Closed whedon closed 6 months ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @enkera it looks like you're currently assigned to review this paper :tada:.
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Wordcount for paper.md
is 1504
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.09 s (498.6 files/s, 48211.7 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Markdown 26 372 0 1427
Python 7 342 230 1063
TeX 1 22 0 233
R 4 52 39 161
YAML 3 30 54 126
make 1 28 29 67
JSON 1 0 0 57
Ruby 1 3 1 7
Bourne Shell 1 2 2 4
-------------------------------------------------------------------------------
SUM: 45 851 355 3145
-------------------------------------------------------------------------------
Statistical information for the repository '1ac5fffa9be4e8bd17f6359c' was
gathered on 2023/06/01.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Andy Boughton 1 5 4 0.03
Francois Michonneau 1 2306 0 6.45
François Michonneau 5 22 130 0.43
Gabriel A. Devenyi 1 5 3 0.02
Greg Wilson 47 12802 13284 73.01
Joseph Stachelek 1 1 1 0.01
Katrin Leinweber 3 6 6 0.03
Maxim Belkin 14 55 55 0.31
Michael R. Crusoe 1 74 70 0.40
Raniere Silva 20 262 687 2.66
Rémi Emonet 2 49 17 0.18
Tracy Teal 4 3817 1950 16.14
W. Trevor King 1 0 1 0.00
William L. Close 3 53 56 0.31
naught101 1 4 2 0.02
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
Andy Boughton 3 60.0 10.3 0.00
François Michonneau 95 431.8 9.8 0.00
Greg Wilson 506 4.0 32.1 11.26
Joseph Stachelek 1 100.0 10.2 0.00
Katrin Leinweber 1 16.7 10.0 0.00
Maxim Belkin 46 83.6 10.3 2.17
Michael R. Crusoe 62 83.8 11.2 4.84
Raniere Silva 58 22.1 13.4 10.34
Tracy Teal 873 22.9 20.1 12.37
naught101 1 25.0 16.3 0.00
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.5281/ZENODO.3585993 is OK
- 10.1101/2021.06.17.448726 is OK
- 10.1101/2021.06.15.448091 is OK
- 10.21105/jose.00049 is OK
- 10.7554/eLife.49816 is OK
- 10.5281/ZENODO.3260309 is OK
- 10.3389/fmicb.2020.578600 is OK
MISSING DOIs
- 10.21105/jose.00049 may be a valid DOI for title: A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching
- 10.21105/jose.00027 may be a valid DOI for title: An Introduction to Applied Bioinformatics: a free, open, and interactive text.
- 10.21105/jose.00021 may be a valid DOI for title: CFD Python: the 12 steps to Navier-Stokes equations
- 10.3389/fmicb.2020.578600 may be a valid DOI for title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R
- 10.1002/bmb.21387 may be a valid DOI for title: Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education
- 10.1525/abt.2021.83.1.33 may be a valid DOI for title: Introducing Python Programming into Undergraduate Biology
INVALID DOIs
- None
:wave: @enkera, please update us on how your review is going (this is an automated reminder).
Hello @JasonJWilliamsNY and @enkera Please could you share if there is any news in the review process?
Hello @JasonJWilliamsNY. I've had a look at the workshop and it satisfies most of the criteria needed for publication. There seem to be several broken or indirect URL links, in particular the Instructor Notes, Setup, and Metagenomics Workshop Setup page links are dead or not working properly. Other than that, everything looks good.
Hello @enkera , We have updated Setup and instructor notes in Metagenomics Workshop, I think they broke when we change the repo from carpentries-incubator to carpentries-lab, thank you for noticing that.
Hello, @enkera and @JasonJWilliamsNY Is it something else needed for the workshop to be accepted?
Hi @nselem I'll take one last look so we can move to the acceptance step. Thanks @enkera for review!
@enkera can you check off the items in the checklist at the top of this page; don't worry if some don't apply.
@whedon unassign @enkera as reviewer
@editorialbot remove @enkera from reviewers
@enkera added to the reviewers list!
@enkera I removed and added you - if that does not work, I will consult with @labarba
I still can't check the boxes unfortunately.
On Wed, Jul 26, 2023 at 11:00 AM Jason Williams @.***> wrote:
@enkera https://github.com/enkera I removed and added you - if that does not work, I will consult with @labarba https://github.com/labarba
— Reply to this email directly, view it on GitHub https://github.com/openjournals/jose-reviews/issues/209#issuecomment-1651988209, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETX4ADNFYTE4C4CCAZXHA3XSEWJTANCNFSM6AAAAAAYXBTHXI . You are receiving this because you were mentioned.Message ID: @.***>
@labarba can you help us out here?
@JasonJWilliamsNY – I would suggest that @enkera generates a new checklist with @editorialbot by typing the following in a new comment: @editorialbot generate my checklist
Pinging @enkera and will follow up by email.
@editorialbot generate my checklist
@openjournals/dev – On this review thread, reviewer @enkera was added before we moved JOSE to the new editorial workflow and bot, and I suspect he didn't accept the invitation in time to get the necessary permissions to edit the review auto-generated checklist. He now tried the command @editorialbot generate my checklist
to get a new one, but it didn't work. Can you help us?
I can't see anything obviously wrong here @xuanxu. Any thoughts?
Just a heads up - we're having the same issue in #221
There was a problem with the bot not knowing which checklist to create (software or learning module review). It should be fixed now.
@enkera: can you try again the @editorialbot generate my checklist
command?
paper.md
file include a list of authors with their affiliations?@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.5281/ZENODO.3585993 is OK
- 10.1101/2021.06.17.448726 is OK
- 10.1101/2021.06.15.448091 is OK
- 10.21105/jose.00049 is OK
- 10.7554/eLife.49816 is OK
- 10.5281/ZENODO.3260309 is OK
- 10.3389/fmicb.2020.578600 is OK
MISSING DOIs
- 10.21105/jose.00049 may be a valid DOI for title: A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching
- 10.21105/jose.00027 may be a valid DOI for title: An Introduction to Applied Bioinformatics: a free, open, and interactive text.
- 10.21105/jose.00021 may be a valid DOI for title: CFD Python: the 12 steps to Navier-Stokes equations
- 10.3389/fmicb.2020.578600 may be a valid DOI for title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R
- 10.1002/bmb.21387 may be a valid DOI for title: Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education
- 10.1525/abt.2021.83.1.33 may be a valid DOI for title: Introducing Python Programming into Undergraduate Biology
INVALID DOIs
- None
Hi @ @nselem I have made a few optional suggestions via a pull request https://github.com/carpentries-lab/metagenomics-workshop/pull/20
Once you are ready, the next step is for you to create an archive on either https://zenodo.org/ or https://figshare.com/ and obtain a DOI (which you'll need to give to us). I can then move to the final acceptance and publication steps.
Tip: Here is a nice guide on doing the above with Zenodo: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content#:~:text=Making%20Your%20Code%20Citable%201%20Choose%20your%20repository.,a%20shiny%20new%20badge%20showing%20your%20new%20DOI%21
Do note that the instructions provided in the link above result in the following behavior:
Zenodo archives your repository and issues a new DOI each time you create a new GitHub release.
This may or may not be behavior that you want for your project. Also note that the automatic Zenodo archives are titled with your repository name, and list every committer to the repo as an author. We request that authors edit the metadata of the Zenodo deposit so title and author list match the JOSE paper. It's just cleaner that way as readers see these as part of the "same scholarly object."
Thank you @JasonJWilliamsNY and @labarba
We had already made these archives in Zenodo for each repository of the lesson: Metagenomics R: https://zenodo.org/badge/latestdoi/315204217 Metagenomics Analysis: https://zenodo.org/badge/latestdoi/287395428 Metagenomics shell: https://zenodo.org/badge/latestdoi/344547242 Metagenomics organization: https://zenodo.org/badge/latestdoi/349858841 Metagenomics workshop: https://zenodo.org/badge/latestdoi/315250269
Are those what you need? Or should I make something differently? They do have long lists of authors, I'll see if it can be edited without affecting the DOI.
I think you can issue a new version; we try and make sure the Zenodo and the paper authors are the same. Since this is new maybe @labarba can comment.
Yes I think you are right Jason, because our links conserve as authors "Raniere Silva; François Michonneau; Maxim Belkin; Nelly Sélem; Andy Boughton; Claudia Zirión Martínez; Erin Becker; Abby Cabunoc Mayes; Katrin Leinweber @gitlabhq; W. Trevor King; Aaron O'Leary; maneesha sane; Toby Hodges; João Rodrigues; Diego Garfias Gallegos; Rayna M Harris; Jonah Duckles; Kate Hertweck; John Blischak; Trevor Bekolay; Jemma Stachelek; AbrahamAvelar; Piotr Banaszkiewicz; aaronejaime; Edward Wallace; David Mawdsley; Ivan Gonzalez; Naupaka Zimmerman; Zhian N. Kamvar; Michael R. Crusoe" and we need to keep only the authors of this lesson.
"
To change the list of authors, you edit the metadata of the archive, which does not issue a new DOI.
Thank you all, I have edited the list of authors in all the Zenodo archives. The links are the ones above.
"all the Zenodo archives"—I'm confused. We can only link the paper to one Zenodo archive. Are the materials spread out over several archives for this work?
The contents of the lesson itself are spread out in several GitHub repositories and each of those has a Zenodo archive. The paper.md is in the landing repo of the lesson, whose Zenodo archive is https://zenodo.org/record/7713380
Is it possible to make one fat .zip with everything and deposit in its own Zenodo archive?
I did this Zenodo archive https://doi.org/10.5281/zenodo.8306876
Does it work?
@editorialbot set 10.5281/zenodo.8306876 as archive
Done! archive is now 10.5281/zenodo.8306876
@JasonJWilliamsNY – when this is ready to be published, please run the recommend-accept
command
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.5281/ZENODO.3585993 is OK
- 10.1101/2021.06.17.448726 is OK
- 10.1101/2021.06.15.448091 is OK
- 10.21105/jose.00049 is OK
- 10.7554/eLife.49816 is OK
- 10.5281/ZENODO.3260309 is OK
- 10.3389/fmicb.2020.578600 is OK
MISSING DOIs
- 10.21105/jose.00049 may be a valid DOI for title: A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching
- 10.21105/jose.00027 may be a valid DOI for title: An Introduction to Applied Bioinformatics: a free, open, and interactive text.
- 10.21105/jose.00021 may be a valid DOI for title: CFD Python: the 12 steps to Navier-Stokes equations
- 10.3389/fmicb.2020.578600 may be a valid DOI for title: A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R
- 10.1002/bmb.21387 may be a valid DOI for title: Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education
- 10.1525/abt.2021.83.1.33 may be a valid DOI for title: Introducing Python Programming into Undergraduate Biology
INVALID DOIs
- None
The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.
citation becker_datacarpentrygenomics-workshop:2019 not found
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
IDREFS attribute rid references an unknown ID "ref-becker_datacarpentrygenomics-workshopU003A2019"
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
IDREFS attribute rid references an unknown ID "ref-becker_datacarpentrygenomics-workshopU003A2019"
@labarba any clues? I'm not at a computer now but can look into later if not resolved.
Submitting author: !--author-handle-->@nselem<!--end-author-handle-- (Nelly Selem) Repository: https://github.com/carpentries-lab/metagenomics-workshop Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@JasonJWilliamsNY<!--end-editor-- Reviewers: !--reviewers-list-->@enkera<!--end-reviewers-list-- Archive: 10.5281/zenodo.8306876 Paper kind: learning module
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
@enkera, 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 @JasonJWilliamsNY 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 @enkera
Conflict of interest
Code of Conduct
General checks
Documentation
Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)
JOSE paper
paper.md
file include a list of authors with their affiliations?