Joss-reviews: [PRE REVIEW]: REGENS: an open source Python package for simulating realistic autosomal genotypes

[whedon]

Submitting author: @greggj2016 (John Gregg)
Repository: https://github.com/EpistasisLab/regens
Version: v0.1.0
Editor: @fboehm
Reviewers: @raivivek, @dwinter
Managing EiC: Kevin M. Moerman

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

Thanks for submitting your paper to JOSS @greggj2016. Currently, there isn't an JOSS editor assigned to your paper.

@greggj2016 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=10.49 s (5.8 files/s, 50407.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SQL                              1              0              0         500001
C                                1           1768           8513          15245
Python                           8            224            293            860
Bourne Shell                    32             70            204            654
Markdown                         7            106              0            417
R                               10             30              0            260
TeX                              1             16              0            112
Cython                           1              5              0             50
-------------------------------------------------------------------------------
SUM:                            61           2219           9010         517599
-------------------------------------------------------------------------------


Statistical information for the repository '2716' was gathered on 2020/10/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
John Gregg                       4         51848          51426           99.96
greggj2016                       1             0             41            0.04

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
John Gregg                52597          101.4          0.0               34.35

[Kevin-Mattheus-Moerman]

@fboehm @mikldk @lpantano @will-rowe @majensen could one of you handle this submission? Thanks

[Kevin-Mattheus-Moerman]

FYI :point_up: I closed an apparent duplicate submission. @greggj2016 can you confirm you submitted twice perhaps by mistake? I want to check if this was a hiccup in our system or not.

[greggj2016]

Yes, actually this is the first paper I submitted here. I wasn't sure how to submit my reformatted draft, so I had attempted to resubmit the reformatted draft and withdraw the previous submission. However, clicking the button to withdraw the previous submission did not seem to do anything after multiple attempts. I was then advised to wait for your response, so this is not a hiccup in your system (Unless you count the withdraw submission button not working. You might want to look at that.)

[Kevin-Mattheus-Moerman]

@greggj2016 Okay thanks for clarifying. In the future you can make changes to your paper on your repository and then call @whedon generate pdf (on its own, without any other text) here, to update the paper.

[greggj2016]

Yes, but what does that mean to "call @whedon generate pdf"?

[Kevin-Mattheus-Moerman]

Like this :point_down: , whedon is a bot that helps our review process

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[greggj2016]

yes, but where do I input that? Is there a place where I can read more details?

[whedon]

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

[greggj2016]

@whedon generate pdf

[greggj2016]

Did your comment make that?

[Kevin-Mattheus-Moerman]

yes, but where do I input that? Is there a place where I can read more details?

Right here. Like you just did :+1:

[whedon]

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

[Kevin-Mattheus-Moerman]

Did your comment make that?

Yep, and yours did too

[greggj2016]

Got it thanks!

[Kevin-Mattheus-Moerman]

We will also use whedon like that to assign reviewers, start the review etc.

[greggj2016]

Is there a place i can read more about the full functionality of whedon, or do I not need to know anything else?

[Kevin-Mattheus-Moerman]

Is there a place i can read more about the full functionality of whedon, or do I not need to know anything else?

See here: https://joss.readthedocs.io/en/latest/

Let me know if you have any more questions.

[fboehm]

Yes, @Kevin-Mattheus-Moerman - I can take this on as editor.

[fboehm]

@whedon assign @fboehm as editor

[whedon]

OK, the editor is @fboehm

[fboehm]

@whedon list reviewers

[whedon]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[fboehm]

@whedon assign @raivivek as reviewer

[whedon]

OK, @raivivek is now a reviewer

[fboehm]

@whedon add @dwinter as reviewer

[whedon]

OK, @dwinter is now a reviewer

[fboehm]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2743.