking issue #67 in the target repository that will contain replies and lengthier discussions from the review process. I have also added the 'under review' badge to the README.

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arfon commented May 4, 2024

@bozaah – please take a look at the compiled PDF linked above and make fixes where you can. There are a number of issues with formatting and some of the references not rendering properly (likely a mis-match between your BibTeX keys in the paper.md and paper.bib files).

You can check if things are fixed by asking @editorialbot for a new draft with @editorialbot generate pdf as a standalone comment in this thread.

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arfon commented May 9, 2024

@JanLauGe – thanks for your enthusiasm here, but as I mentioned in the pre-review thread, there's no need to do an additional review here (JOSS accepts the rOpenSci review).

I'm currently just waiting on @bozaah's response to this comment to proceed.

@bozaah
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bozaah commented May 9, 2024

Thanks @arfon for moving our review process quickly. I am away from office on holidays until the 14th May and I will attend to the issues with the references and submit the editorial check. Much appreciated.

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bozaah commented May 28, 2024

@editorialbot generate pdf

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

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bozaah commented May 28, 2024

@editorialbot check references

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

OK DOIs

- 10.21105/joss.00411 is OK
- 10.1016/s1364-8152(01)00008-1 is OK
- 10.1016/S1474-7065(02)00140-7 is OK
- 10.1016/j.rser.2005.12.002 is OK
- 10.1016/j.landurbplan.2008.10.006 is OK
- 10.1016/S0169-2046(02)00076-2 is OK
- 10.1094/PHYTO.2003.93.4.428 is OK
- 10.1201/9780429459016 is OK

MISSING DOIs

- No DOI given, and none found for title: Weather Data Services
- No DOI given, and none found for title: apsimx: Inspect, Read, Edit and Run ’APSIM’ "Next ...
- No DOI given, and none found for title: WINS: Crop Stress Weather Information Delivery Sys...
- No DOI given, and none found for title: terra: Spatial Data Analysis
- No DOI given, and none found for title: data.table: Extension of ‘data.frame‘
- No DOI given, and none found for title: magick: Advanced Graphics and Image-Processing in ...
- No DOI given, and none found for title: SILO - Australian climate data from 1898 to yester...

INVALID DOIs

- None

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arfon commented Jun 2, 2024

@editorialbot generate pdf

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

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arfon commented Jun 2, 2024

@bozaah – this all looks good now. The only issue I can see now is that all of the software names that are wrapped in {} should be updated to be simply wrapped in backticks. e.g.:

Change from this:

`{weatherOz}`

...to this:

`weatherOz`

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bozaah commented Jun 4, 2024

Thanks @arfon, we have updated the manuscript to have the package names use backticks and removed the {} (thanks @adamhsparks!). It should be all good now. Thank you.

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bozaah commented Jun 4, 2024

@editorialbot generate pdf

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

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arfon commented Jun 6, 2024

@editorialbot recommend-accept

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Paper is not ready for acceptance yet, the archive is missing

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arfon commented Jun 6, 2024

@editorialbot set 10.5281/zenodo.8191283 as archive

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Done! archive is now 10.5281/zenodo.8191283

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arfon commented Jun 6, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.21105/joss.00411 is OK
- 10.1016/s1364-8152(01)00008-1 is OK
- 10.1016/S1474-7065(02)00140-7 is OK
- 10.1016/j.rser.2005.12.002 is OK
- 10.1016/j.landurbplan.2008.10.006 is OK
- 10.1016/S0169-2046(02)00076-2 is OK
- 10.1094/PHYTO.2003.93.4.428 is OK
- 10.5281/zenodo.11363275 is OK
- 10.1201/9780429459016 is OK

MISSING DOIs

- No DOI given, and none found for title: Weather Data Services
- No DOI given, and none found for title: apsimx: Inspect, Read, Edit and Run ’APSIM’ "Next ...
- No DOI given, and none found for title: terra: Spatial Data Analysis
- No DOI given, and none found for title: data.table: Extension of ‘data.frame‘
- No DOI given, and none found for title: magick: Advanced Graphics and Image-Processing in ...
- No DOI given, and none found for title: SILO - Australian climate data from 1898 to yester...

INVALID DOIs

- None

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⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

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arfon commented Jun 6, 2024

@bozaah – can you merge this PR please? It should fix the XML validation above: ropensci/weatherOz#76

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I’ve merged it, thanks @arfon

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arfon commented Jun 7, 2024

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.21105/joss.00411 is OK
- 10.1016/s1364-8152(01)00008-1 is OK
- 10.1016/S1474-7065(02)00140-7 is OK
- 10.1016/j.rser.2005.12.002 is OK
- 10.1016/j.landurbplan.2008.10.006 is OK
- 10.1016/S0169-2046(02)00076-2 is OK
- 10.1094/PHYTO.2003.93.4.428 is OK
- 10.5281/zenodo.11363275 is OK
- 10.1201/9780429459016 is OK

MISSING DOIs

- No DOI given, and none found for title: Weather Data Services
- No DOI given, and none found for title: apsimx: Inspect, Read, Edit and Run ’APSIM’ "Next ...
- No DOI given, and none found for title: terra: Spatial Data Analysis
- No DOI given, and none found for title: data.table: Extension of ‘data.frame‘
- No DOI given, and none found for title: magick: Advanced Graphics and Image-Processing in ...
- No DOI given, and none found for title: SILO - Australian climate data from 1898 to yester...

INVALID DOIs

- None

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👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5464, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 7, 2024
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arfon commented Jun 7, 2024

@editorialbot accept

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

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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: Pires
  given-names: Rodrigo
  orcid: "https://orcid.org/0000-0001-7384-6849"
- family-names: Hepworth
  given-names: Anna
  orcid: "https://orcid.org/0000-0003-0204-6347"
- family-names: O'Leary
  given-names: Rebecca
- family-names: Carroll
  given-names: Jonathan
  orcid: "https://orcid.org/0000-0002-1404-5264"
- family-names: Goldie
  given-names: James
  orcid: "https://orcid.org/0000-0002-5024-6207"
- family-names: Marchiori
  given-names: Dean
  orcid: "https://orcid.org/0000-0002-3430-7225"
- family-names: Melloy
  given-names: Paul
  orcid: "https://orcid.org/0000-0003-4253-7167"
- family-names: Padgam
  given-names: Mark
  orcid: "https://orcid.org/0000-0003-2172-5265"
- family-names: Parsonage
  given-names: Hugh
  orcid: "https://orcid.org/0000-0003-4055-0835"
- family-names: Sparks
  given-names: Adam H.
  orcid: "https://orcid.org/0000-0002-0061-8359"
doi: 10.5281/zenodo.8191283
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Pires
    given-names: Rodrigo
    orcid: "https://orcid.org/0000-0001-7384-6849"
  - family-names: Hepworth
    given-names: Anna
    orcid: "https://orcid.org/0000-0003-0204-6347"
  - family-names: O'Leary
    given-names: Rebecca
  - family-names: Carroll
    given-names: Jonathan
    orcid: "https://orcid.org/0000-0002-1404-5264"
  - family-names: Goldie
    given-names: James
    orcid: "https://orcid.org/0000-0002-5024-6207"
  - family-names: Marchiori
    given-names: Dean
    orcid: "https://orcid.org/0000-0002-3430-7225"
  - family-names: Melloy
    given-names: Paul
    orcid: "https://orcid.org/0000-0003-4253-7167"
  - family-names: Padgam
    given-names: Mark
    orcid: "https://orcid.org/0000-0003-2172-5265"
  - family-names: Parsonage
    given-names: Hugh
    orcid: "https://orcid.org/0000-0003-4055-0835"
  - family-names: Sparks
    given-names: Adam H.
    orcid: "https://orcid.org/0000-0002-0061-8359"
  date-published: 2024-06-07
  doi: 10.21105/joss.06717
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6717
  title: "weatherOz: An API Client for Australian Weather and Climate
    Data Resources in R"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06717"
  volume: 9
title: "weatherOz: An API Client for Australian Weather and Climate Data
  Resources in R"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06717 joss-papers#5465
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06717
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 7, 2024
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arfon commented Jun 7, 2024

@JanLauGe, @rogerssam – many thanks for your reviews here! JOSS (and rOpenSci) relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@bozaah – your paper is now accepted and published in JOSS ⚡🚀💥

@arfon arfon closed this as completed Jun 7, 2024
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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06717/status.svg)](https://doi.org/10.21105/joss.06717)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06717">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06717/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06717/status.svg
   :target: https://doi.org/10.21105/joss.06717

This is how it will look in your documentation:

DOI

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