Closed whedon closed 2 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @emilydolson, @TimKam it looks like you're currently assigned to review this paper :tada:.
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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Wordcount for paper.md
is 629
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btt772 is OK
- 10.7554/eLife.61288 is OK
- 10.1101/2021.05.29.446280 is OK
- 10.1016/j.zool.2019.02.007 is OK
- 10.1098/rstb.2019.0248 is OK
- 10.1101/053405 is OK
- 10.3389/fmicb.2015.00728 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.27 s (428.6 files/s, 285181.1 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
HTML 67 22318 315 19027
SVG 9 0 0 16611
JavaScript 27 1465 3089 9484
JSON 1 0 0 1794
CSS 6 199 68 1230
TeX 1 8 0 75
Markdown 2 32 0 64
Bourne Shell 1 17 9 54
-------------------------------------------------------------------------------
SUM: 114 24039 3481 48339
-------------------------------------------------------------------------------
Statistical information for the repository '41d513f16f9bdba7c5f10c3d' was
gathered on 2021/11/23.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Bram van Dijk 24 3508 1172 0.47
bramvandijk88 153 490986 472663 96.80
jeroenmeijer 2 26 24 0.01
root 4 24015 3150 2.73
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
bramvandijk88 16747 3.4 3.4 23.08
jeroenmeijer 4 15.4 1.6 0.00
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: :wave: :wave: @bramvandijk88 @emilydolson @TimKam this is the review thread for the paper. All of our communications will happen here from now on.
Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3948
so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
We aim for reviews to be completed within about 4-6 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.
Please feel free to ping me (@bisaloo) if you have any questions/concerns.
@Bisaloo should I be able to edit this issue to check things off? I don't seem to be able to. I suspect this has to do with me not having accepted the invitation to collaborate on this repository before it expired.
@emilydolson, yes, you should be able to edit the checklist once you have accepted the invitation. I'll re-invite you :relaxed:
@whedon re-invite @emilydolson as reviewer
OK, the reviewer has been re-invited.
@emilydolson please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
:wave: @TimKam, please update us on how your review is going (this is an automated reminder).
:wave: @emilydolson, please update us on how your review is going (this is an automated reminder).
Heya,
Just checking in after the holidays, is this review still in progress? I'm not at all in a hurry, but just wanted to make sure it wasn't forgotten.
Yes! Apologies for being slow - my university switched teaching modalities and I've been scrambling to adjust my course.
Yes! Apologies for being slow - my university switched teaching modalities and I've been scrambling to adjust my course.
No need to apologise, there have been holidays + a new year of teaching, so nobody should expect to stay within standardised deadlines. Thanks for your time! :)
Okay, done with my initial review! Really cool project! @bramvandijk88 already added the contributing guidelines, so in my mind the only two issues currently blocking acceptance are:
Thank you for your very insighful comments @emilydolson and thanks @bramvandijk88 for sending a reminder (Sorry for my lack of activity, I'm still on leave without reliable internet access until next week)
I'm satisfied that all items on the review checklist are complete!
Thanks @emilydolson!
@TimKam, could you give us an update for your review of this library+paper please? Please let me know if you need anything.
Sorry, I should be able to complete the review within roughly (but perhaps not exactly) one week.
I have completed the review and have created an issue in the source code repository that outlines some shortcomings/improvements, with respect to some issues around installation & instructions, automated tests, community guidelines, and the software paper (minor comments). Conceptually/w.r.t. scholarly effort, I assess the paper as reasonable (from an engineering point of view, I do not have any expertise in ecology and evolution).
@bramvandijk88 responded rather promptly and we have concluded the revisions and discussions regarding my review. I have now completed the review checklist.
@TimKam not sure if this is intended, but one of your checkboxes is still unticked.
Thx, now it's ticked!
Great! Thank you again @emilydolson and @TimKam for your valuable comments!
@bramvandijk88, I'll now do a last review for typos. I encourage you to do the same because there is no proofing after acceptance at JOSS. Once this is done, we can take the final steps to accept this submission.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btt772 is OK
- 10.7554/eLife.61288 is OK
- 10.1101/2021.05.29.446280 is OK
- 10.1016/j.zool.2019.02.007 is OK
- 10.1098/rstb.2019.0248 is OK
- 10.1101/053405 is OK
- 10.3389/fmicb.2015.00728 is OK
MISSING DOIs
- 10.1098/rstb.2020.0460 may be a valid DOI for title: Introduction: the secret lives of microbial mobile genetic elements
INVALID DOIs
- None
Shouldn't https://github.com/bramvandijk88/cacatoo/blob/65b6e7a2daac8175d65a6052b4f2f6d3652d08b7/paper/paper.bib#L1-L10 be @article
instead of @misc
anyways?
I've added the DOI of "Introduction: the secret lives of Mobile genetic Elements".
Google indexed that citation as @misc, probably because it's not an article in the strict sense, it's just an overview of the content in the special issue.
I've checked the proof for typos (caught a few!) Please let me know what happens next.
At this point could you:
I can then move forward with accepting the submission.
At this point could you:
- [x] Make a tagged release of your software, and list the version tag of the archived version here.
- [x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
- [x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
- [x] Please list the DOI of the archived version here.
Done. The archived Zenodo DOI is 10.5281/zenodo.5918404
@whedon set 1.0.1 as version
OK. 1.0.1 is the version.
@bramvandijk88, there is a mismatch in the version listed in Zenodo and the actual tag in GitHub. If you can easily fix it, it would be great. But if it's too difficult, then we can ignore it and proceed.
Additionally, could you please edit the license on Zenodo. It's listed as 'Other' when it should be 'GPL-3'?
What mismatch is there? They are both 1.0.1 as far as I can tell.
I've changed the licence to "GPL-3" in the zenodo.json file, but it only updates this upon republishing the package. Zenodo complains when I do that without bumping the version, but I actually don't want to bump the version without having any changes in the code. Is there a way around this?
Here is what I see. And the link to 1.0.3 on GitHub doesn't work because this version doesn't exist.
Not sure what's going on here. V1.0.3 was the result of me testing the metadata, for which I was forced to publish (or Zenodo wouldn't reindex them).
I'm not sure how to resolve this. There's no way to edit these things after publication as far as I can tell, but the DOI-link on the github page itself should get you to version 1.0.1.
Okay, let's go with this then. It's not super important. The most important thing is that the submission is actually archived.
@whedon recommend-accept
No archive DOI set. Exiting...
@whedon set 10.5281/zenodo.5918404 as archive
OK. 10.5281/zenodo.5918404 is the archive.
@whedon recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1098/rstb.2020.0460 is OK
- 10.1093/bioinformatics/btt772 is OK
- 10.7554/eLife.61288 is OK
- 10.1101/2021.05.29.446280 is OK
- 10.1016/j.zool.2019.02.007 is OK
- 10.1098/rstb.2019.0248 is OK
- 10.1101/053405 is OK
- 10.3389/fmicb.2015.00728 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2921
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2921, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@whedon set 1.0.3 as version
Submitting author: @bramvandijk88 (Bram van Dijk) Repository: https://github.com/bramvandijk88/cacatoo Version: 1.0.3 Editor: @Bisaloo Reviewer: @emilydolson, @TimKam Archive: 10.5281/zenodo.5918404
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
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
@emilydolson & @TimKam, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Bisaloo 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 ✨
Review checklist for @emilydolson
✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @TimKam
✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper