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[PRE REVIEW]: AgriFoodPy: a package for modelling food systems #6080

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editorialbot opened this issue Nov 21, 2023 · 52 comments
Closed

[PRE REVIEW]: AgriFoodPy: a package for modelling food systems #6080

editorialbot opened this issue Nov 21, 2023 · 52 comments
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@jsun @crvernon @kanishkan91
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pre-review Python TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Nov 21, 2023 •
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Submitting author: @jucordero (Juan P. Cordero)
Repository: https://github.com/FixOurFood/AgriFoodPy/
Branch with paper.md (empty if default branch): joss-paper
Version: v0.1.1
Editor: @crvernon
Reviewers: @kanishkan91, @jsun
Managing EiC: Kevin M. Moerman

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271"><img src="https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271/status.svg)](https://joss.theoj.org/papers/0c6438d4f2627ede5b2562b362e81271)

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

@jucordero 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Nov 21, 2023
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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (638.7 files/s, 58896.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0              0            493
Python                          13            171            289            392
Markdown                         2             43              0            199
TeX                              1              9              0            116
YAML                             2              3              4             33
-------------------------------------------------------------------------------
SUM:                            19            226            293           1233
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1133

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Failed to discover a valid open source license

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

OK DOIs

- 10.1126/science.aaq0216 is OK
- 10.5334/jors.148 is OK
- 10.5285/d6f8c045-521b-476e-b0d6-b3b97715c138 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5194/gmd-14-3007-2021 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.envsoft.2014.07.009 is INVALID because of 'https://doi.org/' prefix

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⚠️ An error happened when generating the pdf. Problem with ORCID (XXXX-XXXX-XXXX-XXXX) for Kevin Donkers. Invalid ORCID digit (X).

@Kevin-Mattheus-Moerman
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Running cloc on the main branch gives me:

github.com/AlDanial/cloc v 1.90  T=0.02 s (2351.3 files/s, 203681.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          25            678            833           1420
Markdown                         4             63              0            182
reStructuredText                 5             34             21             61
YAML                             3             10             22             51
INI                              1              7              0             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40            804            884           1777

@Kevin-Mattheus-Moerman
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@jucordero I am the AEiC on this track and here to help with initial steps. For the moment can you please try to address the DOI and paper compilation errors? ☝️

@jucordero
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@Kevin-Mattheus-Moerman thanks! I'll work on these as soon as I possible.

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My name is now @editorialbot

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

@jucordero
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@editorialbot generate pdf

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

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Five most similar historical JOSS papers:

PEFAP : Estimating the environmental footprint of food products from packaging data
Submitting author: @GustaveCoste
Handling editor: @vissarion (Active)
Reviewers: @marvinjonathcn, @simonom
Similarity score: 0.8043

SkyPy: A package for modelling the Universe
Submitting author: @rrjbca
Handling editor: @arfon (Active)
Reviewers: @cescalara, @rmorgan10
Similarity score: 0.8022

Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle
Submitting author: @barneydobson
Handling editor: @crvernon (Active)
Reviewers: @cheginit, @jlarsen-usgs
Similarity score: 0.7963

pyam: a Python Package for the Analysis and Visualization of Models of the Interaction of Climate, Human, and Environmental Systems
Submitting author: @gidden
Handling editor: @lheagy (Retired)
Reviewers: @jtmiclat, @Chilipp
Similarity score: 0.7954

epipack: An infectious disease modeling package for Python
Submitting author: @benmaier
Handling editor: @fboehm (Active)
Reviewers: @chrisvoncsefalvay, @esteinig
Similarity score: 0.7949

⚠️ 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.

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@editorialbot check references

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

OK DOIs

- 10.1126/science.aaq0216 is OK
- 10.5334/jors.148 is OK
- 10.5285/d6f8c045-521b-476e-b0d6-b3b97715c138 is OK
- 10.5281/zenodo.3946761 is OK
- 10.5194/gmd-14-3007-2021 is OK
- 10.1016/j.envsoft.2014.07.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Dec 4, 2023
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@jucordero thanks for making those changes. I will now be looking for a handling editor. Note however that many editors are busy handling other submissions. I've therefore waitlisted this submission for now. We will assign an editor as soon as one becomes available.

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Kevin-Mattheus-Moerman commented Dec 5, 2023 •
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@fraukewiese this sounds like it might be your cup of tea. However, I see you are handling several other submissions already. Do you think this submission is something you could help with once you are available? Also, let me know if we could perhaps assign it to you now, and then leave it waitlisted until you are available.

@jucordero
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@Kevin-Mattheus-Moerman Thanks!
Quick question: Is it okay to modify the .md for the paper at this stage? Some coauthors have provided updated ORCID numbers and affiliations.

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Kevin-Mattheus-Moerman commented Dec 5, 2023 •
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@jucordero Yes, that is absolutely fine. You can call @editorialbot generate pdf here in a comment to update the paper draft then as well.

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@editorialbot generate pdf

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⚠️ An error happened when generating the pdf. Author (Bob Doherty) is missing affiliation.

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@editorialbot generate pdf

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

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@editorialbot invite @dfm as editor

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Invitation to edit this submission sent!

@Kevin-Mattheus-Moerman
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@dfm do you think that your data science expertise would allow you to help edit this one?

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Or perhaps @fraukewiese?

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dfm commented Jan 12, 2024

@Kevin-Mattheus-Moerman unfortunately I can't help with this one since we have a backlog over in the AASS track too that I'll need to cover. Sorry!

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@editorialbot invite @fraukewiese as editor

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Invitation to edit this submission sent!

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Thank you for the invitation. Sounds super interesting but currently I cannot edit any additional papers before others are finished

@Kevin-Mattheus-Moerman
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@fraukewiese okay thanks for getting back to me. Would you be okay with me assigning this submission to you at this time, and that we'll leave this "waitlisted" such that you'll start once you've finished processing one of the other submissions?

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@fraukewiese do you mind if I assign this one to you now, and that you pick it up once you are ready?

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@editorialbot invite @crvernon as editor

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Invitation to edit this submission sent!

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@editorialbot assign me as editor

No problem @Kevin-Mattheus-Moerman

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Assigned! @crvernon is now the editor

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👋 @kanishkan91 - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

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kanishkan91 commented Jan 29, 2024 •
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@crvernon happy to review. Would it be ok if I returned a review in 2-3 weeks?

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@editorialbot add @kanishkan91 as reviewer

@kanishkan91 that will be fine. Thanks!

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@kanishkan91 added to the reviewers list!

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👋 @jsun - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

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👋 @dlebauer - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

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jsun commented Jan 29, 2024

@crvernon sure!

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@editorialbot add @jsun as reviewer

Thanks @jsun !

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@jsun added to the reviewers list!

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👋 - Alright @jucordero , @kanishkan91 , and @jsun- I am going to close this Pre-Review and kick off the full review which you should receive a notification for. Thanks!

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@editorialbot start review

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OK, I've started the review over in #6305.

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