[REVIEW]: Pherosensor-toolbox: a Python package for Biology-Informed Data Assimilation

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@slabarthe@Nikoleta-v3<!--end-editor-- Reviewers: @Shreyas911, @mrazomej Archive: 10.5281/zenodo.13834137

Status

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Markdown: [![status](https://joss.theoj.org/papers/c01d64d23d66cfdfa3017abc5776e1de/status.svg)](https://joss.theoj.org/papers/c01d64d23d66cfdfa3017abc5776e1de)

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

@Shreyas911 & @mrazomej, 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 @Nikoleta-v3 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 @mrazomej

📝 Checklist for @Shreyas911

Nikoleta-v3 commented 1 week ago

@editorialbot recommend-accept

editorialbot commented 1 week ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 week ago

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

✅ OK DOIs

- 10.1126/science.1183899 is OK
- 10.5281/ZENODO.11506617 is OK
- 10.1142/9789812701831_0006 is OK
- 10.1017/S0021859605005708 is OK
- 10.21105/joss.05150 is OK
- 10.1016/j.envsoft.2014.02.008 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 week ago

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

editorialbot commented 1 week ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5907, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 6 days ago

@slabarthe as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I will now process some final checks:

Checks on repository

[x] Project has OSI approved license
[x] Project features contributing guidelines

Checks on review issue

[x] Review completed
[x] Software license tag listed here matches a tagged release

Checks on archive

[x] Archive listed title and authors matches paper
[x] Archive listed license matches software license
[x] Archive listed version tag matches tagged release (and includes a potential v).

Checks on paper

[x] Checked paper formatting
[x] Check affiliations to make sure country acronyms are not used
[x] Checked reference rendering
[x] Checked if pre-print citations can be updated by published versions
[x] Checked for typos

Remaining points:

The above seems in order, however the below are some points that require your attention :point_down: :

[x] In the paper, can you check the spelling for epidemio? Should that be epidemic?

Kevin-Mattheus-Moerman commented 6 days ago

@mrazomej thanks for your help with this review. Because the editor recommended acceptance, and you said "I completed my checklist, and I approved the submission.", I am happy to proceed with acceptance. However, if for completeness you could tick the last two boxes in your checklist that would be great. Thanks.

Nikoleta-v3 commented 6 days ago

@mrazomej thanks for your help with this review. Because the editor recommended acceptance, and you said "I completed my checklist, and I approved the submission.", I am happy to proceed with acceptance. However, if for completeness you could tick the last two boxes in your checklist that would be great. Thanks.

😮 I never realised that was required @Kevin-Mattheus-Moerman ! I'll make sure to check from now on.

slabarthe commented 6 days ago

Hi @Kevin-Mattheus-Moerman. I changed epidemio to epidemic. Thank you for your remark.

Kevin-Mattheus-Moerman commented 6 days ago

@mrazomej thanks for your help with this review. Because the editor recommended acceptance, and you said "I completed my checklist, and I approved the submission.", I am happy to proceed with acceptance. However, if for completeness you could tick the last two boxes in your checklist that would be great. Thanks.

😮 I never realised that was required @Kevin-Mattheus-Moerman ! I'll make sure to check from now on.

@Nikoleta-v3 no worries. It is not a strict requirement that all boxes have to be ticked, in some cases for instance 1 reviewer feels a box should remain unticked while several others believe all should be ticked. However, where possible they should all be ticked. In this case it looks like they are not "open or unresolved issues" but more like boxes that were forgotten to be ticked.

Kevin-Mattheus-Moerman commented 6 days ago

@editorialbot accept

editorialbot commented 6 days ago

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

editorialbot commented 6 days ago

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: Malou given-names: Thibault orcid: "https://orcid.org/0009-0002-3540-8789" - family-names: Labarthe given-names: Simon orcid: "https://orcid.org/0000-0002-5463-7256" contact: - family-names: Labarthe given-names: Simon orcid: "https://orcid.org/0000-0002-5463-7256" doi: 10.5281/zenodo.13834137 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Malou given-names: Thibault orcid: "https://orcid.org/0009-0002-3540-8789" - family-names: Labarthe given-names: Simon orcid: "https://orcid.org/0000-0002-5463-7256" date-published: 2024-09-26 doi: 10.21105/joss.06863 issn: 2475-9066 issue: 101 journal: Journal of Open Source Software publisher: name: Open Journals start: 6863 title: "Pherosensor-toolbox: a Python package for Biology-Informed Data Assimilation" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06863" volume: 9 title: "Pherosensor-toolbox: a Python package for Biology-Informed Data Assimilation" ```

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 commented 6 days ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 6 days ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5915
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06863
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 5 days ago

@slabarthe congratulations on this JOSS publication!

@Nikoleta-v3 thanks for editing this one!

And a special thank you to the reviewers: @Shreyas911, @mrazomej !!!

editorialbot commented 5 days ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.06863/status.svg)](https://doi.org/10.21105/joss.06863)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06863/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06863/status.svg
   :target: https://doi.org/10.21105/joss.06863

This is how it will look in your documentation:

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