Joss-reviews: [PRE REVIEW]: BioGears: A C++ library for whole body physiology simulations

[whedon]

Submitting author: @ajbaird (Austin Baird)
Repository: https://github.com/BioGearsEngine/core
Version: v7.3.1
Editor: @meg-simula
Reviewers: @fcooper8472, @MiroK
Managing EiC: Arfon Smith

: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 @ajbaird. Currently, there isn't an JOSS editor assigned to your paper.

@ajbaird 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

[arfon]

@whedon check repository

[arfon]

@whedon generate pdf from branch f/abard-JOSSPaper

[whedon]

Attempting PDF compilation from custom branch f/abard-JOSSPaper. Reticulating splines etc...

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=54.74 s (36.7 files/s, 34676.3 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
XML                                    500           3914           1916        1485366
C++                                    555          12083          23612         106323
JavaScript                              57           9145          10418          45077
C                                       97           8355           7246          40103
C/C++ Header                           532           9800          17125          35874
CSS                                     14            317            379          16002
Markdown                                62           3348           1614          12112
TeX                                      1            844              2           7293
MSBuild script                           7              1              0           4675
CMake                                   29            594           1254           4566
XSD                                     31            440            701           4020
Assembly                                 8           1033           1471           2755
HTML                                    11            101             52           2257
Python                                  11            326            421           1986
Ada                                     10            599            560           1681
Sass                                    13             26             24           1352
LESS                                    13             26             33           1343
Pascal                                   5            219            551           1200
Bourne Shell                             2            156            146            985
C#                                       9            230            506            879
SVG                                      2              0              0            794
JSON                                    11              0              0            664
Windows Module Definition                3             16             17            265
make                                     7             60             40            165
YAML                                     2              5              0            133
Perl                                     1             33             14            105
Windows Resource File                    2              3              2             67
Ruby                                     1              7              5             48
SAS                                      1             14             22             32
Dockerfile                               4              8              7             31
m4                                       1              5              0             27
Bourne Again Shell                       1             18              7             26
NAnt script                              1              7              0             26
Visual Basic                             1              1              0             15
DOS Batch                                2              0              0              4
---------------------------------------------------------------------------------------
SUM:                                  2007          51734          68145        1778251
---------------------------------------------------------------------------------------


Statistical information for the repository '2611' was gathered on 2020/08/30.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Austin                          19           439            206            0.05
Austin Baird                    23          1213            304            0.13
Lucas Marin                    130        171256           3309           14.82
Matthew McDaniel               261         23573          17360            3.48
Nathan Tatum                   205         11061           4487            1.32
Shashank                         1          1772           8196            0.85
Steven A White                 313        578694         355408           79.31
Steven White                     4           361            192            0.05

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
Austin Baird               1087           89.6          7.2               16.38
Lucas Marin               78548           45.9         11.7               17.09
Matthew McDaniel          11639           49.4         12.2               14.14
Nathan Tatum               6582           59.5         17.8                4.79
Shashank                   1772          100.0          3.0                5.42
Steven A White           228526           39.5          6.5               22.24
Steven White                332           92.0          0.8               14.16

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ajbaird]

looks like there were a few updates to the acknowledgements that i had
forgotten to push up before submission. Just pushed those up. Should be
good to go on our end.

Thanks!

Austin

On Sun, Aug 30, 2020 at 10:33 AM whedon [e-mail] wrote:

👉 Check article proof 📄 👈
https://raw.githubusercontent.com/openjournals/joss-papers/joss.02611/joss.02611/10.21105.joss.02611.pdf

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/2611#issuecomment-683427828,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAG4QLYESSHJ33SPLXDRW5DSDJPKTANCNFSM4QPUY36Q
.

--
Regards,

Austin Baird

[kthyng]

@meg-simula Could you edit this submission?

[kthyng]

@whedon invite @meg-simula as editor

[whedon]

@meg-simula has been invited to edit this submission.

[meg-simula]

@whedon assign @meg-simula as editor

[whedon]

OK, the editor is @meg-simula

[meg-simula]

@ajbaird Thanks for submitting BioGears to JOSS. Do you have any suggestions for reviewers?

[meg-simula]

@whedon generate pdf from branch f/abard-JOSSPaper

[whedon]

Attempting PDF compilation from custom branch f/abard-JOSSPaper. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[meg-simula]

Also, @ajbaird, could you please take a look at (and fix) the code formatting?

[ajbaird]

Hi @meg-simula, no special comments for the reviews. So sorry about that formatting, I'll have a new document submitted tonight!

[ajbaird]

Hi @meg-simula , just updated the code formatting, shouldn't be overrun any longer. Really sorry about this, we are very verbose with a lot of function calls! :)

[meg-simula]

Thanks @ajbaird!This looks very much ready for review. I'll reach out to reviewers, and get back to you

[meg-simula]

@mirok @fcooper8472 Would you be available to review this submission for JOSS?

Feel free to take a look at our reviewer guidelines here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

[fcooper8472]

Yes, happy to review.

[MiroK]

Same here.

[meg-simula]

Thanks @MiroK and @fcooper8472 for the rapid and positive response. I'll get the review issue started.

[meg-simula]

@whedon assign @fcooper8472 as reviewer

[whedon]

OK, @fcooper8472 is now a reviewer

[meg-simula]

@whedon add @MiroK as reviewer

[whedon]

OK, @MiroK is now a reviewer

[meg-simula]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2645.