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editorialbot opened this issue Apr 6, 2025 · 52 comments
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pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Apr 6, 2025

Submitting author: @jennifersteeden (Jennifer Steeden)
Repository: https://github.com/mrphys/tensorflow-mri
Branch with paper.md (empty if default branch): master
Version: v0.23.1
Editor: @Kevin-Mattheus-Moerman
Reviewers: Pending
Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/1fedf5675ade9e9cd8a9cf85896dd346/status.svg)](https://joss.theoj.org/papers/1fedf5675ade9e9cd8a9cf85896dd346)

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@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Apr 6, 2025
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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:

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

✅ OK DOIs

- 10.1038/s41598-024-62294-7 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare

❌ MISSING DOIs

- 10.1137/18m120885x may be a valid DOI for title: A parallel nonuniform fast Fourier transform libra...
- 10.1109/ipdpsw52791.2021.00105 may be a valid DOI for title: cuFINUFFT: a load-balanced GPU library for general...

❌ INVALID DOIs

- https://doi.org/10.1016/j.mri.2024.04.027 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.24389 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.29855 is INVALID because of 'https://doi.org/' prefix

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Software report:

github.com/AlDanial/cloc v 1.98  T=5.57 s (455.0 files/s, 260937.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
JavaScript                      988          43041          78912         348745
C/C++ Header                    452          12323          22832          65126
JSON                            245              6              0          55449
Python                          186           9772          18994          40953
Markdown                        159           9269             19          25609
HTML                             85           1816              0          24923
YAML                            230           1434            170          13088
TypeScript                       51            817           1609           5446
Jupyter Notebook                 14              0         667650           1549
Bourne Shell                     44            202             86           1177
Bourne Again Shell                6            100             86            562
SVG                               4              1              1            459
PowerShell                       16             26             74            356
C++                               4             56             45            232
reStructuredText                 12            112            112            203
C#                                1             55              9            186
DOS Batch                        21             18              3            169
Text                              8             10              0            141
TOML                              1              8             31             80
TeX                               1              8              0             80
make                              3             26              7             63
Dockerfile                        3             16              9             49
XML                               1              0              0             31
Fish Shell                        1              5             14             21
--------------------------------------------------------------------------------
SUM:                           2536          79121         790663         584697
--------------------------------------------------------------------------------

Commit count by author:

   392	Javier Montalt Tordera
    47	jennifersteeden
     4	Michele Pascale

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Paper file info:

📄 Wordcount for paper.md is 886

✅ The paper includes a Statement of need section

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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

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

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Five most similar historical JOSS papers:

DIRECT: Deep Image REConstruction Toolkit
Submitting author: @georgeyiasemis
Handling editor: @osorensen (Active)
Reviewers: @estenhl, @sairamgeethanath
Similarity score: 0.7470

Virtual Scanner: MRI on a Browser
Submitting author: @imr-framework
Handling editor: @arokem (Retired)
Reviewers: @nstikov, @vsoch, @mathieuboudreau
Similarity score: 0.7457

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7447

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.7428

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.7390

⚠️ 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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jennifersteeden commented Apr 13, 2025 via email

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@editorialbot assign me as editor

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Assigned! @Kevin-Mattheus-Moerman is now the editor

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@jennifersteeden Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. I will also be the handling editor. Before we proceed, please can you have a look at the following points:

  • Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
  • Although your project has a basic statement on receiving contributions we recommend that you add more detailed contributing guidelines. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

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jennifersteeden commented Apr 29, 2025 via email

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@editorialbot check references

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

✅ OK DOIs

- 10.1038/s41598-024-62294-7 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare

❌ MISSING DOIs

- 10.1137/18m120885x may be a valid DOI for title: A parallel nonuniform fast Fourier transform libra...
- 10.1109/ipdpsw52791.2021.00105 may be a valid DOI for title: cuFINUFFT: a load-balanced GPU library for general...

❌ INVALID DOIs

- https://doi.org/10.1016/j.mri.2024.04.027 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.24389 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.29855 is INVALID because of 'https://doi.org/' prefix

@jennifersteeden
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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:

DIRECT: Deep Image REConstruction Toolkit
Submitting author: @georgeyiasemis
Handling editor: @osorensen (Active)
Reviewers: @estenhl, @sairamgeethanath
Similarity score: 0.7473

Virtual Scanner: MRI on a Browser
Submitting author: @imr-framework
Handling editor: @arokem (Retired)
Reviewers: @nstikov, @vsoch, @mathieuboudreau
Similarity score: 0.7465

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7460

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.7447

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.7398

⚠️ 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.

@jennifersteeden
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@editorialbot check references

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

✅ OK DOIs

- 10.1038/s41598-024-62294-7 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare

❌ MISSING DOIs

- 10.1137/18m120885x may be a valid DOI for title: A parallel nonuniform fast Fourier transform libra...
- 10.1109/ipdpsw52791.2021.00105 may be a valid DOI for title: cuFINUFFT: a load-balanced GPU library for general...

❌ INVALID DOIs

- https://doi.org/10.1016/j.mri.2024.04.027 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.24389 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.29855 is INVALID because of 'https://doi.org/' prefix

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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

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@editorialbot set master as branch

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Done! branch is now master

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

@editorialbot
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Five most similar historical JOSS papers:

DIRECT: Deep Image REConstruction Toolkit
Submitting author: @georgeyiasemis
Handling editor: @osorensen (Active)
Reviewers: @estenhl, @sairamgeethanath
Similarity score: 0.7471

Virtual Scanner: MRI on a Browser
Submitting author: @imr-framework
Handling editor: @arokem (Retired)
Reviewers: @nstikov, @vsoch, @mathieuboudreau
Similarity score: 0.7463

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7456

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.7448

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.7402

⚠️ 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.

@jennifersteeden
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@editorialbot set v0.23.2 as branch

@editorialbot generate pdf

@editorialbot check references

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Done! branch is now v0.23.2

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@editorialbot set master as branch

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Done! branch is now master

@jennifersteeden
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@editorialbot generate pdf

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

@editorialbot
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Five most similar historical JOSS papers:

DIRECT: Deep Image REConstruction Toolkit
Submitting author: @georgeyiasemis
Handling editor: @osorensen (Active)
Reviewers: @estenhl, @sairamgeethanath
Similarity score: 0.7472

Virtual Scanner: MRI on a Browser
Submitting author: @imr-framework
Handling editor: @arokem (Retired)
Reviewers: @nstikov, @vsoch, @mathieuboudreau
Similarity score: 0.7464

PyQMRI: An accelerated Python based Quantitative MRI toolbox
Submitting author: @maieroli2010
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @agahkarakuzu, @DARSakthi
Similarity score: 0.7458

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.7449

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.7400

⚠️ 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.

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

✅ OK DOIs

- 10.1038/s41598-024-62294-7 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Fidgit: An ungodly union of GitHub and Figshare

❌ MISSING DOIs

- 10.1137/18m120885x may be a valid DOI for title: A parallel nonuniform fast Fourier transform libra...
- 10.1109/ipdpsw52791.2021.00105 may be a valid DOI for title: cuFINUFFT: a load-balanced GPU library for general...

❌ INVALID DOIs

- https://doi.org/10.1016/j.mri.2024.04.027 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.24389 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/mrm.29855 is INVALID because of 'https://doi.org/' prefix

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@editorialbot set v0.23.2 as version

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I'm sorry @jennifersteeden, I'm afraid I can't do that. That's something only editors are allowed to do.

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The PDF generated is from the older version of the files. The files have been updated to correct the references, but the PDF generated still seems to be accessing the older versions. I cant seem to find a way around this. Please help.
The vserion in 'master', or branch 0.23.2 are the corrected files.

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Hello @jennifersteeden, 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 check repository

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Software report:

github.com/AlDanial/cloc v 1.98  T=5.74 s (457.2 files/s, 262897.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
JavaScript                      996          43237          80725         369903
JSON                            254              6              0          73424
C/C++ Header                    516          12881          24529          68414
Python                          188           9795          19067          41984
Markdown                        163          10180             30          31418
HTML                             85           1816              0          24923
YAML                            230           1434            170          13088
TypeScript                       51            817           1609           5446
Jupyter Notebook                 14              0         667650           1549
Bourne Shell                     45            231             95           1318
Bourne Again Shell                6            100             86            562
SVG                               4              1              1            459
PowerShell                       16             26             74            356
C++                               4             56             45            232
reStructuredText                 12            112            112            203
C#                                1             55              9            186
DOS Batch                        21             18              3            169
TeX                               2             14              0            154
Text                              8             10              0            141
TOML                              1              8             31             80
make                              3             26              7             63
Dockerfile                        3             16              9             49
XML                               1              0              0             31
Fish Shell                        1              5             14             21
--------------------------------------------------------------------------------
SUM:                           2625          80844         794266         634173
--------------------------------------------------------------------------------

Commit count by author:

   392	Javier Montalt Tordera
    50	jennifersteeden
     4	Michele Pascale

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Paper file info:

📄 Wordcount for paper.md is 886

✅ The paper includes a Statement of need section

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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

@jennifersteeden
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@editorialbot generate pdf

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