Closed editorialbot closed 3 months ago
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=0.06 s (659.0 files/s, 223895.7 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 13 1226 1167 3746
JSON 3 0 0 3452
CSS 2 322 53 1938
CSV 4 1 0 581
Markdown 5 164 0 270
TOML 2 45 12 239
HTML 2 54 13 143
JavaScript 3 40 28 118
TeX 1 9 0 85
make 2 37 26 78
YAML 2 11 4 64
DOS Batch 1 0 0 2
SVG 1 0 0 1
-------------------------------------------------------------------------------
SUM: 41 1909 1303 10717
-------------------------------------------------------------------------------
Commit count by author:
211 Istvan Albert
2 aswathy
Paper file info:
π Wordcount for paper.md
is 844
β
The paper includes a Statement of need
section
License info:
β
License found: MIT License
(Valid open source OSI approved license)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@sridhar0605 and @j-andrews7 - Thank you for agreeing to review this submission.
This is the review thread for the paper. All of our communications will happen here from now on.
As mentioned above, you can use the command @editorialbot generate my checklist to create your review checklist. 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 (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html)
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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6624 so that a link is created to this thread for visibility. 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 2-4 weeks. Please let me know if you require additional time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period.
Please feel free to ping me (@mahfuz05062) if you have any questions/concerns.
I've done a first pass review detailed more thoroughly in the project's issue tracker. It's generally in pretty good shape, and I expect Istvan will have little trouble addressing most of my points.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@j-andrews7 @sridhar0605
Based on reviewer suggestions, the software has been rewritten to be deployed as Shiny app and is now also available at
A few minor alterations were made to the paper, citing Networkx and Shiny, additional screenshot of the Shiny interface was also added. All other suggestions were addressed. (See PDF above for updated paper).
Additional genomes were also added to the default distribution.
I see that the reviews are going well. Please feel free to ask any questions that may arise!
Istvan has addressed all of my (relatively minor) concerns, and I consider my review complete.
@sridhar0605 Hey Shridar, would you mind finishing your review? It seems the process is waiting for you to finalize it.
@sridhar0605 Please let us know if anything is blocking you or if you need any assistance.
@sridhar0605 @j-andrews7 all issues brought up by reviewers have been addressed, the interface has been reworked to Shiny app, and the app went through numerous iterations regarding the user interface elements and reporting.
@sridhar0605 Please let us know if anything is blocking you or if you need any assistance.
@ialbert has addressed all the issues that were raised by me.
@sridhar0605 if you are satisfied with it, can you also mark the reproducibility tab? I will then go over the updated submission and take the next steps.
@mahfuz05062 Done.
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@sridhar0605 and @j-andrews7 , thank you for completing your reviews.
@ialbert can you make sure to complete the post-review tasks from above? Thanks!
@mahfuz05062 ok, I am planning to make a new software release for the paper, so will be doing that in a few days and tag here when done
@mahfuz05062 Checklist completed.
Software release: 1.0.4
Zenodo DOI for the software: 10.5281/zenodo.11245263
Thank you reviewers @j-andrews7 @sridhar0605 for the suggestions. The software is now so much more usable.
Thanks @ialbert . I will go through my list and take the next steps
@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 set v1.0.4 as version
Done! version is now v1.0.4
@editorialbot set 10.5281/zenodo.11245263 as archive
Done! archive is now 10.5281/zenodo.11245263
@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
- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK
MISSING DOIs
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: shiny: Web Application Framework for R
INVALID DOIs
- None
@ialbert - please change the title of your zenodo deposit to match the title of the paper. This is a change of metadata only, which doesn't require a new deposit or new DOI.
@mahfuz05062 ok, done, zenodo deposit title matches the paper.
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK
MISSING DOIs
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: shiny: Web Application Framework for R
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.
@editorialbot set 10.5281/zenodo.11245264 as archive
Done! archive is now 10.5281/zenodo.11245264
@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 recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK
MISSING DOIs
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: shiny: Web Application Framework for R
INVALID DOIs
- None
:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.
Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.
Submitting author: !--author-handle-->@ialbert<!--end-author-handle-- (Istvan Albert) Repository: https://github.com/ialbert/genescape-central Branch with paper.md (empty if default branch): Version: v1.0.4 Editor: !--editor-->@mahfuz05062<!--end-editor-- Reviewers: @sridhar0605, @j-andrews7 Archive: 10.5281/zenodo.11245264
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
@sridhar0605 & @j-andrews7, 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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mahfuz05062 know.
β¨ 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 β¨
Checklists
π Checklist for @j-andrews7
π Checklist for @sridhar0605