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

[editorialbot]

Submitting author: @JeffreyMinucci (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

Status

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[editorialbot]

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]

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]

Paper file info:

📄 Wordcount for paper.md is 720

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[arfon]

@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]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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[kthyng]

@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]

@editorialbot reject

[editorialbot]

Paper rejected.

[JeffreyMinucci]

@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:

• This software makes the BeePop+ model developed by the US Environmental Protection Agency and US Department of Agriculture widely available and accessible to the scientific community, government regulators and the public for the first time. The pybeepop+ package will be the primary way that US EPA scientists install and interact with the underlying model to support regulation of pesticides and protection of pollinators. Therefore, it is of great public interest that the software and accompanying paper receive rigorous peer review.
• The software (in an early version) has already been used and cited in two scientific publications from the US EPA, with at least one other in prep and several more studies on the horizon: paper 1 paper 2. This demonstrates that it has substantial utility to advance research and shape regulatory decisions.
• The software is more than a 'thin API client' or similar because it includes features not available in the underlying C++ interface: multiple output formats (DataFrame, JSON), validation of parameters, informative error messages, API documentation, tests, example notebooks and automated installation of BeePop+ for a wider range of systems via Python wheels and pre-compilation of BeePop+ on many platforms (implemented via GitHub CIs).
• The software is over 1000 lines of code with CSV files removed, which is the number cited on the Submitting a paper to JOSS article as the cutoff for flagging.

Thank you for your further consideration.

[kthyng]

@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
-------------------------------------------------------------------------------