editorialbot commented 7 months ago

Submitting author: !--author-handle-->@kmcdono2@emdupre<!--end-editor-- Reviewers: @geekysquirrel, @PipGrylls, @jordibc Archive: 10.5281/zenodo.13643609

Status

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Markdown: [![status](https://joss.theoj.org/papers/96e2d51da2c283a40c38101856f1f15c/status.svg)](https://joss.theoj.org/papers/96e2d51da2c283a40c38101856f1f15c)

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

@geekysquirrel & @PipGrylls & @jordibc, 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 @emdupre 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 @PipGrylls

📝 Checklist for @jordibc

📝 Checklist for @geekysquirrel

emdupre commented 3 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

rwood-97 commented 3 months ago

Hi, just wanted to check whether these are tasks we should do now or wait until the editor tasks are complete?

emdupre commented 3 months ago

Hi @rwood-97, and thanks for checking ! Apologies for being unclear : You can go ahead and work on the author tasks. I will have requests for the accompanying software paper (which should be ready shortly), but these can be handled independently from versioning and archiving the software.

emdupre commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

emdupre commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

OK DOIs

- 10.1145/3557919.3565812 is OK
- 10.5281/ZENODO.7147906 is OK
- 10.1093/jvcult/vcab009 is OK
- 10.1016/j.regsciurbeco.2021.103711 is OK
- 10.48550/ARXIV.2101.12478 is OK
- 10.21105/joss.01800 is OK

MISSING DOIs

- No DOI given, and none found for title: mapKurator
- No DOI given, and none found for title: Automated extraction of dynamic phenotype data fro...

INVALID DOIs

- None

emdupre commented 3 months ago

Thank you for your patience, @rwood-97 ! I've now finished reviewing both the paper as well as the references and have a only a few remaining editorial requests on both :

I've opened a pull request with minor edits to the text of the paper. Please review these and let me know if you have any concerns or questions !
Could you please update the mapkurator citation to include the references they request in their documentation, as described here ?
It looks like the Corcoran citation is listed as "in preparation." Is there a preprint or another source that could be directly cited, here ?

kmcdono2 commented 3 months ago

I reviewed your pull request and made 1 request to not edit as suggested, otherwise fine.

I have made the update to the mapkurator citation here: https://github.com/Living-with-machines/MapReader/pull/449

I have emailed Corcoran about whether her citation can be updated.

kmcdono2 commented 3 months ago

Corcoran can be updated to 'under review'. I'll make this change now.

rwood-97 commented 3 months ago

Just updated the repo with a release for the JOSS paper. This is v1.3.3 and can be found here.

Link for draft of zenodo release: https://zenodo.org/uploads/12636179?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImU0MjI2ZDEzLThhZjUtNDZkZS1iMTFmLTQ0NDU3NTBkZGI4MCIsImRhdGEiOnt9LCJyYW5kb20iOiIzOTFiOWYzMWI0NWRkNThhYTJjNjc0M2YyMmViYTcxZCJ9.vAW3VwdfXQbzYqWhZySYN7KXDjoj8PHf7ETCW_-pqTtxtCyH9HjHEb94AAkMUR66qS390ASkgSpWpMLXiigepQ

Is this correct? I can edit if not

kmcdono2 commented 3 months ago

@rwood-97 I don't have permission to see the zenodo draft...

emdupre commented 2 months ago

Hi all,

Thanks for sending these updates, @kmcdono2 and @rwood-97 !

Confirming that I also cannot see the Zenodo draft and so cannot check the archive. Please let me know when this is accessible (usually by publishing the record).

On my side, I'm happy to update or close the PR if you'd like to make the remaining changes to the software paper. Of note, for the Corcoran reference, the bibtex entry will need to be updated to the following :

@unpublished{Corcoran,
    title = {Automated extraction of dynamic phenotype data from whole plant images collected under controlled conditions},
    author = {Corcoran, E and Hosseini, K and Siles, L and Kurup, S and Ahnert, S},
    note = {Under review},
}

rwood-97 commented 2 months ago

Hi,

Sorry for being a bit slow to action this.

Here is the published record: https://zenodo.org/records/12636179 Katie is on holiday at the moment - I'll check with her about the PR when she's back and then make any changes/merge.

emdupre commented 2 months ago

@editorialbot set 10.5281/zenodo.12636179 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.12636179

emdupre commented 2 months ago

@editorialbot set v1.3.3 as version

editorialbot commented 2 months ago

Done! version is now v1.3.3

emdupre commented 2 months ago

Thank you, @rwood-97 !

On the archive, it looks like there's one missing ORCID for Rosie Wood (that is present in the software paper). Could you please add this ? You can usually do so by editing the archive metadata. If you hit any issues, of course, please let me know.

Otherwise, to move things along, I'll go ahead and modify my existing PR to incorporate the last reference edit.

rwood-97 commented 2 months ago

Ah woops, yes all done :)

rwood-97 commented 2 months ago

@emdupre Let us know when this is done.

Is there anything else on our end?

emdupre commented 2 months ago

Apologies, this is now pushed. Please let me know when you have merged these changes (or otherwise committed them to the code), and this should be ready to process.

rwood-97 commented 2 months ago

Hi thanks, this is merged now.

emdupre commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

emdupre commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- 10.1145/3557919.3565812 is OK
- 10.5281/ZENODO.7147906 is OK
- 10.1093/jvcult/vcab009 is OK
- 10.1016/j.regsciurbeco.2021.103711 is OK
- 10.48550/ARXIV.2101.12478 is OK
- 10.21105/joss.01800 is OK

MISSING DOIs

- 10.1145/3394486.3403381 may be a valid DOI for title: An automatic approach for generating rich, linked ...
- No DOI given, and none found for title: Automated extraction of dynamic phenotype data fro...

INVALID DOIs

- None

emdupre commented 2 months ago

Thank you, @rwood-97 !

It looks like there is one identified DOI that is not currently included in the bib file entry. From my review, it looks like this is indeed associated with the correct reference and should be added. Could you please include this ?

Otherwise, please let me know if you see any remaining issues with the current article proofs before we proceed !

rwood-97 commented 2 months ago

@emdupre Could you check this is updated correctly? PR is here

rwood-97 commented 2 months ago

PR is merged.

One last thing is that we restructured the documentation last week (after zenodo record) so may want to reword the documentation paragraph. @kmcdono2 and I will chat about this and update you asap.

rwood-97 commented 2 months ago

@emdupre We are considering moving the MapReader repo into its own MapReader org (as opposed to being under Living-with-machines). Would your preference be for us to do this before or after publicationo of the JOSS paper?

Otherwise we think we are done

emdupre commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

emdupre commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

OK DOIs

- 10.1145/3557919.3565812 is OK
- 10.5281/ZENODO.7147906 is OK
- 10.1093/jvcult/vcab009 is OK
- 10.1016/j.regsciurbeco.2021.103711 is OK
- 10.1145/3394486.3403381 is OK
- 10.48550/ARXIV.2101.12478 is OK
- 10.21105/joss.01800 is OK

MISSING DOIs

- No DOI given, and none found for title: Dynamic phenotyping of whole oilseed rape (Brassic...

INVALID DOIs

- None

emdupre commented 2 months ago

Hi @rwood-97 -- thank you for these updates. There are two remaining issues I see :

Given that you've updated the documentation significantly, it would make sense to also generate a new version of the software that includes these updates (and can be referenced in the paper). If you would like to do that at the same time as transferring the repo under a new org, that makes sense to me. Otherwise, the archive itself is the persistent record of the software.
On the software paper itself, it looks like the Cocoran reference was modified in the last pull request from the text I had provided. As this is currently an unpublished reference, we should include it as :

@unpublished{Corcoran,
    title = {Automated extraction of dynamic phenotype data from whole plant images collected under controlled conditions},
    author = {Corcoran, E and Hosseini, K and Siles, L and Kurup, S and Ahnert, S},
    note = {Under review},
}

rather than listing the current year or journal where it is currently under review. From the most recent changes it looks like the article title has since been updated as well !

rwood-97 commented 1 month ago

Okay thanks. I think the consensus among the team is that we may need to take some time to make sure we do the transfer to the new org properly but want to make sure it won't delay publication too much (i.e. we'd do it after if it looks like it will take a long time to organise the transfer). In the meantime, should I update the current zenodo record with recent updates or would it be better to create a new record?
Ah sorry! I thought this could be updated to include the extra info but I will change it back. The title was changed just before submission so I will keep that as the new one.

emdupre commented 1 month ago

Thank you for confirming !

You should be able to mint a new version of the software. If you have the Zenodo-GitHub integration enabled, this should then automatically create a new Zenodo record. If not, you can create a new version (with a matching version number to your GitHub release) directly on Zenodo: https://help.zenodo.org/docs/deposit/manage-versions/

If you can then share the resulting version number and doi here, I can move this forward ! 🚀

emdupre commented 1 month ago

Hi @rwood-97, please let me know if you're able to create this new DOI, or if you're hitting any issues I can help in troubleshooting !

rwood-97 commented 1 month ago

Hi, sorry for being slow on this - I'll do the updated zenodo record today. We are still trying to move MapReader to its own repo but are trying to get in touch with a github user called MapReader (who has been inactive for 2 years) to ask if we can steal his username.

rwood-97 commented 1 month ago

Hi,

Here is the updated record: https://zenodo.org/records/13354851

emdupre commented 1 month ago

@editorialbot set v1.3.3 as version

editorialbot commented 1 month ago

Done! version is now v1.3.3

emdupre commented 1 month ago

@editorialbot set v1.3.9 as version

editorialbot commented 1 month ago

Done! version is now v1.3.9

emdupre commented 1 month ago

@editorialbot set 10.5281/zenodo.13354851 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13354851

emdupre commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1145/3557919.3565812 is OK
- 10.5281/ZENODO.7147906 is OK
- 10.1093/jvcult/vcab009 is OK
- 10.1016/j.regsciurbeco.2021.103711 is OK
- 10.1145/3394486.3403381 is OK
- 10.48550/ARXIV.2101.12478 is OK
- 10.21105/joss.01800 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Dynamic phenotyping of whole oilseed rape (Brassic...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

emdupre commented 1 month ago

@editorialbot generate pdf

openjournals / joss-reviews

[REVIEW]: MapReader: v1.1.0 #6434

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance