[REVIEW]: Pyafscgap.org: Open source multi-modal Python-based tools for NOAA AFSC RACE GAP #5593

editorialbot · 2023-06-26T15:48:03Z

Submitting author: @sampottinger (A Samuel Pottinger)
Repository: https://github.com/SchmidtDSE/afscgap
Branch with paper.md (empty if default branch):
Version: 1.0.4
Editor: @Kevin-Mattheus-Moerman
Reviewers: @Kevin-Mattheus-Moerman
Archive: 10.5281/zenodo.8091843

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2b48c80992a67325863aa2fa9b51ae76"><img src="https://joss.theoj.org/papers/2b48c80992a67325863aa2fa9b51ae76/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2b48c80992a67325863aa2fa9b51ae76/status.svg)](https://joss.theoj.org/papers/2b48c80992a67325863aa2fa9b51ae76)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2023-06-26T15:48:05Z

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:

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editorialbot · 2023-06-26T15:48:07Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (889.2 files/s, 204715.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             9              0              0           6657
Python                          29           1524           2993           3447
JavaScript                      14            535           1010           2327
Markdown                        16            364              0            993
CSS                              2            103              0            443
HTML                             6             16              0            392
SQL                             10              5              0            324
Jupyter Notebook                 1              0            894            191
TeX                              1             22              0            189
YAML                             4              8              2            162
SVG                              1              0              1             54
TOML                             1              5              0             54
Dockerfile                       1              9              8             28
Bourne Shell                     4              5              8             19
-------------------------------------------------------------------------------
SUM:                            99           2596           4916          15280
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-06-26T15:48:08Z

Wordcount for paper.md is 1007

editorialbot · 2023-06-26T15:48:26Z

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

OK DOIs

- 10.1023/a:1016528631593 is OK

MISSING DOIs

- 10.1007/978-1-4842-6011-1_12 may be a valid DOI for title: Oracle Rest Data Services

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2023-06-26T15:48:37Z

This is a pyopensci related submission which was reviewed here: pyOpenSci/software-submission#93

editorialbot · 2023-06-26T15:49:17Z

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

Kevin-Mattheus-Moerman · 2023-06-26T15:49:20Z

@sampottinger please try to address the potentially missing DOI listed ☝️ , you can use @editorialbot check references to check the DOIs again.

Kevin-Mattheus-Moerman · 2023-06-26T15:56:51Z

@sampottinger I have checked your paper and noticed some minor typos, please address them, see below. I also recommend that you proof read your paper once more and amend where needed.

Please add California, United States of America to your affiliation
Fix compliation -> compilation
Fix compatability -> compatibility
Fix speices -> species
Fix synchoronous -> synchronous

Relating to the ZENODO archive:

Please edit it to ensure the title matches your paper title
Please edit it to ensure the license listed matches your software license

Kevin-Mattheus-Moerman · 2023-06-26T15:57:10Z

Kevin-Mattheus-Moerman · 2023-06-26T15:57:35Z

@editorialbot set 10.5281/zenodo.7991875 as archive

editorialbot · 2023-06-26T15:57:42Z

Done! archive is now 10.5281/zenodo.7991875

Kevin-Mattheus-Moerman · 2023-06-26T15:58:10Z

@editorialbot set 1.0.2 as version

editorialbot · 2023-06-26T15:58:11Z

Done! version is now 1.0.2

sampottinger · 2023-06-26T16:33:19Z

Thanks for all of this @Kevin-Mattheus-Moerman!

some minor typos

Thank you for flagging those I’ll address shortly.

Relating to the ZENODO archive:

I’ll confirm these items shortly!

please try to address the potentially missing DOI listed

Thanks! ORDS does not have a DOI as far as I can tell. The one suggested is a book for Oracle Cloud Services. Please advise how you want to continue but the current citation may be best.

Kevin-Mattheus-Moerman · 2023-06-27T13:08:25Z

@sampottinger On the DOI, if you believe not having the DOI is correct then just leave it the way it is.

sampottinger · 2023-06-27T14:49:10Z

Phenomenal! I’ll take care of the other items today or tomorrow. Thanks again!

sampottinger · 2023-06-28T15:03:05Z

@editorialbot set 1.0.3 as version

editorialbot · 2023-06-28T15:03:07Z

I'm sorry @sampottinger, I'm afraid I can't do that. That's something only editors are allowed to do.

sampottinger · 2023-06-28T15:03:40Z

@editorialbot generate pdf

editorialbot · 2023-06-28T15:05:17Z

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

editorialbot · 2023-06-28T15:28:02Z

Wordcount for paper.md is 1042

sampottinger · 2023-06-28T15:28:06Z

@editorialbot generate pdf

sampottinger · 2023-06-28T15:28:25Z

Hello @Kevin-Mattheus-Moerman! Thank you for your comments. I have:

Addressed the typos you found. Appreciate it!
Updated our affiliations as you requested.
Corrected the zenodo metadata as you indicated.
Performed another read-through with minor expansion while still trying to remain close to the JOSS word count limits.

My apologies but can you please update the version to 1.0.4 (@editorialbot set 1.0.4 as version)? Thanks!

editorialbot · 2023-06-28T15:29:45Z

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

Kevin-Mattheus-Moerman · 2023-06-28T15:37:06Z

@editorialbot check references

editorialbot · 2023-06-28T15:37:35Z

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

OK DOIs

- 10.1023/a:1016528631593 is OK

MISSING DOIs

- 10.1007/978-1-4842-6011-1_12 may be a valid DOI for title: Oracle Rest Data Services

INVALID DOIs

- None

sampottinger · 2023-06-28T15:38:13Z

(Sorry that DOI check keeps catching ORDS which doesn't have a DOI... the DOI it recommends is incorect)

Kevin-Mattheus-Moerman · 2023-06-28T15:39:02Z

@editorialbot accept

editorialbot · 2023-06-28T15:39:03Z

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

sampottinger · 2023-06-28T15:39:33Z

@Kevin-Mattheus-Moerman - can you change to version 1.0.4 ?

Sorry I should have bolded that request in my earlier message. 😬 The only practical difference is a typo fix in the paper and correction of zenodo metadata.

editorialbot · 2023-06-28T15:40:43Z

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: Pottinger
  given-names: A Samuel
  orcid: "https://orcid.org/0000-0002-0458-4985"
- family-names: Zarpellon
  given-names: Giulia
  orcid: "https://orcid.org/0000-0002-9122-4709"
doi: 10.5281/zenodo.7991875
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Pottinger
    given-names: A Samuel
    orcid: "https://orcid.org/0000-0002-0458-4985"
  - family-names: Zarpellon
    given-names: Giulia
    orcid: "https://orcid.org/0000-0002-9122-4709"
  date-published: 2023-06-28
  doi: 10.21105/joss.05593
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5593
  title: "Pyafscgap.org: Open source multi-modal Python-based tools for
    NOAA AFSC RACE GAP"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05593"
  volume: 8
title: "Pyafscgap.org: Open source multi-modal Python-based tools for
  NOAA AFSC RACE GAP"

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 · 2023-06-28T15:40:47Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-06-28T15:40:48Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05593 joss-papers#4359
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05593
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

sampottinger · 2023-06-28T15:45:19Z

@Kevin-Mattheus-Moerman - My apologies we should be good to go... you can ignore my earlier message unless you want to update the reference here. We reference latest in linking to zenodo 10.5281/zenodo.7991875. Either way, thanks so much for your review!

Kevin-Mattheus-Moerman · 2023-06-29T08:33:03Z

@sampottinger it would be better to update the version and archive DOI here. We should be able to do that. Sorry I missed that in your comment!

@openjournals/dev @arfon can you help process the following changes for this paper:

@editorialbot set 1.0.4 as version
@editorialbot set 10.5281/zenodo.8091843 as archive

xuanxu · 2023-06-29T09:42:27Z

@Kevin-Mattheus-Moerman: Running those two commands to update the version and the archive values and then @editorialbot reaccept should work.

Kevin-Mattheus-Moerman · 2023-06-29T09:53:58Z

@editorialbot set 1.0.4 as version

editorialbot · 2023-06-29T09:54:00Z

Done! version is now 1.0.4

Kevin-Mattheus-Moerman · 2023-06-29T09:54:11Z

@editorialbot set 10.5281/zenodo.8091843 as archive

editorialbot · 2023-06-29T09:54:13Z

Done! archive is now 10.5281/zenodo.8091843

Kevin-Mattheus-Moerman · 2023-06-29T09:54:20Z

@editorialbot reaccept

editorialbot · 2023-06-29T09:54:22Z

Rebuilding paper!

editorialbot · 2023-06-29T09:56:01Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4361

Kevin-Mattheus-Moerman · 2023-06-29T10:01:07Z

@sampottinger this looks good to me now, and the paper available on the website points to the updated archive already. I'll close this issue now shortly. Congratulations again!

editorialbot · 2023-06-29T10:01:09Z

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.05593/status.svg" alt="DOI badge" >
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editorialbot added Dockerfile pyOpenSci Submissions associated with pyOpenSci Python review Shell Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jun 26, 2023

editorialbot assigned Kevin-Mattheus-Moerman Jun 26, 2023

editorialbot mentioned this issue Jun 26, 2023

[PRE REVIEW]: Pyafscgap.org: Open source multi-modal Python-based tools for NOAA AFSC RACE GAP #5516

Closed

sampottinger mentioned this issue Jun 27, 2023

Respond to JOSS editor comments. SchmidtDSE/afscgap#103

Merged

sampottinger mentioned this issue Jun 28, 2023

Move to 1.0.4 SchmidtDSE/afscgap#104

Merged

editorialbot added accepted published Papers published in JOSS labels Jun 28, 2023

This was referenced Jun 28, 2023

Add JOSS badge. SchmidtDSE/afscgap#105

Merged

afscgap: Ocean health tools for NOAA AFSC GAP species presence data pyOpenSci/software-submission#93

Closed

Kevin-Mattheus-Moerman closed this as completed Jun 29, 2023

[REVIEW]: Pyafscgap.org: Open source multi-modal Python-based tools for NOAA AFSC RACE GAP #5593

[REVIEW]: Pyafscgap.org: Open source multi-modal Python-based tools for NOAA AFSC RACE GAP #5593

Comments

editorialbot commented Jun 26, 2023 • edited

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Reviewer instructions & questions

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Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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edited

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