[REVIEW]: MicroTracker.jl: A Julia package for microbot research

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@czimm79@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @roflmaostc, @mkitti, @BioTurboNick Archive: 10.5281/zenodo.10578580

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3e805508dffadd68e665a81c3498d103"><img src="https://joss.theoj.org/papers/3e805508dffadd68e665a81c3498d103/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3e805508dffadd68e665a81c3498d103/status.svg)](https://joss.theoj.org/papers/3e805508dffadd68e665a81c3498d103)

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

@roflmaostc & @mkitti & @BioTurboNick, 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 @Kevin-Mattheus-Moerman 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 @roflmaostc

📝 Checklist for @mkitti

📝 Checklist for @BioTurboNick

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:

Kevin-Mattheus-Moerman 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

- 10.1126/scirobotics.aav4317 is OK
- 10.1126/sciadv.aat4388 is OK
- 10.1137/141000671 is OK
- 10.1038/nmeth.2019 is OK
- 10.1126/scirobotics.aba5726 is OK
- 10.1002/adma.202002047 is OK
- 10.1006/jcis.1996.0217 is OK
- 10.1038/s41598-022-09177-x is OK
- 10.1002/nano.202100353 is OK
- 10.1021/acsomega.3c00886 is OK
- 10.1038/nmeth.2089 is OK
- 10.5281/zenodo.7670439 is OK
- 10.5281/zenodo.6234110 is OK
- 10.1021/acs.langmuir.3c00701 is OK
- 10.5281/zenodo.6234110 is OK
- 10.5281/zenodo.8028030 is OK
- 10.1038/nmeth.2808 is OK
- 10.1115/1.3662552 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ymeth.2016.09.016 is INVALID because of 'https://doi.org/' prefix

czimm79 commented 9 months ago

On it.

@editorialbot check references

czimm79 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

- 10.1126/scirobotics.aav4317 is OK
- 10.1126/sciadv.aat4388 is OK
- 10.1137/141000671 is OK
- 10.1038/nmeth.2019 is OK
- 10.1126/scirobotics.aba5726 is OK
- 10.1002/adma.202002047 is OK
- 10.1006/jcis.1996.0217 is OK
- 10.1038/s41598-022-09177-x is OK
- 10.1002/nano.202100353 is OK
- 10.1021/acsomega.3c00886 is OK
- 10.1038/nmeth.2089 is OK
- 10.5281/zenodo.7670439 is OK
- 10.1016/j.ymeth.2016.09.016 is OK
- 10.5281/zenodo.6234110 is OK
- 10.1021/acs.langmuir.3c00701 is OK
- 10.5281/zenodo.6234110 is OK
- 10.5281/zenodo.8028030 is OK
- 10.1038/nmeth.2808 is OK
- 10.1115/1.3662552 is OK

MISSING DOIs

- None

INVALID DOIs

- None

czimm79 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:

czimm79 commented 9 months ago

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)

[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.

In addition:

[x] Please add a References heading prior to the reference list.

[x] Please spell out USA as United States of America

[x] The second affiliation contains |, can you reformat this? This should perhaps be a comma instead.

[x] Check the potentially invalid DOI's

Latest version: 0.3.2 Zenodo archive DOI:

@Kevin-Mattheus-Moerman Finished. Thanks!

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot generate pdf

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot set v0.3.2 as version

editorialbot commented 9 months ago

Done! version is now v0.3.2

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:

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot set 10.5281/zenodo.10547472 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10547472

Kevin-Mattheus-Moerman commented 9 months ago

@czimm79 please edit the archive title to match the paper title.

czimm79 commented 9 months ago

@Kevin-Mattheus-Moerman Done.

Kevin-Mattheus-Moerman commented 9 months ago

@czimm79 all seems in order. At this point I will proceed to process this for acceptance in JOSS.

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- 10.1126/scirobotics.aav4317 is OK
- 10.1126/sciadv.aat4388 is OK
- 10.1137/141000671 is OK
- 10.1038/nmeth.2019 is OK
- 10.1126/scirobotics.aba5726 is OK
- 10.1002/adma.202002047 is OK
- 10.1006/jcis.1996.0217 is OK
- 10.1038/s41598-022-09177-x is OK
- 10.1002/nano.202100353 is OK
- 10.1021/acsomega.3c00886 is OK
- 10.1038/nmeth.2089 is OK
- 10.5281/zenodo.7670439 is OK
- 10.1016/j.ymeth.2016.09.016 is OK
- 10.5281/zenodo.6234110 is OK
- 10.1021/acs.langmuir.3c00701 is OK
- 10.5281/zenodo.6234110 is OK
- 10.5281/zenodo.8028030 is OK
- 10.1038/nmeth.2808 is OK
- 10.1115/1.3662552 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-plas_fonspplutojl_2022 already defined

Kevin-Mattheus-Moerman commented 9 months ago

@czimm79 it looks like you have that reference twice in your .bib file. Can you check this please?

czimm79 commented 9 months ago

Corrected. Released a new version v0.3.3 with the change. Updated Zenodo with v0.3.3: 10.5281/zenodo.10578580

czimm79 commented 9 months ago

@Kevin-Mattheus-Moerman Anything else I should do?

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot set v.0.3.3 as version

editorialbot commented 9 months ago

Done! version is now v.0.3.3

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot set 10.5281/zenodo.10578580 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10578580

Kevin-Mattheus-Moerman commented 9 months ago

@czimm79 thanks, note that if any further changes to the paper are needed, there is no need for a new version tag/archive link, if you prefer just sticking with the ones we've set.

Kevin-Mattheus-Moerman commented 9 months ago

@czimm79 I have checked your paper, the archive link, and you repository again. It looks like most is in order, I only have the below point that requires your attention.

[x] Please edit the archive link license to match your software license.

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- 10.1126/scirobotics.aav4317 is OK
- 10.1126/sciadv.aat4388 is OK
- 10.1137/141000671 is OK
- 10.1038/nmeth.2019 is OK
- 10.1126/scirobotics.aba5726 is OK
- 10.1002/adma.202002047 is OK
- 10.1006/jcis.1996.0217 is OK
- 10.1038/s41598-022-09177-x is OK
- 10.1002/nano.202100353 is OK
- 10.1021/acsomega.3c00886 is OK
- 10.1038/nmeth.2089 is OK
- 10.5281/zenodo.7670439 is OK
- 10.1016/j.ymeth.2016.09.016 is OK
- 10.1021/acs.langmuir.3c00701 is OK
- 10.5281/zenodo.6234110 is OK
- 10.5281/zenodo.8028030 is OK
- 10.1038/nmeth.2808 is OK
- 10.1115/1.3662552 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 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/4990, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 8 months ago

@czimm79 Can you please edit the archive link license to match your software license? Thanks

czimm79 commented 8 months ago

@Kevin-Mattheus-Moerman Done! Sorry for the delay.

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: Zimmermann given-names: Coy J. - family-names: Neeves given-names: Keith B. - family-names: Marr given-names: David W. M. doi: 10.5281/zenodo.10578580 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Zimmermann given-names: Coy J. - family-names: Neeves given-names: Keith B. - family-names: Marr given-names: David W. M. date-published: 2024-02-13 doi: 10.21105/joss.05804 issn: 2475-9066 issue: 94 journal: Journal of Open Source Software publisher: name: Open Journals start: 5804 title: "MicroTracker.jl: A Julia package for microbot research" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05804" volume: 9 title: "MicroTracker.jl: A Julia package for microbot research" ```

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/5008
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05804
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

@czimm79 congratulations on this JOSS publication !! :tada:

I'd like to thank the stellar efforts of the reviewers: @roflmaostc, @mkitti, @BioTurboNick! :robot:

editorialbot commented 8 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:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05804/status.svg)](https://doi.org/10.21105/joss.05804)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05804">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05804/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05804/status.svg
   :target: https://doi.org/10.21105/joss.05804

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:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews