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[PRE REVIEW]: pybeepop+: A Python wrapper for the BeePop+ honey bee colony model #7335

Closed editorialbot closed 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@JeffreyMinucci<!--end-author-handle-- (Jeffrey Minucci) Repository: https://github.com/USEPA/pybeepop Branch with paper.md (empty if default branch): Version: v0.1.1 Editor: Pending Reviewers: Pending Managing EiC: Arfon Smith

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Markdown: [![status](https://joss.theoj.org/papers/f012d5fd9b575eecf46b9ba296cf39cb/status.svg)](https://joss.theoj.org/papers/f012d5fd9b575eecf46b9ba296cf39cb)

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Thanks for submitting your paper to JOSS @JeffreyMinucci. Currently, there isn't a JOSS editor assigned to your paper.

@JeffreyMinucci if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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editorialbot commented 1 month ago

Hello human, 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

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1060.5 files/s, 114711.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           5             74            129            404
CSV                              2              0              0            226
YAML                             6             29             25            220
Markdown                         2             73              0            177
TeX                              1             13              0            149
TOML                             1              6              0             62
Jupyter Notebook                 1              0            329             31
-------------------------------------------------------------------------------
SUM:                            18            195            483           1269
-------------------------------------------------------------------------------

Commit count by author:

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

✅ OK DOIs

- 10.5281/zenodo.6856426 is OK
- 10.1002/ece3.1293 is OK
- 10.1016/j.tim.2011.09.003 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1098/rspb.2020.0922 is OK
- 10.1126/science.aaa1190 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Dask: Library for dynamic task scheduling
- No DOI given, and none found for title: The population dynamics of varroa mites in honey b...
- No DOI given, and none found for title: Simulating the effects of pesticides on honey bee ...
- No DOI given, and none found for title: BEEPOP+

❌ MISSING DOIs

- 10.1126/science.1255957 may be a valid DOI for title: Bee declines driven by combined stress from parasi...
- 10.1093/bioinformatics/bty361 may be a valid DOI for title: pyABC: distributed, likelihood-free inference
- 10.1016/j.ecolmodel.2018.02.010 may be a valid DOI for title: Sensitivity analyses for simulating pesticide impa...
- 10.1002/eap.2442 may be a valid DOI for title: Inferring pesticide toxicity to honey bees from a ...
- 10.1111/gcb.17219 may be a valid DOI for title: Advances and knowledge gaps on climate change impa...

❌ INVALID DOIs

- None
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 720

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

arfon commented 1 month ago

@JeffreyMinucci – due to the relatively small size of this code and the fact it looks like an API/library wrapper, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. We should get back to you sometime next week. If you want to fix the DOIs (noting that @editorialbot's suggestions are not always right), you can, then use the following commands (one at a time, as the first line of a new comment) to regenerate the PDF and check the references.

@editorialbot generate pdf @editorialbot check references

arfon commented 1 month ago

@editorialbot query scope

editorialbot commented 1 month ago

Submission flagged for editorial review.

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:

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

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⚠️ 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.

kthyng commented 1 month ago

@JeffreyMinucci Thanks again for your submission. Unfortunately the JOSS editorial board has determined that it is too small in scope to pass for substantial scholarly effort. However, note that if you were to expand the functionality of your library quite a bit over time, you could consider submitting to JOSS again in the future.

Alternatively, there are other ways to publish your software now we can suggest, notes here: https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages.

Thanks for your interest in JOSS.

kthyng commented 1 month ago

@editorialbot reject

editorialbot commented 1 month ago

Paper rejected.

JeffreyMinucci commented 1 month ago

@kthyng @arfon I thank the editorial board for their review. Respectfully, am I able to appeal this decision?

I would like to provide additional rationale that this work represents significant scholarly effort:

Thank you for your further consideration.

kthyng commented 1 month ago

@JeffreyMinucci I agree with you on many of your points, them feeding into the reason JOSS exists and that we put our time into it. However, we also have to have a lower bound for enough effort and it gets into the nitty gritty at some point. We count the Python lines of code but not the other bits as being related to docs, workflows, etc, rather than fundamental code. Therefore we see your package as 404 LOC, not 1000. We also look at how long a project has been under development and want a minimum of 3 months, which this is just over. All of this pushes in the same direction. However, I'd still like to see it resubmitted if there is more, useful functionality that would make sense for you or your team to add over time. Thanks again.

github.com/AlDanial/cloc v 1.90  T=0.02 s (1060.5 files/s, 114711.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           5             74            129            404
CSV                              2              0              0            226
YAML                             6             29             25            220
Markdown                         2             73              0            177
TeX                              1             13              0            149
TOML                             1              6              0             62
Jupyter Notebook                 1              0            329             31
-------------------------------------------------------------------------------
SUM:                            18            195            483           1269
-------------------------------------------------------------------------------