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[PRE REVIEW]: Pylinac: Image analysis for routine quality assurance in radiotherapy #5980

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editorialbot opened this issue Oct 24, 2023 · 28 comments
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pre-review Python TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Oct 24, 2023

Submitting author: @jrkerns (James Kerns)
Repository: https://github.com/jrkerns/pylinac
Branch with paper.md (empty if default branch): joss_paper
Version: 3.16
Editor: @kellyrowland
Reviewers: @ProfLeao, @SimonBiggs
Managing EiC: Kevin M. Moerman

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status

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HTML: <a href="https://joss.theoj.org/papers/fbef391df8cf35d0a374003fc25952b2"><img src="https://joss.theoj.org/papers/fbef391df8cf35d0a374003fc25952b2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fbef391df8cf35d0a374003fc25952b2/status.svg)](https://joss.theoj.org/papers/fbef391df8cf35d0a374003fc25952b2)

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

@jrkerns 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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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 Oct 24, 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=0.35 s (384.5 files/s, 162678.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          83           5316           7355          29759
reStructuredText                30           3932           3070           6005
YAML                             7             24             21            496
TeX                              1              0              0            374
HTML                             8             64              0            280
DOS Batch                        1             34              2            227
make                             1             30              6            156
SVG                              1              9              0            133
Markdown                         3             40              0            132
TOML                             1              8              1             69
-------------------------------------------------------------------------------
SUM:                           136           9457          10455          37631
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1012

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

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Five most similar historical JOSS papers:

PyMedPhys: A community effort to develop an open, Python-based standard library for medical physics applications
Submitting author: @Matthew-Jennings
Handling editor: @osorensen (Active)
Reviewers: @ProfLeao, @gbaltz
Similarity score: 0.8468

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.8431

PyLithics: A Python package for stone tool analysis
Submitting author: @JasonGellis
Handling editor: @Nikoleta-v3 (Active)
Reviewers: @MichaelHoltonPrice, @steko
Similarity score: 0.8415

Pyoints: A Python package for point cloud, voxel and raster processing.
Submitting author: @laempy
Handling editor: @lheagy (Retired)
Reviewers: @kbevers, @scivision
Similarity score: 0.8340

The Vascular Modeling Toolkit: A Python Library for the Analysis of Tubular Structures in Medical Images
Submitting author: @rlizzo
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @wouterpotters, @brainstorm
Similarity score: 0.8312

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

@Kevin-Mattheus-Moerman
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@jrkerns I am the AEiC on this track and here to help with initial steps. I will be looking for a handling editor next. Note however we have a bit of a backlog and many editors are currently preoccupied with other submissions. Hence it may take a bit longer than usual to find a handling editor.

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@editorialbot invite @AJQuinn as editor

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Invitation to edit this submission sent!

@Kevin-Mattheus-Moerman
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@AJQuinn this may be a bit off topic, but do you think you can help edit this one?

@kellyrowland
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@Kevin-Mattheus-Moerman I could edit this if needed.

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@editorialbot set @kellyrowland as editor

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

@editorialbot commands

@Kevin-Mattheus-Moerman
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@editorialbot assign @kellyrowland as editor

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Assigned! @kellyrowland is now the editor

@kellyrowland
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hi @jrkerns do you have any suggested reviewers for this submission? if not, I can ping some folks from our reviewer list.

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jrkerns commented Oct 30, 2023

There are people I can think of but they are co-workers or past co-workers, so I'd assume that's a conflict of interest? Otherwise, no, sorry!

@kellyrowland
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no worries, I'll ping some folks from our volunteers list.

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hi @ProfLeao @SimonBiggs 👋 would you be available for and interested in reviewing this JOSS submission?

@ProfLeao
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Yes, I can!

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@editorialbot add @ProfLeao to reviewers

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@ProfLeao added to the reviewers list!

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@editorialbot commands

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Hello @ProfLeao, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

@SimonBiggs
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Hi @kellyrowland,

I absolutely also can :) (I am also familiar with the library, so can probably review quite quickly)

@kellyrowland
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@editorialbot add @SimonBiggs to reviewers

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@SimonBiggs added to the reviewers list!

@kellyrowland
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@editorialbot start review

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OK, I've started the review over in #6001.

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