[REVIEW]: PCRedux: A Quantitative PCR Machine Learning Toolkit

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@devSJR@csoneson<!--end-editor-- Reviewers: @jaybee84, @markziemann Archive: 10.5281/zenodo.7009124

Status

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HTML: <a href="https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b"><img src="https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b/status.svg)](https://joss.theoj.org/papers/860ed94423d2d9908209c37ed8aec46b)

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 & @markziemann, 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:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @csoneson 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 @jaybee84

📝 Checklist for @markziemann

csoneson commented 2 years ago

Thanks @devSJR! I went through the paper again and I think this looks good - I sent another small PR with a couple of minor fixes. Regarding the attachment, I would suggest that you upload the current vignette to e.g. Zenodo or FigShare, and refer to that (you would get a DOI).

Once these things are sorted, the next steps are as follows:

[ ] Make a tagged release of the software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service
[ ] Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper. You can also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

devSJR commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

devSJR commented 2 years ago

Thanks @devSJR! I went through the paper again and I think this looks good - I sent another small PR with a couple of minor fixes. Regarding the attachment, I would suggest that you upload the current vignette to e.g. Zenodo or FigShare, and refer to that (you would get a DOI).

Once these things are sorted, the next steps are as follows:
* [ ]  Make a tagged release of the software, and list the version tag of the archived version here.

* [ ]  Archive the reviewed software in Zenodo or a similar service

* [ ]  Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper. You can also add the authors' ORCID.

* [ ]  Please list the DOI of the archived version here.
I can then move forward with accepting the submission.

@csoneson, finally here are the missing bits.

version tag of the archived version: 1.1-2 DOI of the archived version 10.5281/zenodo.7009124 https://doi.org/10.5281/zenodo.7009124

csoneson commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.6957714 is OK
- 10.32614/RJ-2015-011 is OK
- 10.32614/RJ-2013-024 is OK
- 10.3233/JCB-15025 is OK
- 10.1373/clinchem.2014.230656 is OK
- 10.1093/bioinformatics/btx528 is OK
- 10.1093/bioinformatics/btv205 is OK
- 10.1016/j.bdq.2018.08.001 is OK
- 10.1038/srep38951 is OK
- 10.1038/s41598-021-00827-0 is OK
- 10.3390/life11111163 is OK
- 10.1198/106186007X178663 is OK
- 10.1186/gb-2004-5-10-r80 is OK
- 10.1186/1471-2105-9-221 is OK
- 10.1093/bioinformatics/btn227 is OK
- 10.1016/j.bdq.2014.08.002 is OK
- 10.1016/j.ymeth.2009.12.006 is OK
- 10.32614/rj-2011-002 is OK
- 10.18637/jss.v023.i03 is OK
- 10.18637/jss.v062.i07 is OK
- 10.18637/jss.v032.i03 is OK
- 10.1016/j.ymeth.2012.08.011 is OK
- 10.1016/j.bdq.2015.07.001 is OK
- 10.1261/rna.059063.116 is OK
- 10.1016/j.bdq.2017.11.002 is OK
- 10.1016/S0304-3940(02)01423-4 is OK
- 10.1093/clinchem/hvab052 is OK
- 10.1016/j.tibtech.2018.12.002 is OK
- 10.1186/1471-2105-15-138 is OK
- 10.32614/rj-2014-015 is OK
- 10.1093/gigascience/giy077 is OK
- 10.1111/anzs.12200 is OK
- 10.3390/life11111163 is OK
- 10.18637/jss.v049.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson commented 2 years ago

@editorialbot set 10.5281/zenodo.7009124 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7009124

csoneson commented 2 years ago

@editorialbot set 1.1-2 as version

editorialbot commented 2 years ago

Done! version is now 1.1-2

csoneson commented 2 years ago

@devSJR Thanks! I'll hand over now to an associate EiC for the final steps. Thanks for submitting to JOSS!

csoneson commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.6957714 is OK
- 10.32614/RJ-2015-011 is OK
- 10.32614/RJ-2013-024 is OK
- 10.3233/JCB-15025 is OK
- 10.1373/clinchem.2014.230656 is OK
- 10.1093/bioinformatics/btx528 is OK
- 10.1093/bioinformatics/btv205 is OK
- 10.1016/j.bdq.2018.08.001 is OK
- 10.1038/srep38951 is OK
- 10.1038/s41598-021-00827-0 is OK
- 10.3390/life11111163 is OK
- 10.1198/106186007X178663 is OK
- 10.1186/gb-2004-5-10-r80 is OK
- 10.1186/1471-2105-9-221 is OK
- 10.1093/bioinformatics/btn227 is OK
- 10.1016/j.bdq.2014.08.002 is OK
- 10.1016/j.ymeth.2009.12.006 is OK
- 10.32614/rj-2011-002 is OK
- 10.18637/jss.v023.i03 is OK
- 10.18637/jss.v062.i07 is OK
- 10.18637/jss.v032.i03 is OK
- 10.1016/j.ymeth.2012.08.011 is OK
- 10.1016/j.bdq.2015.07.001 is OK
- 10.1261/rna.059063.116 is OK
- 10.1016/j.bdq.2017.11.002 is OK
- 10.1016/S0304-3940(02)01423-4 is OK
- 10.1093/clinchem/hvab052 is OK
- 10.1016/j.tibtech.2018.12.002 is OK
- 10.1186/1471-2105-15-138 is OK
- 10.32614/rj-2014-015 is OK
- 10.1093/gigascience/giy077 is OK
- 10.1111/anzs.12200 is OK
- 10.3390/life11111163 is OK
- 10.18637/jss.v049.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/joss-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/3454, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years 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/3455
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04407
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@jaybee84, @markziemann – many thanks for your reviews here and to @csoneson for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@devSJR – your paper is now accepted and published in JOSS :zap::rocket::boom:

editorialbot commented 2 years ago

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

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Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04407/status.svg)](https://doi.org/10.21105/joss.04407)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04407">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04407/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04407/status.svg
   :target: https://doi.org/10.21105/joss.04407

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devSJR commented 2 years ago

@arfon @jaybee84 @markziemann @csoneson

Thanks!

openjournals / joss-reviews