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[REVIEW]: biopixR: Extracting Insights from Biological Images #7074

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@Brauckhoff<!--end-author-handle-- (Tim Brauckhoff) Repository: https://github.com/Brauckhoff/biopixR Branch with paper.md (empty if default branch): Version: 1.1.0 Editor: !--editor-->@fabian-s<!--end-editor-- Reviewers: @ColemanRHarris, @tijeco Archive: Pending

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status

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Markdown: [![status](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68/status.svg)](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68)

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

@ColemanRHarris & @tijeco, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fabian-s 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 @tijeco

📝 Checklist for @ColemanRHarris

editorialbot commented 1 month 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
editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.06394 is OK
- 10.32614/CRAN.package.biopixR is OK
- 10.21037/jlpm.2019.04.05 is OK
- 10.1016/j.biosx.2024.100484 is OK
- 10.32614/rj-2011-002 is OK
- 10.32614/RJ-2012-018 is OK
- 10.32614/CRAN.package.countcolors is OK
- 10.21105/joss.01012 is OK
- 10.32614/CRAN.package.magick is OK
- 10.1007/978-0-387-75936-4 is OK
- 10.1109/tsmc.1973.4309314 is OK
- 10.18637/jss.v021.i05 is OK
- 10.32614/CRAN.package.cluster is OK
- 10.1007/s00604-019-3449-y is OK
- 10.1080/17425247.2016.1192122 is OK
- 10.1007/s10544-018-0314-4 is OK
- 10.1007/s00604-014-1243-4 is OK
- 10.1038/76469 is OK
- 10.1007/s11356-020-08127-2 is OK
- 10.1038/s41598-019-41136-x is OK
- 10.1021/ac103277s is OK
- 10.3390/molecules201219766 is OK
- 10.1007/s00216-019-02199-x is OK
- 10.1007/10_2011_132 is OK
- 10.21037/jlpm.2018.11.01 is OK
- 10.21037/jlpm.2018.04.10 is OK
- 10.18637/jss.v049.i09 is OK
- 10.1198/106186007X178663 is OK
- 10.32614/RJ-2015-011 is OK
- 10.5281/ZENODO.12744222 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Tcl/Tk Interface
- No DOI given, and none found for title: RStudio: Integrated Development Environment for R
- No DOI given, and none found for title: Advanced R
- No DOI given, and none found for title: ’Radiomic’ Image Processing Toolbox
- No DOI given, and none found for title: R Markdown
- No DOI given, and none found for title: foodwebr: Visualise Function Dependencies

INVALID DOIs

- None
editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1134.5 files/s, 257540.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               35            472           1159           2524
TeX                              2            161              0           1868
HTML                             1            338              5           1725
Rmd                              7            624           2084           1241
Markdown                         5            171              0            580
YAML                             2             29             18            128
CSV                              6              0              0             40
-------------------------------------------------------------------------------
SUM:                            58           1795           3266           8106
-------------------------------------------------------------------------------

Commit count by author:

   236  Brauckhoff
    70  devSJR
     2  Michael Chirico
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1986

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: GNU Lesser General Public License v3.0 (Check here for OSI approval)

editorialbot commented 1 month ago

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

fabian-s commented 1 month ago

hi @tijeco & @ColemanRHarris,

this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

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 pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7074 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. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

tijeco commented 1 month ago

Review checklist for @tijeco

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

fabian-s commented 1 month ago

@Brauckhoff
while we wait for reviewers to start working on this, please start fixing the missing DOIs the bot pointed out above.

devSJR commented 1 month ago

@editorialbot generate pdf

devSJR commented 1 month ago

Dear @fabian-s, thanks for pointing out the issue with the DOIs. We are eager to cite everything we use or refer to with state-of-the-art technologies. Therefore, we fixed most missing DOIs shortly after submission during the PRE REVIEW. It appears, that we missed a DOI for RMarkown, which I just added.

However, we fear, there is little we can do for the others, since these items have no DOI. For example:

Is this acceptable, or do you see another solution to this?

editorialbot commented 1 month ago

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

devSJR commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

ColemanRHarris commented 1 month ago

Review checklist for @ColemanRHarris

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

fabian-s commented 1 month ago

However, we fear, there is little we can do for the others, since these items have no DOI. For example:

* [foodwebr](https://github.com/lewinfox/foodwebr) is on GitHub only and

* [radiomics is archived on CRAN](https://cran.r-project.org/web/packages/radiomics/index.html). We cite radiomics because it is an R package, which allows extracting Haralick features and clusters information using Partitioning Around Medoids (PAM). However, we will remove the reference to the package since the reader is still guided to appropriate literature.

Is this acceptable, or do you see another solution to this?

@devSJR thanks, perfect!

devSJR commented 1 month ago

Just a short note. We have added a new function to the package, which didn't end up in a branch but in main. Sorry for that, we will fix that. The package submitted for review is the stable version 1.x after bug fixes (→ 1.1.0).

devSJR commented 4 weeks ago

Dear @fabian-s, @tijeco and @ColemanRHarris,

we forgot to mention that we already moved our latest commit, which caused a problem:

Just a short note. We have added a new function to the package, which didn't end up in a branch but in main. Sorry for that, we will fix that. The package submitted for review is the stable version 1.x after bug fixes (→ 1.1.0).

For the moment being, we decided to halt all pending commits of experimental new functions and new data sets, since we haven't tested them intensively in our current research. We decided it is also better not to submit anything until the review process is finished. Better than saying, “Let's commit. What could possibly go wrong?”, in my humble opinion. I hope you consent with this approach.

tijeco commented 3 weeks ago

@fabian-s , for clarity, we should be reviewing https://github.com/Brauckhoff/biopixR/tree/1880095c8bca6701b5363857f1cf4bba9738379b, corresponding to their release 1.1.0?

tijeco commented 3 weeks ago

@devSJR Could you provide clarification about contribution and authorship? The authors in the manuscript are Tim Brauckhoff, Coline Kieffer, and Stefan Rödiger. The first and last authors appear to have made contributions in the commit history. I don't see the middle author's contribution. Also, it looks like Michael Chirico contributed to the software via pull request, but I don't see them in the manuscript.

devSJR commented 3 weeks ago

Dear @tijeco, sure, I can do that.

Tim does the main programming and documentation of biopixR.

I lead this project (active project direction) and usually review the code (sometimes we even did paired programming), make contributions, fixes, and help with the documentation.

Coline Kieffer contributes the various datasets that are central to the package. For this, she prepared wet lab samples, did the imaging and subsequent insight into the data jointly with us. So to speak, she provided the oil. She also, raised issues (albeit personally in the lab or by decentralized digital messaging) and reflects part of the target audience (biologists in the wet lab). We also specifically mention her in the supplement to this paper https://zenodo.org/doi/10.5281/zenodo.12744222 on page 78 (this supplement is referenced as Brauckhoff, T., & Rödiger, S. (2024). biopixR: Extracting insights from biological images. https://doi.org/10.5281/ZENODO.12744222). You will certainly notice that there are more people mentioned. However, considering invested time and dedication, Coline certainly contributed significantly.

Michael Chirico contributed, indeed a software pull request. But truth to be told, I don't know if we should/must include him. @fabian-s, would you be so kind and tell me how to deal with this?

I hope this answers your question.

fabian-s commented 3 weeks ago

@tijeco

for clarity, we should be reviewing https://github.com/Brauckhoff/biopixR/tree/1880095c8bca6701b5363857f1cf4bba9738379b, corresponding to their release 1.1.0?

that's how i understood @devSJR 's remark, too.

fabian-s commented 3 weeks ago

@devSJR

Michael Chirico contributed, indeed a software pull request. But truth to be told, I don't know if we should/must include him. @fabian-s, would you be so kind and tell me how to deal with this?

I looked at their 2 commits, seems like very small housekeeping stuff to me. I don't think their contribs warrant a co-authorship.