[REVIEW]: Chi: A Python package for treatment response modelling

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@DavAug@ppxasjsm<!--end-editor-- Reviewers: @shahmoradi, @ns-rse Archive: 10.5281/zenodo.10510572

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ab102a087414584c19a7aeccc85fe3b2/status.svg)](https://joss.theoj.org/papers/ab102a087414584c19a7aeccc85fe3b2)

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

@shahmoradi, 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 @ppxasjsm 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 @ns-rse

📝 Checklist for @shahmoradi

DavAug commented 9 months ago

Super thank and no problem at all. Let me copy-paste the list, so I can tick it off while working on it :)

[x] add missing references
[x] Double check your author affiliation including ORCID
- [x] 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.
- [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
- [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

DavAug commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

DavAug commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK

MISSING DOIs

- None

INVALID DOIs

- None

DavAug commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

DavAug commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

DavAug commented 9 months ago

Thank you @ppxasjsm for all your help so far! I have now completed the outstanding tasks.

The release of the software with the latest changes from the review has the version number: 1.0.0
I have archived the release on Zenodo and the DOI is: 10.5281/zenodo.10510572

DavAug commented 9 months ago

Just some minor wording tweaks:

DavAug commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

DavAug commented 8 months ago

Hi @ppxasjsm ,

I hope you are doing well and you had a great week since coming back from your holidays.

I just wanted to kindly follow up on this review.

Best, David

ppxasjsm commented 8 months ago

@editorialbot set 10.5281/zenodo.10510572 as archive

editorialbot commented 8 months ago

Done! archive is now 10.5281/zenodo.10510572

ppxasjsm commented 8 months ago

@editorialbot set 1.0.0 as version

editorialbot commented 8 months ago

Done! version is now 1.0.0

ppxasjsm commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

ppxasjsm commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ppxasjsm commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months ago

:warning: 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'.

ppxasjsm commented 8 months ago

@Kevin-Mattheus-Moerman can you help with this error? I don't know what to make of this.

DavAug commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

DavAug commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

DavAug commented 8 months ago

Hi @ppxasjsm @Kevin-Mattheus-Moerman

Thank you so much for recommending the acceptance of my article. I really appreciate it! :)

I just had a quick look into the error message, and while I am not sure why the error occured, I noticed that it was related to "wrong" ISBN in one of my BibTeX entries. Since the ISBN is not actually included in the reference that appear on the rendered article, I simply removed it.

@ppxasjsm would you, perhaps, be able to trigger the acceptance again? I hope that this will remove the error (I saw that an article was successfully published yesterday, so the error does seem to be specific to my article).

Thank you so much and best wishes, David

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1093/bioinformatics/btg015 is OK
- 10.1371/journal.pcbi.1011135 is OK
- 10.1208/s12248-014-9716-2 is OK
- 10.1038/nrd.2017.244 is OK
- 10.1016/j.ddtec.2016.11.005 is OK
- 10.3389/fphar.2023.1270443 is OK
- 10.5334/jors.252 is OK
- 10.1038/psp.2013.24 is OK
- 10.1007/s10928-017-9562-9 is OK
- 10.1007/s11095-021-03065-1 is OK
- 10.1101/2020.11.28.402297 is OK
- 10.1093/aje/kwt245 is OK
- 10.1007/s11222-013-9416-2 is OK
- 10.1101/2022.03.19.483454 is OK
- 10.1016/j.pbiomolbio.2015.12.008 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 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/4979, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

DavAug commented 8 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/4979, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Hi @Kevin-Mattheus-Moerman , thank you so much for recommending the acceptance.

I just wanted to kindly confirm that accepting the submission is not in my mandate? I.e. we are not waiting for me to approve the final version of the article.

Best, David

Kevin-Mattheus-Moerman commented 8 months ago

@DavAug As AEiC I will now help process this submission for acceptance in JOSS. I have just checked your repository, the archive link, this review, and the paper. Most seems in order. I do however have the below points that require your attention:

[x] In your affiliation, please spell out UK as United Kingdom
[x] Please edit the ZENODO archive version tag to be v1.0.0
[x] Check methdological which should read methodological

DavAug commented 8 months ago

@DavAug As AEiC I will now help process this submission for acceptance in JOSS. I have just checked your repository, the archive link, this review, and the paper. Most seems in order. I do however have the below points that require your attention:

[ ] In your affiliation, please spell out UK as United Kingdom

[ ] Please edit the ZENODO archive version tag to be v1.0.0

[ ] Check methdological which should read methodological

Hi @Kevin-Mattheus-Moerman , Thank you so much for the thorough review! Requested updates are now completed.

[x] In your affiliation, please spell out UK as United Kingdom
[x] Please edit the ZENODO archive version tag to be v1.0.0
[x] Check methdological which should read methodological

DavAug commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 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 8 months ago

@DavAug great, thanks, now all looks in order, ready to proceed.

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot accept

editorialbot commented 8 months ago

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

editorialbot commented 8 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: Augustin given-names: David orcid: "https://orcid.org/0000-0002-4885-1088" contact: - family-names: Augustin given-names: David orcid: "https://orcid.org/0000-0002-4885-1088" doi: 10.5281/zenodo.10510572 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Augustin given-names: David orcid: "https://orcid.org/0000-0002-4885-1088" date-published: 2024-02-07 doi: 10.21105/joss.05925 issn: 2475-9066 issue: 94 journal: Journal of Open Source Software publisher: name: Open Journals start: 5925 title: "Chi: A Python package for treatment response modelling" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05925" volume: 9 title: "Chi: A Python package for treatment response modelling" ```

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 8 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 8 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/4991
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05925
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 8 months ago

@DavAug congrats on this publication with JOSS!

Thanks for editing @ppxasjsm!

And a special thank you to the reviewers: @shahmoradi, @ns-rse!!

editorialbot commented 8 months ago

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05925/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05925/status.svg
   :target: https://doi.org/10.21105/joss.05925

This is how it will look in your documentation:

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