Closed editorialbot closed 6 months ago
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1089/genedge.5.1.39 is OK
- 10.1016/j.apsb.2022.02.002 is OK
- 10.1038/s41598-019-54849-w is OK
- 10.1186/s13321-020-00450-7 is OK
- 10.1016/j.eswa.2017.05.004 is OK
- 10.1093/bib/bbab581 is OK
- 10.1186/s12859-019-2983-2 is OK
- 10.1109/icdm.2010.127 is OK
- 10.1186/s12859-020-03898-4 is OK
- 10.1109/TCBB.2022.3212051 is OK
- 10.1109/TCBB.2023.3254163 is OK
- 10.1016/j.patter.2023.100804 is OK
- 10.1007/3-540-44886-1_25 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/cid/ciab350 is OK
- 10.5281/zenodo.8038847 is OK
- 10.5281/zenodo.8241505 is OK
- 10.5281/zenodo.7982964 is OK
- 10.5281/zenodo.7982969 is OK
- 10.1038/msb.2011.26 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/bioinformatics/btw770 is OK
- 10.3389/fphar.2021.784171 is OK
- 10.1093/bioinformatics/btz965 is OK
- 10.1016/j.asoc.2021.107135 is OK
- 10.1093/bioinformatics/btz331 is OK
- 10.1093/bioinformatics/btw228 is OK
- 10.1145/3308558.3313562 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
ID ref-luo2018computational already defined
Dear @Nikoleta-v3 I have just fixed the reference issue mentioned above (commit d7bdc43). The process should end up successfully now.
Thank you; that was fast 😄
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1089/genedge.5.1.39 is OK
- 10.1016/j.apsb.2022.02.002 is OK
- 10.1038/s41598-019-54849-w is OK
- 10.1186/s13321-020-00450-7 is OK
- 10.1016/j.eswa.2017.05.004 is OK
- 10.1093/bib/bbab581 is OK
- 10.1186/s12859-019-2983-2 is OK
- 10.1109/icdm.2010.127 is OK
- 10.1186/s12859-020-03898-4 is OK
- 10.1109/TCBB.2022.3212051 is OK
- 10.1109/TCBB.2023.3254163 is OK
- 10.1016/j.patter.2023.100804 is OK
- 10.1007/3-540-44886-1_25 is OK
- 10.1093/bioinformatics/bty013 is OK
- 10.1093/cid/ciab350 is OK
- 10.5281/zenodo.8038847 is OK
- 10.5281/zenodo.8241505 is OK
- 10.5281/zenodo.7982964 is OK
- 10.5281/zenodo.7982969 is OK
- 10.1038/msb.2011.26 is OK
- 10.1093/bioinformatics/btw770 is OK
- 10.3389/fphar.2021.784171 is OK
- 10.1093/bioinformatics/btz965 is OK
- 10.1016/j.asoc.2021.107135 is OK
- 10.1093/bioinformatics/btz331 is OK
- 10.1093/bioinformatics/btw228 is OK
- 10.1145/3308558.3313562 is OK
MISSING DOIs
- None
INVALID DOIs
- None
: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/4938, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@clreda as AEiC I will now help to process this work for acceptance in JOSS. Since this concerns two packages, i.e. stanscofi
and benchscofi
, we need to re-do/change a couple of things here first.
Please can you complete the following:
stanscofi
and benchscofi
. Next report back here with the version tags used for these releases, for both software packages. I am guessing this will be v.2.0.0
and v.2.0.0
? I will proceed with this just now, but let me know if this needs to be amended. The version tag we'll assign here will be a a collection of the two separated by a comma, e.g. v.2.0.0, v.2.0.0
. stanscofi
and benchscofi
, and report back here with the DOI. Next ensure its title matches the paper title, and that you assign the MIT license. For the version tag use the merged one, i.e. v.2.0.0, v.2.0.0
. In addition:
stanscofi and benchscofi: A new standard for drug repurposing by collaborative filtering
. This is only a recommendation, but let me know if you are in agreement. If so, please amend the paper and ensure the archive title matches. @editorialbot set v.2.0.0, v.2.0.0 as version
Done! version is now v.2.0.0, v.2.0.0
Dear @Kevin-Mattheus-Moerman, thanks for your help.
Release version for stanscofi
: v2.0.0
Release version for benchscofi
: v2.0.0
Joint archive DOI: Version v2.0.0,v2.0.0
10.5281/zenodo.10561760
I agree with your suggestion, and I have changed the title accordingly (commit c1e0260) in both the paper and the Zenodo archive.
Please let me know if there is anything else needed.
@editorialbot generate pdf
@editorialbot set 10.5281/zenodo.10561760 as archive
Done! archive is now 10.5281/zenodo.10561760
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
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:
``` cff-version: "1.2.0" authors: - family-names: Réda given-names: Clémence orcid: "https://orcid.org/0000-0003-3238-0258" - family-names: Vie given-names: Jill-Jênn orcid: "https://orcid.org/0000-0002-9304-2220" - family-names: Wolkenhauer given-names: Olaf orcid: "https://orcid.org/0000-0001-6105-2937" doi: 10.5281/zenodo.10561760 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Réda given-names: Clémence orcid: "https://orcid.org/0000-0003-3238-0258" - family-names: Vie given-names: Jill-Jênn orcid: "https://orcid.org/0000-0002-9304-2220" - family-names: Wolkenhauer given-names: Olaf orcid: "https://orcid.org/0000-0001-6105-2937" date-published: 2024-01-25 doi: 10.21105/joss.05973 issn: 2475-9066 issue: 93 journal: Journal of Open Source Software publisher: name: Open Journals start: 5973 title: "stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05973" volume: 9 title: "stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering" ```
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.
🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
Any issues? Notify your editorial technical team...
Congralations on this publication @clreda !
Thanks for editing @Nikoleta-v3
And a special thank you to the reviewers: @jaybee84, @abhishektiwari
: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.05973/status.svg)](https://doi.org/10.21105/joss.05973)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05973">
<img src="https://joss.theoj.org/papers/10.21105/joss.05973/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05973/status.svg
:target: https://doi.org/10.21105/joss.05973
This is how it will look in your documentation:
We need your help!
The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Thank you very much for coordinating the publication @Kevin-Mattheus-Moerman and a lot of thanks to @Nikoleta-v3, @jaybee84 and @abhishektiwari for their help in considerably improving the use of the softwares!
Submitting author: !--author-handle-->@clreda<!--end-author-handle-- (Clémence Réda) Repository: https://github.com/RECeSS-EU-Project/stanscofi/ Branch with paper.md (empty if default branch): Version: v.2.0.0, v.2.0.0 Editor: !--editor-->@Nikoleta-v3<!--end-editor-- Reviewers: @jaybee84, @abhishektiwari Archive: 10.5281/zenodo.10561760
Status
Status badge code:
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
@jaybee84 & @abhishektiwari, 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:
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 @abhishektiwari
📝 Checklist for @jaybee84