editorialbot commented 1 year ago

Submitting author: !--author-handle-->@patquem@phibeck<!--end-editor-- Reviewers: @maurov, @FCMeng Archive: 10.5281/zenodo.10812332

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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

@maurov & @FCMeng, 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 @phibeck 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 @maurov

📝 Checklist for @FCMeng

phibeck commented 8 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

patquem commented 8 months ago

Hi @phibeck,

Regarding the last draft published the 05/02/24 with ID : 10.21105.joss.05868.pdf the authors and affiliations (including ORCIDs) are OK for me. The reference Fitspy version for JOSS is the 2024.4. This release has been archived on Zenodo : https://zenodo.org/doi/10.5281/zenodo.10812332 with title and author list matching those in the JOSS paper. The license listed for the archive is the same as the software license.

Hoping it will be okay with you to finalize the article publishing :)

phibeck commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago

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

OK DOIs

- 10.1107/S0021889810030499 is OK
- 10.1002/cmtd.202100094 is OK
- 10.5281/zenodo.11813 is OK
- 10.5281/zenodo.8092679 is OK

MISSING DOIs

- No DOI given, and none found for title: Full wafer-scale characterization method for 2D ma...

INVALID DOIs

- None

phibeck commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

phibeck commented 7 months ago

Hi @patquem. A couple of comments:

the version is somehow tagged as v2024.4 in the git repo link to the pypi package. Just want to confirm that the version is 2024.4. Additionally, it may help to tag the same version in git.
we do require the licenses to match between the archive and the software repo, but they are GPLv3 for zenodo/pypi and AGPL-3.0 for the repo. Please correct this and let me know
reference Meyer et al. 2023 doesn't have a DOI, and doesn't contain the image used in the manuscript. Is there a paper draft on the arxiv that can be used instead?

patquem commented 7 months ago

Hello @phibeck,

Regarding the first and second points, I have standardized the version number between the PyPI repository and the badges (it is version 2024.4), as well as the license (it is GPLv3). On the last point, apart from the abstract referenced in the article, Thibault Meyer's work presented at the RamanFest2023 conference has not yet been published in a paper.

phibeck commented 7 months ago

@patquem Thank you for correcting the version number and unifying the license! Here are a few more comments/suggestions for the manuscript. Please have a look when you have a moment.

Throughout the text: I find it more intuitive to speak of a single "user" instead of "users", but this is a personal preference
line 5: I would merge this sentence with the following paragraph, it looks unusual to me to have this separate
line 7f.: I would add at the end of the sentence "as peak models"
Fig. 1: It would be helpful to add a little more detail, i.e. that the noisy line is some experimental measurement and the solid lines of different colors are returned after running Fitspy
line 14f.: I am not sure I would say "chemical" composition here, but rather just composition. There are certainly use cases for tools like Fitspy where peak positions aren't a matter of chemical composition, but other parameters.
line 42: none of them "seem" (without "s")
line 47: at the time of writing
line 49: "two-column base format"
line 49: I would rephrase slightly: "base format, with the first column containing the physical support..."
line 52: "is associated with"
line 53: "identified by its grid coordinates (X,Y)"
line 55 and 56: "file selection widget"
line 59f: please correct if this isn't what you mean: "...Attractors capability, which automatically returns the local maxima.."
line 64: "...so that the spectra have a common, flat zero-intensity level"
line 65: either "user, who positions" or "users, who position"
line 66: "with the (mouse) cursor" (mouse not necessary)
line 78f.: I would say "for an asymmetric model the width can be further divided into left and right"
line 84: "with each other" instead of together
line 102: "when performing repeated analyses, users familiar with Python may find it helpful to use Fitspy as follows:"
line 107: "This approach has recently been used by Meyer et al., 2023..."

phibeck commented 7 months ago

@editorialbot set 10.5281/zenodo.10812332 as archive

editorialbot commented 7 months ago

Done! archive is now 10.5281/zenodo.10812332

phibeck commented 7 months ago

@editorialbot set 2024.4 as version

editorialbot commented 7 months ago

Done! version is now 2024.4

matbryan52 commented 7 months ago

@patquem test mention (checking notifications)

patquem commented 7 months ago

@phibeck I have taken into account all your remarks/suggestions.

(I noticed that I have not been receiving any notifications since your last two messages from this 'JOSS' page, even though my notification settings are correctly set up (?).)

phibeck commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

phibeck commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago

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

OK DOIs

- 10.1107/S0021889810030499 is OK
- 10.1002/cmtd.202100094 is OK
- 10.5281/zenodo.11813 is OK
- 10.5281/zenodo.8092679 is OK

MISSING DOIs

- No DOI given, and none found for title: Full wafer-scale characterization method for 2D ma...

INVALID DOIs

- None

phibeck commented 7 months ago

@editorialbot recommend-accept

editorialbot commented 7 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 7 months ago

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

OK DOIs

- 10.1107/S0021889810030499 is OK
- 10.1002/cmtd.202100094 is OK
- 10.5281/zenodo.11813 is OK
- 10.5281/zenodo.8092679 is OK

MISSING DOIs

- No DOI given, and none found for title: Full wafer-scale characterization method for 2D ma...

INVALID DOIs

- None

editorialbot commented 7 months 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/5203, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 7 months ago

@patquem as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

[x] Please create a tagged release on your repository (i.e. one that will be listed here: https://github.com/CEA-MetroCarac/fitspy/tags), its version tag should match what we listed here and what is listed for the archive here which is currently 2024.4 (if you end up creating a new version/archive, let us know then we can update the version tag and archive link here to match).
[x] In the paper replace softwares by software e.g. one could phrase your sentence using ...although other open-source software packages are much more....
[x] Change visualization, characterize, customize (which is American English) to visualisation, characterise, and customise, to be consistent with the rest of the European English used throughout the paper.

Kevin-Mattheus-Moerman commented 7 months ago

@patquem :wave:

patquem commented 7 months ago

Hi @Kevin-Mattheus-Moerman, I have created the tag and put the corrections you mentioned in the article. Let me know if something is wrong/missing.

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

Kevin-Mattheus-Moerman commented 7 months ago

@patquem thanks for making those changes. All looks good now to proceed.

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot accept

editorialbot commented 7 months ago

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

editorialbot commented 7 months 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: Quéméré given-names: Patrick orcid: "https://orcid.org/0009-0008-6936-1249" doi: 10.5281/zenodo.10812332 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Quéméré given-names: Patrick orcid: "https://orcid.org/0009-0008-6936-1249" date-published: 2024-04-15 doi: 10.21105/joss.05868 issn: 2475-9066 issue: 96 journal: Journal of Open Source Software publisher: name: Open Journals start: 5868 title: "Fitspy: A Python package for spectral decomposition" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05868" volume: 9 title: "Fitspy: A Python package for spectral decomposition" ```

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 7 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 7 months 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/5243
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05868
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 7 months ago

@patquem congratulations on this JOSS publication! :tada:

At this point I would like to thank @phibeck for editing this submission.

A special thank you also to the reviewers: @maurov, @FCMeng !!!

editorialbot commented 7 months 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:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05868/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05868/status.svg
   :target: https://doi.org/10.21105/joss.05868

This is how it will look in your documentation:

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patquem commented 6 months ago

Thank you all (@maurov , @FCMeng , @phibeck and @Kevin-Mattheus-Moerman ) for reviewing, editing, and publishing the article. The Citations and the Acknowlegments section of the Github FITSPY site have been updated :)

openjournals / joss-reviews

[REVIEW]: Fitspy: A Python package for spectral decomposition #5868

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance