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:
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Software report:
github.com/AlDanial/cloc v 1.88 T=0.18 s (379.9 files/s, 21894.5 lines/s)
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Language files blank comment code
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R 55 555 825 1376
Markdown 4 163 0 283
TeX 1 27 0 205
YAML 4 24 11 107
Dockerfile 1 11 10 53
HTML 1 1 0 15
Bourne Shell 1 1 2 8
JSON 2 0 0 2
Rmd 1 100 255 0
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SUM: 70 882 1103 2049
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1106
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/s41598-021-02545-z is OK
- 10.25225/jvb.21016 is OK
- 10.32614/RJ-2018-009 is OK
- 10.21105/joss.02948 is OK
- 10.5281/ZENODO.4317946 is OK
- 10.1007/s10109-020-00336-0 is OK
- 10.2307/1218258 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
ππΌ @jlacko, @nickbearman, @paleolimbot this is the review thread for the paper. All of our communications will happen here from now on.
All reviewers should create checklists with the JOSS requirements using the command @editorialbot generate my 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.
As you know, 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 small pull requests if needed) on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5082 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 2-4 weeks, feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use editorialbot
to set automatic reminders if you know you'll be away for a known period of time.
Given the nature of the paper, it would also be great if you can compare its functionality to previously published packages like rgugik for Polish data or tigris for the US.
Please feel free to ping me (@martinfleis) if you have any questions/concerns.
Thanks!
@jlacko I have added quite a few issues above - feel free to ask questions if they are not clear. Thanks for all of your work with this :-)
Re License https://github.com/jlacko/RCzechia/issues/55 there seems to be a conflict between CRAN's license requirements and JOSS's license requirements. Personally I would say I am fine with how @jlacko has approached this, but I would also like: a) a second opinion from another reviewer and/or b) a view from @martinfleis
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
there seems to be a conflict between CRAN's license requirements and JOSS's license requirements
This solution seems to be a standard way of dealing with the issue of having a human-readable License file JOSS requires as well as CRAN version. So I am fine with the solution. Thanks for pointing it out!
I have amended the dev version of RCzechia package for the issues raised by @nickbearman. This included update of the journal article (adding library calls to code samples). I am thankful for the comments, as they led to improvement of the package for users.
I am not sure what the usual practice is, but I would like to add @nickbearman as [rev] in package description in a future version, as I really appreciated his view.
@editorialbot generate pdf
@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 amended the dev version of RCzechia package for the issues raised by @nickbearman. This included update of the journal article (adding library calls to code samples). I am thankful for the comments, as they led to improvement of the package for users.
I am not sure what the usual practice is, but I would like to add @nickbearman as [rev] in package description in a future version, as I really appreciated his view.
Thanks @jlacko that's very kind, I really appreciate that.
@martinfleis I think I have now completed my review. Do let me know if I have missed any steps :-D
Sorry this review took me a while to get to!
As a quick summary - this package is great! Data access packages are difficult to get right but make life so much easier...I'll note that the work that the author did here is two-fold (if I understand the workflow correctly): you've both provided cleaned up data AND written the R package to access that data (in addition to providing the hosting). The package does indeed have very high test coverage and has been on CRAN for many years (which is no small feat for a package like this one with a lot of dependencies that depends on internet access being available).
I do have some high-level suggestions having maintained a few data access packages in the past. None of these are blockers on accepting this paper.
readr::read_rds("https://rczechia.jla-data.net/"Okresy-R-2021-06.rds")
. I wonder if you can lean into that a bit more (e.g., maybe printing that call or the URL when calling the function)...while calling RCzechia::okresy()
is nice for interactive use and prototyping, a straight download + read_rds()
might be more appropriate.Using okresy(version = "2023-01-01")
if this version
unspecified). You should have the freedom to update the data when you find a better way to clean it (or when sf updates and invalidates the object that you saved), and users should have a path to a stable dataset (e.g., to avoid surprises when rebuilding a paper that you wrote six months ago).R_RCZECHIA_MIRROR=file://path/to/pending/change
and run R CMD check
).Happy to follow up on any of those...just let me know!
Thank you @paleolimbot for your kind words!
Regarding the high level suggestions I have a few comments, if I may:
rds
files. Instead a generic downloader function https://github.com/jlacko/RCzechia/blob/master/R/downloader.R is implemented to concentrate the logic in a single place. It first tries to serve a locally cached copy and downloads the remote file only if required.rds
files is implemented - several versions of the files are stored on AWS in parallel, and the path is hardcoded in R code. Meaning that to access a lower version of rds
file a lower version of entire package needs to be installed.A more performant versioning of datasets is planned, but as this will require rewriting of a lot of the internal logic I am saving this idea for a future major version. What kind of helps is that the Czech admin area definitions are not changing too fast. But it definitely is high on my list for future improvements.
I really appreciate the suggestion for a configurable mirror - the benefit to debugging is obvious, especially when linked to a local (and not remote) file location. I will certainly implement this!
@jlacko I see that from the standpoint of JOSS, nothing stands in the way of moving one step closer towards acceptance. Do you want to make some other changes as per suggestions or do you consider existing version ready?
I think it would be the best to leave the article as it stands now. The short term impacts from the review process are already integrated in the development version of the package, and I will push them to CRAN shortly (hopefully with an updated citation). The more longer term impacts will require a more thorough revision of the codebase and it seems impractical to keep the article on hold for much longer.
@jlacko Cool!
Thank you @paleolimbot and @nickbearman for your reviews!
The submission is now almost ready to be published.
@jlacko the next steps you need to do now:
I can then move forward with accepting the submission.
@editorialbot check references
@editorialbot generate pdf
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/s41598-021-02545-z is OK
- 10.25225/jvb.21016 is OK
- 10.32614/RJ-2018-009 is OK
- 10.21105/joss.02948 is OK
- 10.5281/ZENODO.4317946 is OK
- 10.1007/s10109-020-00336-0 is OK
- 10.2307/1218258 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Perfect; I will do that.
The current version is tagged as v1.10.2 / https://github.com/jlacko/RCzechia/releases/tag/v1.10.2
It is listed on Zenodo as https://zenodo.org/record/7665574
The metadata on Zenodo is the same as in the article / in particular the author is me (using the same ORCID as the JOSS article) and the title is the same as of the JOSS article.
The Zenodo tagged version has DOI 10.5281/zenodo.7665574
@editorialbot set 10.5281/zenodo.7665574 as archive
Done! Archive is now 10.5281/zenodo.7665574
@editorialbot set v1.10.2 as version
Done! version is now v1.10.2
Thanks @jlacko! That is all done from my side. I am going to recommend acceptance and pass the submission to the editor in chief.
Big thanks to @nickbearman and @paleolimbot for their reviews! We couldn't run JOSS without you!
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Couldn't check the bibtex because branch name is incorrect: joss-paper
:warning: Error preparing paper acceptance.
@editorialbot set master as branch
Done! branch is now master
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
I am sorry; this is my fault - I have closed the branch; as finalized.
:wave: @openjournals/sbcs-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4008, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/s41598-021-02545-z is OK
- 10.25225/jvb.21016 is OK
- 10.32614/RJ-2018-009 is OK
- 10.21105/joss.02948 is OK
- 10.5281/ZENODO.4317946 is OK
- 10.1007/s10109-020-00336-0 is OK
- 10.2307/1218258 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@jlacko no worries, that was na easy fix :)
@martinfleis thanks for your understanding!
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
π¦π¦π¦ π Tweet for this paper π π¦π¦π¦
π¨π¨π¨ THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! π¨π¨π¨
Here's what you must now do:
Any issues? Notify your editorial technical team...
Submitting author: !--author-handle-->@jlacko<!--end-author-handle-- (Jindra Lacko) Repository: https://github.com/jlacko/RCzechia Branch with paper.md (empty if default branch): master Version: v1.10.2 Editor: !--editor-->@martinfleis<!--end-editor-- Reviewers: @nickbearman, @paleolimbot Archive: 10.5281/zenodo.7665574
Status
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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
@nickbearman & @paleolimbot, 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 @martinfleis 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
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