[PRE REVIEW]: abc

[med-oc]

Submitting author: !--author-handle-->@max-anu<!--end-author-handle-- (Max Proft) Repository: https://github.com/max-anu/example-medportal3 Branch with paper.md (empty if default branch): Version: v1 Editor: !--editor-->@max-anu<!--end-editor-- Reviewers: !--reviewers-list-->@max-anu<!--end-reviewers-list-- Managing EiC: Max Proft

Status

Status badge code:

HTML: <a href="https://medportal-dev-6a745f452687.herokuapp.com/papers/41811bc6f54d1a70cb4c97dd1a4884a2"><img src="https://medportal-dev-6a745f452687.herokuapp.com/papers/41811bc6f54d1a70cb4c97dd1a4884a2/status.svg"></a>
Markdown: [![status](https://medportal-dev-6a745f452687.herokuapp.com/papers/41811bc6f54d1a70cb4c97dd1a4884a2/status.svg)](https://medportal-dev-6a745f452687.herokuapp.com/papers/41811bc6f54d1a70cb4c97dd1a4884a2)

Author instructions

Thanks for submitting your recipe to medportal @max-anu. Currently, there isn't a medportal editor assigned to your recipe.

The AEiC suggestion for the handling editor is @max-anu.

@max-anu 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 medportal submission bot @med-oc is here to help you find and assign reviewers and start the main review. To find out what @med-oc can do for you type:

@med-oc commands

[med-oc]

Hello humans, I'm @med-oc, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@med-oc help

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@med-oc generate pdf

[max-anu]

@med-oc generate pdf

[max-anu]

@med-oc add @max-anu as reviewer

[med-oc]

@max-anu added to the reviewers list!

[max-anu]

@med-oc assign @max-anu as editor

[med-oc]

Assigned! @max-anu is now the editor

[med-oc]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[max-anu]

@med-oc start review

[max-anu]

@med-oc hello

[med-oc]

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

@med-oc help

[max-anu]

@med-oc start review

[max-anu]

@med-oc start review

[max-anu]

hello @med-oc

[med-oc]

Hi!

[max-anu]

hello @med-oc

[med-oc]

Hi!

[max-anu]

@med-oc start review

[max-anu]

@med-oc start review

[max-anu]

hello @med-oc

[med-oc]

Hi!

[max-anu]

hello @med-oc

[med-oc]

Hi!

[max-anu]

@med-oc start review

[med-oc]

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

@med-oc help

[max-anu]

@med-oc help

[med-oc]

Hello @max-anu, here are the things you can ask me to do:

# List all available commands
@med-oc help

# Show our community Code of Conduct and Guidelines
@med-oc code of conduct

# Replies to 'list editors'
@med-oc list editors

# Check the references of the paper for missing DOIs
# Optionally, it can be run on a non-default branch 
@med-oc check references
@med-oc check references from branch custom-branch-name

# Perform checks on the repository
# Optionally, it can be run on a non-default branch 
@med-oc check repository
@med-oc check repository from branch custom-branch-name

# Random facts about cats
@med-oc tell me something about cats

# Adds a checklist for the reviewer using this command
@med-oc generate my checklist

[max-anu]

@med-oc list editors

[max-anu]

@med-oc start review

[med-oc]

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

@med-oc help

[max-anu]

@med-oc start review

[med-oc]

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

@med-oc help

[max-anu]

@med-oc start review

[med-oc]

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

@med-oc help

[max-anu]

@med-oc help

[med-oc]

Hello @max-anu, here are the things you can ask me to do:

# List all available commands
@med-oc help

# Show our community Code of Conduct and Guidelines
@med-oc code of conduct

# Replies to 'list editors'
@med-oc list editors

# Check the references of the paper for missing DOIs
# Optionally, it can be run on a non-default branch 
@med-oc check references
@med-oc check references from branch custom-branch-name

# Perform checks on the repository
# Optionally, it can be run on a non-default branch 
@med-oc check repository
@med-oc check repository from branch custom-branch-name

# Random facts about cats
@med-oc tell me something about cats

# Adds a checklist for the reviewer using this command
@med-oc generate my checklist

[max-anu]

@med-oc check repository

[med-oc]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (359.3 files/s, 54976.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             55              0            280
Markdown                         2             56              0            144
Jupyter Notebook                 1              0             74              3
-------------------------------------------------------------------------------
SUM:                             4            111             74            427
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[med-oc]

Wordcount for paper.md is 2619

[med-oc]

Failed to discover a valid open source license

[max-anu]

@med-oc check references

[med-oc]

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

OK DOIs

- 10.1371/journal.pcbi.1009149 is OK
- 10.25080/majora-212e5952-00e is OK
- 10.1596/978-1-4648-1523-2_ch13 is OK
- 10.12688/gatesopenres.13031.2 is OK
- 10.1186/s12889-018-5294-z is OK
- 10.1371/journal.pcbi.1009255 is OK
- 10.1371/journal.pone.0260247 is OK
- 10.1371/journal.pcbi.1008316 is OK
- 10.1093/femspd/ftz006 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1093/bioinformatics/bty407 is OK
- 10.21105/joss.03021 is OK
- 10.21105/joss.03262 is OK
- 10.21105/joss.01891 is OK
- 10.1038/s41592-018-0137-5 is OK
- 10.21105/joss.01026 is OK
- 10.3389/fninf.2017.00069 is OK
- 10.1109/mcse.2011.35 is OK
- 10.21105/joss.01450 is OK
- 10.1038/d41586-020-02462-7 is OK
- 10.25080/Majora-7b98e3ed-013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[max-anu]

@med-oc list editors

[max-anu]

Review checklist for @max-anu

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/max-anu/example-medportal3?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@max-anu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[max-anu]

@med-oc list editors

[max-anu]

@med-oc list editors

[med-oc]

Current recipe editors

@AndyHoggANU
@CodeGat
@MartinDix
@NBateman-bit
@OKaluza
@Quartzer2
@SeanBryan51
@aidanheerdegen
@anton-seaice
@atteggiani
@bschroeter
@ccarouge
@dougiesquire
@echus
@ezhilsabareesh8
@flicj191
@harshula
@headmetal
@heidinett
@jo-basevi
@kdruken
@kieranricardo
@max-anu
@med-oc
@penguian
@rbeucher
@rogeredberg
@svenbuder
@utkarshgupta95

[max-anu]

@med-oc help

[med-oc]

Hello @max-anu, here are the things you can ask me to do:

# List all available commands
@med-oc help

# Show our community Code of Conduct and Guidelines
@med-oc code of conduct

# Add to this issue's reviewers list
@med-oc add @username as reviewer

# Remove from this issue's reviewers list
@med-oc remove @username from reviewers

# Assign a user as the editor of this submission
@med-oc assign @username as editor

# Remove the editor assigned to this submission
@med-oc remove editor

# Send an invitation to a user to collaborate in the review
@med-oc invite @username

# Add a user to this issue's assignees list
@med-oc add assignee: @username

# Remove a user from this issue's assignees list
@med-oc remove assignee: @username

# Replies to 'list editors'
@med-oc list editors

# Set a value for version
@med-oc set v1.0.0 as version

# Set a value for archive
@med-oc set 10.21105/medportal.12345 as archive

# Label issue with: reviewed, recommend publication, pending publication. Remove labels: ongoing, pending review
@med-oc review successful

# Label issue with: recommend rejection
@med-oc review failed

# Close the issue
@med-oc reject

# Add review checklist for a user
@med-oc add checklist for @username

# Remove the checklist for a user
@med-oc remove checklist for @username

# Generates the pdf paper
@med-oc generate pdf

# Recommends the submission for acceptance
@med-oc recommend-accept

# Accept and publish the paper
@med-oc accept

# Generates a LaTeX preprint file
@med-oc generate preprint

# Open the review issue
@med-oc start review

# Adds a checklist for the reviewer using this command
@med-oc generate my checklist

[max-anu]

@med-oc start review

[max-anu]

@med-oc review successful