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[REVIEW]: bleiglas: An R package for interpolation and visualisation of spatiotemporal data with 3D tessellation #3092

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @nevrome (Clemens Schmid) Repository: https://github.com/nevrome/bleiglas Version: 1.0.0 Editor: @vissarion Reviewer: @corybrunson , @fabian-s Archive: 10.17605/OSF.IO/AGMD6

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Status

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Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/4c33bb2047fb2a38c642bf861d6ece87/status.svg)](https://joss.theoj.org/papers/4c33bb2047fb2a38c642bf861d6ece87)

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

@corybrunson & @fabian-s, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @vissarion 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 @corybrunson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @fabian-s

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @corybrunson , @fabian-s it looks like you're currently assigned to review this paper :tada:.

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whedon commented 3 years ago

Failed to discover a Statement of need section in paper

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (271.8 files/s, 27070.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               19            200            297            975
Markdown                         2             90              0            449
Rmd                              2            111            209            178
JSON                             1              0              0            172
C++                              3             30             30            155
TeX                              1              0              0            121
C                                1              5              5             20
YAML                             1              0              2             19
C/C++ Header                     1              4              2             14
-------------------------------------------------------------------------------
SUM:                            31            440            545           2103
-------------------------------------------------------------------------------

Statistical information for the repository '0fe783203955437192eb8bc8' was
gathered on 2021/03/08.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Clemens Schmid                  11           591            326          100.00

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
Clemens Schmid              265           44.8          0.8               13.96
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.3215722 is OK
- 10.1038/s41598-020-58834-6 is OK
- 10.1016/j.compenvurbsys.2019.101357 is OK
- 10.1093/mnras/staa1379 is OK
- 10.1007/978-3-319-29538-1 is OK
- 10.7287/peerj.preprints.3188v1 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1177/1059712319860842 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

:wave: @fabian-s, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @corybrunson , please update us on how your review is going (this is an automated reminder).

corybrunson commented 3 years ago

Update on my review: I've test-run the software and will review the documentation and paper this week. I've been creating issues on the repo and will post here when i finish—with any additional comments not made in the issues.

fabian-s commented 3 years ago

Current status: I've openend some (minor) issues, waiting for them to be resolved.

vissarion commented 3 years ago

@corybrunson @fabian-s thank you both for the updates!

nevrome commented 3 years ago

@vissarion As the author of the software I thought I would wait with fixing/addressing the raised issues until the first round of review is complete. Thanks already for your very valuable feedback, @corybrunson and @fabian-s!

corybrunson commented 3 years ago

@nevrome that is OK with me! Though it's also OK (and common, in my experience) for the developers to address the issues in an ongoing way. Usually the issues are modular enough that this doesn't cause confusion. But it could also be done in a separate branch just in case.

corybrunson commented 3 years ago

@vissarion should the two "statement of need" requirements in the reviewer checklist be interchanged? The one in the "software paper" section reads like it refers to the documentation, and vice-versa. And could you confirm that a statement of need is indeed expected in both places? Thank you!

corybrunson commented 3 years ago

@vissarion I have completed my initial review. @nevrome this package was well-organized and straightforward to evaluate, and the paper was concise and clearly written, for all of which i thank you! All of the issues i identified have been mentioned in issues, either my own or (often) those by @fabian-s before me. I'll be available to answer follow-up questions and will complete my review checklist as the issues are addressed.

vissarion commented 3 years ago

@vissarion should the two "statement of need" requirements in the reviewer checklist be interchanged? The one in the "software paper" section reads like it refers to the documentation, and vice-versa. And could you confirm that a statement of need is indeed expected in both places? Thank you!

It makes sense to ask for a statement of need both in the documentation and in the JOSS paper but I agree that the text in the checklist should be changed. Of course this would not affect the current review process. I propose to threat each "statement of need" check boxes separately, i.e. one for documentation and one for the paper. Thanks for mentioning this @corybrunson.

fabian-s commented 3 years ago

As far as I'm concerned, this is good to go now.

corybrunson commented 3 years ago

@vissarion My concerns have been addressed and i recommend acceptance of the package and manuscript.

[Edit: Upon merge of the joss_review branch into master.]

vissarion commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

vissarion commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.3215722 is OK
- 10.1038/s41598-020-58834-6 is OK
- 10.1016/j.compenvurbsys.2019.101357 is OK
- 10.1093/mnras/staa1379 is OK
- 10.1007/978-3-319-29538-1 is OK
- 10.7287/peerj.preprints.3188v1 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1177/1059712319860842 is OK

MISSING DOIs

- 10.21105/joss.01096 may be a valid DOI for title: ggvoronoi: Voronoi Diagrams and Heatmaps with ’ggplot2’

INVALID DOIs

- None
vissarion commented 3 years ago

@nevrome there are some minor issues in your bibliography, see https://github.com/nevrome/bleiglas/issues/17

nevrome commented 3 years ago

@vissarion Thanks for the suggestions!

I created a PR to address these small, final proofreading changes: https://github.com/nevrome/bleiglas/pull/18

I also wait for final approval by @stschiff, which might take until after the Easter holidays.

nevrome commented 3 years ago

I believe everything is ready to go now - thank you for your patience!

vissarion commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #3092 with the following error:

Error producing PDF. ! Argument of \caption@ydblarg has an extra }.

\par l.558 project}.\label{fig:plot_map}} Looks like we failed to compile the PDF
vissarion commented 3 years ago

@nevrome it seems there is an issue with your PDF (see message above). Please fix and run @whedon generate pdf to be sure there are not issues left.

nevrome commented 3 years ago

Oh - I think I have an idea where this might be coming from.

nevrome commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

vissarion commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.3215722 is OK
- 10.1038/s41598-020-58834-6 is OK
- 10.1016/j.compenvurbsys.2019.101357 is OK
- 10.1093/mnras/staa1379 is OK
- 10.1007/978-3-319-29538-1 is OK
- 10.7287/peerj.preprints.3188v1 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1177/1059712319860842 is OK
- 10.21105/joss.01096 is OK

MISSING DOIs

- None

INVALID DOIs

- None
vissarion commented 3 years ago

Thanks @nevrome the submission is ready to be accepted.

Could you please make a tagged release and archive (using for example Zenodo or figshare), and report the version number and archive DOI here?

nevrome commented 3 years ago

Release: https://github.com/nevrome/bleiglas/releases/tag/1.0.0 DOI: https://doi.org/10.17605/OSF.IO/AGMD6

vissarion commented 3 years ago

Release: https://github.com/nevrome/bleiglas/releases/tag/1.0.0 DOI: https://doi.org/10.17605/OSF.IO/AGMD6

Thanks. I am checking the metadata of the archive and the list of authors is not the same as in the submitted paper. Could you please update?

stschiff commented 3 years ago

Hi all. I have just created an OSF account and I see myself being listed. Seems all good.

stschiff commented 3 years ago

And thanks to @vissarion and @corybrunson for your careful review!

corybrunson commented 3 years ago

@stschiff and to @fabian-s! The review credits are at the top of the thread in case you missed them there.

vissarion commented 3 years ago

@whedon set https://doi.org/10.17605/OSF.IO/AGMD6 as archive

whedon commented 3 years ago

OK. 10.17605/OSF.IO/AGMD6 is the archive.

vissarion commented 3 years ago

@whedon set 1.0.0 as version

whedon commented 3 years ago

OK. 1.0.0 is the version.

vissarion commented 3 years ago

@whedon accept

whedon commented 3 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1063/1.3215722 is OK
- 10.1038/s41598-020-58834-6 is OK
- 10.1016/j.compenvurbsys.2019.101357 is OK
- 10.1093/mnras/staa1379 is OK
- 10.1007/978-3-319-29538-1 is OK
- 10.7287/peerj.preprints.3188v1 is OK
- 10.32614/RJ-2018-009 is OK
- 10.1177/1059712319860842 is OK
- 10.21105/joss.01096 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 3 years ago

: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/2214

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2214, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
vissarion commented 3 years ago

Thanks @stschiff and @nevrome for your cooperation here!

This is an interesting use case of computational geometry to archeology and I believe the package will be of use by practitioners on that or related fields.

I would like to thank again @corybrunson and @fabian-s for the careful reviews!

I have already recommended acceptance.

At this point, some EiC will take over to make final checks and publish the paper.

nevrome commented 3 years ago

Excellent! Thank you for managing this whole process, @vissarion!

danielskatz commented 3 years ago

@nevrome - As AEiC on duty currently, I've proofread the paper, and have made some suggestions in https://github.com/nevrome/bleiglas/pull/20 Please merge this or let me know what you disagree with, and we can proceed to acceptance and publication.

danielskatz commented 3 years ago

@whedon accept