[PRE REVIEW]: Tree Explorer (T-REX): Bridging Phylogenetic and Phenotypic Data for Enhanced Analysis and Interpretation

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@DamianJM<!--end-author-handle-- (Damian John Magill) Repository: https://github.com/DamianJM/T-REX Branch with paper.md (empty if default branch): main Version: v1.2 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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editorialbot commented 2 months ago

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editorialbot commented 2 months ago

:warning: An error happened when generating the pdf.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot set main as branch

editorialbot commented 2 months ago

Done! branch is now main

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot check repository

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (398.4 files/s, 99891.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2            197            208           1017
Markdown                         3             70              0            156
TeX                              1              6              0             77
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                             7            274            212           1269
-------------------------------------------------------------------------------

Commit count by author:

    19  DamianJM
     1  Damian Magill

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 885

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

editorialbot commented 2 months ago

Five most similar historical JOSS papers:

SuchTree: Fast, thread-safe computations with phylogenetic trees Submitting author: @ryneches Handling editor: @karthik (Retired) Reviewers: @giraola Similarity score: 0.7520

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SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. Submitting author: @andrewjpage Handling editor: @biorelated (Retired) Reviewers: @brainstorm Similarity score: 0.7193

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot query scope

editorialbot commented 2 months ago

Submission flagged for editorial review.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1093/bioinformatics/17.8.754 is OK
- 10.1093/molbev/msw046 is OK
- 10.1038/s41576-020-0233-0 is OK
- 10.1093/nar/gkab301 is OK
- 10.1093/molbev/msu300 is OK
- 10.1093/bioinformatics/btu033 is OK
- 10.1093/molbev/msab120 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 2 months ago

@DamianJM thanks for this resubmission, and for making some changes to address the points we raised. Below is a copy of points raised over at the original submission: https://github.com/openjournals/joss-reviews/issues/7234

The following includes some of the reasons for the rejection and other points on the paper/repository, and should be addressed in full if a future re-submission is of interest:

[x] Please study the above reference check :point_up: and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
[x] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/). -> I recommend linking to the contribution guidelines in the README/documentation.
[x] The project lacks an open source license approved by the Open Source Initiative.
[ ] Given the small size and limited functionality of the project (<1000 lines of code offering basic GUI interactions and predominantly visualizations), its relative immaturity (single developer, few commits), and poor packaging (single Python file, no license), the project doesn't meet our substantial scholarly effort criterion.

As you can see I've ticked the boxes that I think are addressed. For the remaining box, on being in scope for JOSS, I've just asked the editorial board for help (by flagging this submission for a scope query). This scope review should take about 2 weeks to complete.

We agree that having a cutoff e.g. at 1000 LOC is arbitrary, and indeed a small number of LOC could be the sign of highly elegant and optimised code that received a lot of thought/attention. And of course, the number of lines of code for a particular problem will vary from one language to another. However, at JOSS we do receive a large number of packages that are very minor in nature, and which could be <3 months of work. Such packages are often "minor utility" or single functionality packages, and are typically not in scope. Furthermore we also receive many "immature" packages (e.g. single contributor quick dump of code, no license, missing testing/documentation etc.). It can be very hard to make these scope calls, but I hope to convince you it is not solely the number of lines of code that we base our decision on. As I said, I've now asked the board for help, so my colleagues, whose expertise is closer aligned with this topic, will help judge if this work should be in scope as well. Thanks.

DamianJM commented 2 months ago

Hi @Kevin-Mattheus-Moerman,

I appreciate this comment and your rapid reconsideration of the manuscript. I can also appreciate the need for strict screening criteria with JOSS as I can imagine it would be easy to be bombarded with numerous submissions. Thank you for passing on the submission for consideration. Work on the project will continue and regardless of the outcome here I hope for some good feedback on possible improvements.

Thanks

Kevin-Mattheus-Moerman commented 1 month ago

@DamianJM just an update here. Apologies for the delay in processing the scope review. We still need a bit more time I'm afraid, I'll hope to check back in here by the end of the coming week with a conclusion.

DamianJM commented 1 month ago

@Kevin-Mattheus-Moerman thank you for the update. No problem it will take the time it takes!

Kevin-Mattheus-Moerman commented 1 week ago

@DamianJM unfortunately the editorial board has decided this work remains out of scope for JOSS. Besides the small size and the before mentioned points, the core reasons mentioned were the small size, the fact that it represents a simple GUI for visualization, and that it appears to lack a strong analysis component. In addition, given the GUI centered functionality, the work is perhaps insufficiently customizable, and it appears difficult to incorporate in a reproducible workflow.

We will now proceed to reject this submission.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot reject

editorialbot commented 1 week ago

Paper rejected.

openjournals / joss-reviews

[PRE REVIEW]: Tree Explorer (T-REX): Bridging Phylogenetic and Phenotypic Data for Enhanced Analysis and Interpretation #7271

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