Closed editorialbot closed 1 year 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
- 10.1021/acsomega.0c02564 is OK
- 10.1021/pr401264n is OK
- 10.12688/f1000research.27893.1 is OK
- 10.1093/bioinformatics/btx094 is OK
- 10.1093/nar/gkv007 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.88 T=0.21 s (468.2 files/s, 171424.8 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
JavaScript 21 2278 7436 8713
R 45 1394 2229 4807
Markdown 7 553 0 3205
CSS 15 120 176 2551
HTML 1 35 2 855
Rmd 4 173 228 252
TeX 1 13 0 72
YAML 2 1 4 53
-------------------------------------------------------------------------------
SUM: 96 4567 10075 20508
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 525
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Howdy @shahmoradi and @MohmedSoudy!
Thanks for agreeing to review this submission.
The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.
Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html
Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!
Hi @ByrumLab, Thank you for that great software package. The paper is well-written and the package is well-documented, however, I have some comments that may increase the package's feasibility and usability
HI @MohmedSoudy, Thank you for taking time to review our package.
We appreciate your time and helpful suggestions.
@shahmoradi, do you think you'll have a chance to look at this submission soon?
Apologies for my delayed response. I can respond as soon as I am back from an ongoing conference by this weekend if that is not too late.
Hi @ByrumLab Thank you for addressing my comments. For me, the paper and the package now are ready and I think it's acceptable for publication.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
I have a few comments for which I'd appreciate the authors' response before I mark the remaining items in the checklist as approved.
testthat
testing framework. Can you clarify how to run the tests? Normally, I'd expect a README file to exist in the appropriate folder that describes the steps to run the tests. covr
.Thank you @shahmoradi, we appreciate the review! We've made some changes to the package in response to your review:
The testthat
framework is very commonly used across R packages, but it does have some differences to the way tests are distributed with other software packages and languages. In general, R packages do not have their tests bundled with them, so users cannot re-run testthat
locally. See, for example, popular R packages like dplyr and ggplot2, which do not bundle their tests for distribution (that is, the tests are not in the inst/
directory). Instead, testthat
runs package tests locally during development and during automated package checking with R CMD check
. We have set up some GitHub actions to automatically run R CMD check
against the latest R releases for the Mac, Windows, and Unix/Ubuntu operating systems, with the results displayed in a badge on the GitHub README. These tests are also run when packages are submitted to CRAN, which we plan to do upon acceptance.
We have used the R package you suggested to generate a code coverage report: it can be found by clicking on the codecov badge in our README. Currently, we have ~100% test coverage.
We have added community guidelines to our README, and have included a contributor code of conduct (CODE_OF_CONDUCT.md).
We hope these changes address your concerns.
Hi @shahmoradi, I wanted to check if there are anymore concerns you would like us to address for this package?
Thanks!
Hi @shahmoradi, do you have any remaining concerns? If not, would you mind ticking the remaining boxes to let us know you're satisfied? Thanks!
@shahmoradi can you please provide an update?
Thank you for your response @ByrumLab. I am fine with the latest updates and improvements and have approved all items in the checklist.
Great, thanks!
@ByrumLab what is the software version you'd like included in this release, and do you have a DOI for the code+paper, e.g. on Zenodo?
@jmschrei This will be version 1.0.0 for the release. We currently do not have a DOI on Zenodo. Thanks.
@editorialbot set 1.0.0 as version
Done! version is now 1.0.0
@ByrumLab would you mind creating a DOI, following the instructions at https://joss.readthedocs.io/en/latest/submitting.html#the-review-process? We need one to accept the paper.
@jmschrei yes, I'll send this as soon as possible. Thanks!
@jmschrei here is the zenodo DOI: [DOI: 10.5281/zenodo.7962306]. url: "https://doi.org/10.5281/zenodo.7962306"
Thanks, @ByrumLab. Would you mind making the title and author list match the paper exactly?
@jmschrei The title and author list should now match. Thanks!
Great, thank you.
@editorialbot set 10.5281/zenodo.7962306 as archive
Done! archive is now 10.5281/zenodo.7962306
@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
@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
- 10.1021/acsomega.0c02564 is OK
- 10.1021/pr401264n is OK
- 10.12688/f1000research.27893.1 is OK
- 10.1093/bioinformatics/btx094 is OK
- 10.1093/nar/gkv007 is OK
- 10.1109/ACCESS.2020.3047588 is OK
- 10.1093/nar/gkac1040 is OK
- 10.1093/nar/gkab1038 is OK
- 10.1101/2022.08.17.503867 is OK
- 10.1101/2022.06.07.494524 is OK
MISSING DOIs
- None
INVALID DOIs
- https://doi.org/10.1002/bies.201800042 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/pmic.202100103 is INVALID because of 'https://doi.org/' prefix
@ByrumLab would you mind fixing these two invalid DOIs?
@jmschrei I just committed changes to fix the invalid doi references to the main branch.
@jmschrei @ByrumLab I just noticed that my name is incorrectly formatted in the proof as "II Michael S. Robeson" and it should be "Michael S. Robeson II". I'll see if I can fix ASAP.
Author name has been fixed and committed. :-)
Thanks!
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Fixed affiliation 2 from "Biomedical Imaging" to "Biomedical Informatics". Committed changes.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Submitting author: !--author-handle-->@ByrumLab<!--end-author-handle-- (Stephanie D. Byrum) Repository: https://github.com/ByrumLab/proteoDA Branch with paper.md (empty if default branch): main Version: 1.0.0 Editor: !--editor-->@jmschrei<!--end-editor-- Reviewers: @shahmoradi, @MohmedSoudy Archive: 10.5281/zenodo.7962306
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
@shahmoradi & @MohmedSoudy, 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 @jmschrei 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 @shahmoradi