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[PRE REVIEW]: CAD_to_OpenMC: from CAD design to particle transport #7369

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editorialbot opened this issue Oct 18, 2024 · 45 comments
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editorialbot commented Oct 18, 2024

Submitting author: @ebknudsen (Erik B Knudsen)
Repository: https://www.github.com/openmsr/CAD_to_OpenMC
Branch with paper.md (empty if default branch): paper_joss
Version: v1.0.0
Editor: @mbarzegary
Reviewers: @nasserma, @jacobmerson, @bonh
Managing EiC: Kyle Niemeyer

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HTML: <a href="https://joss.theoj.org/papers/fc9555a355e3d399303a371bfce633f5"><img src="https://joss.theoj.org/papers/fc9555a355e3d399303a371bfce633f5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fc9555a355e3d399303a371bfce633f5/status.svg)](https://joss.theoj.org/papers/fc9555a355e3d399303a371bfce633f5)

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

@ebknudsen 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: 3 (PE) Physics and Engineering labels Oct 18, 2024
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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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Checking the BibTeX entries failed with the following error:

No paper file path

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⚠️ An error happened when generating the pdf. Paper file not found.

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1250.2 files/s, 116908.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30            439            433           2758
Markdown                         2             45              0            202
YAML                             4             10              3            148
TOML                             1              2              0             33
reStructuredText                 4             19             11             31
DOS Batch                        1              8              1             26
XML                              1              0              0             17
make                             1              4              7              9
INI                              1              0              0              2
-------------------------------------------------------------------------------
SUM:                            45            527            455           3226
-------------------------------------------------------------------------------

Commit count by author:

   619	Erik B Knudsen
    48	erkn
     8	LukeLabrie
     3	dependabot[bot]
     2	Jonathan Shimwell
     2	Stephen Coleman
     1	Daniel Kozma
     1	Luke Labrie-Cleary

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Paper file info:

⚠️ Failed to find a paper file in https://www.github.com/openmsr/CAD_to_OpenMC

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License info:

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

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Hi @ebknudsen, we will use this issue to assign an editor and find reviewers; any recommendations for the latter would be welcome (though please do not invite/tag them yourself).

Unfortunately, our editors in this area already have a full load of assignments, so I have to place this in our backlog until someone becomes available.

@kyleniemeyer kyleniemeyer added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Oct 18, 2024
@ebknudsen
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ebknudsen commented Nov 22, 2024

Getting back to this with a somewhat silly question: For any suggestions for reviewer, should I just put them here?

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@ebknudsen yes, you can just share some names here, but do not tag them directly with @ (the editor will reach out)

@ebknudsen
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Allright: Here are a few suggestions:
Amalia Chambon, Physics Dept. DTU
Garret Granroth, ORNL
Paul Wilson, U. Wisconsin at Madison
Gunter Muhrer, European Spallation Source

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@editorialbot assign me as editor

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Assigned! @mbarzegary is now the editor

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@editorialbot generate pdf

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⚠️ An error happened when generating the pdf. Paper file not found.

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Wait! Is there any JOSS paper here in this submission?
@ebknudsen

@ebknudsen
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I certainly thought so... if not something must have gone haywire. I'll look into the matter ASAP.

@ebknudsen
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I think I have been confused by repos - the paper lives here: https://github.com/ebknudsen/c2omc_joss
I will have to look through the docs again to see what I need to do in order to make it available to you.

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Hello @ebknudsen, 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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# 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

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@editorialbot set joss-paper as branch

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Done! branch is now joss-paper

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@editorialbot generate pdf

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@editorialbot set paper_joss as branch

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Done! branch is now paper_joss

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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:

model-traits: Model attribute definitions for scientific simulations in C++
Submitting author: @jacobmerson
Handling editor: @diehlpk (Active)
Reviewers: @daniellivingston, @pratikvn
Similarity score: 0.6859

BasicTools: a numerical simulation toolbox
Submitting author: @fbordeu
Handling editor: @diehlpk (Active)
Reviewers: @hvonwah, @sthavishtha
Similarity score: 0.6844

OpenCMP: An Open-Source Computational Multiphysics Package
Submitting author: @nasserma
Handling editor: @lucydot (Active)
Reviewers: @bonh, @WilkAndy
Similarity score: 0.6799

feign: a Python package to estimate geometric efficiency in passive gamma spectroscopy measurements of nuclear fuel
Submitting author: @ezsolti
Handling editor: @katyhuff (Retired)
Reviewers: @kellyrowland, @sskutnik
Similarity score: 0.6763

Efficient Polyhedral Gravity Modeling in Modern C++ and Python
Submitting author: @schuhmaj
Handling editor: @dfm (Active)
Reviewers: @mikegrudic, @santisoler
Similarity score: 0.6673

⚠️ 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

- 10.1016/j.fusengdes.2010.05.030 is OK
- 10.1016/j.net.2024.01.052 is OK
- 10.1145/3272127.3275006 is OK
- 10.1016/S0168-9002(03)01368-8 is OK
- 10.2172/1889957 is OK
- 10.1016/j.nds.2014.07.049 is OK
- 10.2172/4237975 is OK
- 10.1016/j.anucene.2012.06.040 is OK
- 10.1051/epjconf/202023918002 is OK
- 10.1787/7e0ebc50-en is OK
- 10.1080/00295639.2021.1947103 is OK
- 10.3769/radioisotopes.56.497 is OK
- 10.1080/00223131.2015.1062812 is OK
- 10.1016/j.nucengdes.2021.111381 is OK
- 10.1016/j.pnucene.2006.07.005 is OK
- 10.1107/S0021889813007991 is OK
- 10.1145/2487228.2487235 is OK
- 10.1145/2487228.2487235 is OK
- 10.1107/S0021889813007991 is OK
- 10.1016/j.pnucene.2006.07.005 is OK
- 10.1016/j.nucengdes.2021.111381 is OK
- 10.1080/00223131.2015.1062812 is OK
- 10.3769/radioisotopes.56.497 is OK
- 10.1080/00295639.2021.1947103 is OK
- 10.1787/7e0ebc50-en is OK
- 10.1051/epjconf/202023918002 is OK
- 10.1145/2487228.2487235 is OK
- 10.1107/S0021889813007991 is OK
- 10.1016/j.pnucene.2006.07.005 is OK
- 10.1016/j.nucengdes.2021.111381 is OK
- 10.1080/00223131.2015.1062812 is OK
- 10.3769/radioisotopes.56.497 is OK
- 10.1080/00295639.2021.1947103 is OK
- 10.1787/7e0ebc50-en is OK
- 10.1051/epjconf/202023918002 is OK
- 10.1016/j.anucene.2012.06.040 is OK
- 10.2172/4237975 is OK
- 10.1016/j.nds.2014.07.049 is OK
- 10.2172/1889957 is OK
- 10.1016/S0168-9002(03)01368-8 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Zur Theori der Interferenzen der Röntgenstrahlen i...
- No DOI given, and none found for title: Benchmark for Neutronic Analysis of Sodium-cooled ...
- No DOI given, and none found for title: Benchmark for Neutronic Analysis of Sodium-cooled ...
- No DOI given, and none found for title: Highly birefringent index-guiding photonic crystal...
- No DOI given, and none found for title: Macro-bending loss properties of photonic crystal ...
- No DOI given, and none found for title: High-birefringent photonic crystal fiber
- No DOI given, and none found for title: Photonic crystal fiber modelling and applications
- No DOI given, and none found for title: Crystal fibre technology
- No DOI given, and none found for title: Coupling to photonic crystal fibers
- No DOI given, and none found for title: Mapping grains and their dynamics in three dimensi...
- No DOI given, and none found for title: Photonic Crystal Fibres-the State-of-the-Art
- No DOI given, and none found for title: Component Manual for the Neutron Ray-Tracing Packa...
- No DOI given, and none found for title: Cut-off properties of index-guiding photonic cryst...
- No DOI given, and none found for title: Optical waveguide, method of its production, and i...
- No DOI given, and none found for title: Micro-structured optical fiber
- No DOI given, and none found for title: Modeling photonic crystal fibers with localized fu...
- No DOI given, and none found for title: User and programmers guide to the x-ray-tracing pa...
- No DOI given, and none found for title: Modelling of photonic crystal fibres
- No DOI given, and none found for title: Users’ and Programmers’ Guide to the X-ray tracing...
- No DOI given, and none found for title: McXtrace: a Monte Carlo software package for simul...
- No DOI given, and none found for title: McXtrace-An X-ray Monte Carlo Ray-tracing software...
- No DOI given, and none found for title: ESS technical design report
- No DOI given, and none found for title: Component Manual for the Xray-Tracing Package McXt...
- No DOI given, and none found for title: Simulation and modeling of silicon pore optics for...
- No DOI given, and none found for title: McXtrace 1.4: latest developments in the new relea...
- No DOI given, and none found for title: A Monte Carlo simulation of scattering reduction i...
- No DOI given, and none found for title: Monte Carlo Ray Tracing of Scanning Coherent Diffr...
- No DOI given, and none found for title: Coherent X-ray Diffractive Imaging Simulated by Mo...
- No DOI given, and none found for title: Sådan får vi en (endnu) bedre læreruddannelse
- No DOI given, and none found for title: Simulating the optical performances of the ATHENA ...
- No DOI given, and none found for title: Optical simulations for design, alignment, and per...
- No DOI given, and none found for title: Three dimensional polarimetric neutron tomography-...
- No DOI given, and none found for title: McXtrace anno 2020-complex sample geometries and G...
- No DOI given, and none found for title: Magic Analyzer Simulation Report
- No DOI given, and none found for title: Simulations of foil-based spin-echo (modulated) sm...
- No DOI given, and none found for title: Iridium thin-film coatings for the BabyIAXO hybrid...
- No DOI given, and none found for title: AstroX/McXtrace 2021: an update on simulation exam...
- No DOI given, and none found for title: Effect of mirror curvature on the angular resoluti...
- No DOI given, and none found for title: Modelling diffractive effects in silicon pore opti...
- No DOI given, and none found for title: The effect of mirror curvature and wedging on the ...
- No DOI given, and none found for title: Real-time imaging of acoustic waves in bulk materi...
- No DOI given, and none found for title: International Tables for Crystallography (2019). V...
- No DOI given, and none found for title: Photon. Technol. Lett.
- No DOI given, and none found for title: Simultaneous bright-and dark-field X-ray microscop...
- No DOI given, and none found for title: Benchmark for Neutronic Analysis of Sodium-cooled ...
- No DOI given, and none found for title: Zur Theori der Interferenzen der Röntgenstrahlen i...
- No DOI given, and none found for title: Industrial automation systems and integration—Prod...
- No DOI given, and none found for title: OCCT3D Collaborative development portal
- No DOI given, and none found for title: MSRE Design and Operations Report, Part I, Descrip...

❌ MISSING DOIs

- 10.2172/1463583 may be a valid DOI for title: Updating the GODIVA-IV benchmark
- 10.2172/877507 may be a valid DOI for title: FLUKA: a multi-particle transport code
- 10.1107/s002188980601939x may be a valid DOI for title: A discrete tomography algorithm for improving the ...
- 10.1109/jlt.2003.808668 may be a valid DOI for title: Quantitative estimates of mode coupling and differ...
- 10.1049/ip-opt:20020713 may be a valid DOI for title: Spectral macro-bending loss considerations for pho...
- 10.1107/s0021889807001288 may be a valid DOI for title: A stochastic algorithm for reconstruction of grain...
- 10.4028/www.scientific.net/msf.467-470.1363 may be a valid DOI for title: 3DXRD–Mapping grains and their dynamics in 3 dimen...
- 10.1088/1464-4258/2/6/314 may be a valid DOI for title: Polarization properties of honeycomb-structured ph...
- 10.1016/s0030-4018(03)01451-2 may be a valid DOI for title: Modelling photonic crystal fibres with Hermite–Gau...
- 10.1016/j.endm.2005.05.076 may be a valid DOI for title: Resolving ambiguities in reconstructed grain maps ...
- 10.1117/1.2390680 may be a valid DOI for title: Optimized algebraic reconstruction technique for g...
- 10.1080/10238160902819684 may be a valid DOI for title: Virtual experiments: the ultimate aim of neutron r...
- 10.1007/978-0-8176-4543-4_13 may be a valid DOI for title: Discrete tomography for generating grain maps of p...
- 10.3233/jnr-130004 may be a valid DOI for title: McStas: Past, present and future
- 10.1016/j.endm.2005.05.077 may be a valid DOI for title: Discrete tomographic reconstruction of 2D polycrys...
- 10.1109/ecoc.2001.989089 may be a valid DOI for title: Photonic crystal fibres and effective index approa...
- 10.3934/ipi.2009.3.69 may be a valid DOI for title: A greedy method for reconstructing polycrystals fr...
- 10.1117/12.2302167 may be a valid DOI for title: Macro-bending loss estimation for air-guiding phot...
- 10.1109/icsens.2003.1278941 may be a valid DOI for title: Photonic crystal fibers; fundamental properties an...
- 10.1109/ecoc.2001.989648 may be a valid DOI for title: Microbending in photonic crystal fibres-An ultimat...
- 10.1117/12.559602 may be a valid DOI for title: Optimization of an algebraic reconstruction techni...
- 10.1107/s0021889810034114 may be a valid DOI for title: DART: a robust algorithm for fast reconstruction o...
- 10.1117/12.894179 may be a valid DOI for title: McXtrace: a modern ray-tracing package for x-ray i...
- 10.1016/j.nima.2010.06.212 may be a valid DOI for title: Using McStas for modelling complex optics, using s...
- 10.1016/j.nima.2010.06.235 may be a valid DOI for title: Analysing neutron scattering data using McStas vir...
- 10.1016/j.nima.2010.06.261 may be a valid DOI for title: Eliminating line of sight in elliptic guides using...
- 10.1179/174328405x71684 may be a valid DOI for title: 3D grainmap generation with the algebraic reconstr...
- 10.1117/12.894520 may be a valid DOI for title: A monte carlo approach for simulating the propagat...
- 10.4028/www.scientific.net/msf.558-559.389 may be a valid DOI for title: Mapping partially recrystallised structures by 3DX...
- 10.1117/12.893343 may be a valid DOI for title: Advanced simulations of x-ray beam propagation thr...
- 10.1016/j.physb.2010.11.060 may be a valid DOI for title: McStas-model of the delft SESANS
- 10.1109/icton.2002.1007862 may be a valid DOI for title: Photonic crystal fibers: a variety of applications
- 10.1107/s0021889813000150 may be a valid DOI for title: FabIO: easy access to two-dimensional X-ray detect...
- 10.3233/jnr-130003 may be a valid DOI for title: Investigation of propagation algorithms for ray-tr...
- 10.1063/1.4803167 may be a valid DOI for title: Simulation of a suite of generic long-pulse neutro...
- 10.1088/1742-6596/528/1/012032 may be a valid DOI for title: Application of the MCNPX-McStas interface for shie...
- 10.1016/j.nima.2013.11.071 may be a valid DOI for title: McStas event logger: Definition and applications
- 10.1088/1742-6596/528/1/012035 may be a valid DOI for title: New developments in the McStas neutron instrument ...
- 10.1117/12.2061411 may be a valid DOI for title: Novel applications of the x-ray tracing software p...
- 10.1016/j.nimb.2014.10.015 may be a valid DOI for title: Prediction of beam hardening artefacts in computed...
- 10.1117/12.2233060 may be a valid DOI for title: Simulating X-ray telescopes with McXtrace: A case ...
- 10.1016/j.cpc.2017.04.012 may be a valid DOI for title: Monte Carlo particle lists: MCPL
- 10.3233/jnr-150023 may be a valid DOI for title: Simulation of waviness in neutron guides
- 10.1103/physreva.95.023618 may be a valid DOI for title: Zero-order filter for diffractive focusing of de B...
- 10.1038/s41598-017-09717-w may be a valid DOI for title: Time-of-flight three dimensional neutron diffracti...
- 10.1016/j.physb.2018.03.025 may be a valid DOI for title: Simulation tools for detector and instrument desig...
- 10.1117/1.oe.57.3.037105 may be a valid DOI for title: Simulation tools for scattering corrections in spe...
- 10.1117/12.2312272 may be a valid DOI for title: The McXtrace AstroX toolbox: a general ray tracing...
- 10.1080/10448632.2018.1551000 may be a valid DOI for title: Molecular (and lattice) dynamics to analyze neutro...
- 10.1088/1361-6463/ab0aba may be a valid DOI for title: Three dimensional polarimetric neutron tomography—...
- 10.1117/12.2529113 may be a valid DOI for title: Simulating the effects of thermoelastic deformatio...
- 10.1107/s1600576719012858 may be a valid DOI for title: Full-field neutron microscopy based on refractive ...
- 10.1107/s1600577519014425 may be a valid DOI for title: A Monte Carlo ray-tracing simulation of coherent X...
- 10.1109/ecoc.2001.989675 may be a valid DOI for title: Macrobending loss properties of photonic crystal f...
- 10.1117/12.2561372 may be a valid DOI for title: Example telescope simulations with the AstroX tele...
- 10.1117/12.2594461 may be a valid DOI for title: Open-source simulator for ATHENA X-ray telescope o...
- 10.1107/s1600576721012760 may be a valid DOI for title: X-ray free-electron laser based dark-field X-ray m...
- 10.3233/jnr-150023 may be a valid DOI for title: Simulation of waviness in neutron guides
- 10.1117/12.2622220 may be a valid DOI for title: A fully-analytical treatment of stray light in sil...
- 10.1038/s41598-024-59506-5 may be a valid DOI for title: Neutron Instrument Concepts for a High Intensity M...
- 10.2172/877507 may be a valid DOI for title: FLUKA: a multi-particle transport code
- 10.2172/1463583 may be a valid DOI for title: Updating the GODIVA-IV benchmark

❌ INVALID DOIs

- None

@kyleniemeyer kyleniemeyer removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Dec 16, 2024
@mbarzegary
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Hi @fbordeu, @nasserma, @jacobmerson, @schuhmaj 👋
Considering that you have already published your software in JOSS, would any of you be willing to review this submission? As you know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Paper: https://raw.githubusercontent.com/openjournals/joss-papers/joss.07369/joss.07369/10.21105.joss.07369.pdf
Software: https://www.github.com/openmsr/CAD_to_OpenMC

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nasserma commented Jan 6, 2025

@mbarzegary I would be willing to review this submission.

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@nasserma added to the reviewers list!

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jacobmerson commented Jan 13, 2025

@nasserma I'd be happy to review.

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@editorialbot add @jacobmerson as reviewer

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@jacobmerson added to the reviewers list!

@mbarzegary
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Hi @pratikvn, @WilkAndy, @bonh, @daniellivingston👋
Given your expertise and your experience in reviewing for JOSS, would any of you be willing to review this submission? As you know, we carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Paper: https://raw.githubusercontent.com/openjournals/joss-papers/joss.07369/joss.07369/10.21105.joss.07369.pdf
Software: https://www.github.com/openmsr/CAD_to_OpenMC

@bonh
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bonh commented Jan 23, 2025

Looks interesting and I'd be happy to review it

@WilkAndy
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I feel my expertise doesn't quite match with this paper, so i wouldn't be able to provide a holistic review. Therefore, I'll decline to review at present. If you haven't found suitable reviewers by, say, mid-March, please contact me again, and I'll do my best (commenting on the software aspects, rather than the relevance/usefulness of the code).

@mbarzegary
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@WilkAndy thank you for the clarification. I believe we have now secured sufficient number of reviewers for this submission.

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@editorialbot add @bonh as reviewer

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@bonh added to the reviewers list!

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@editorialbot start review

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OK, I've started the review over in #7710.

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