[PRE REVIEW]: Tyssue, en Epithelium simulation library

[whedon]

Submitting author: @glyg (Guillaume Gay)
Repository: https://github.com/damcb/tyssue
Version: v0.8.0
Editor: @pdebuyl
Reviewers: @fcooper8472, @SergeDmi
Managing EiC: Kyle Niemeyer

⚠️ JOSS reduced service mode ⚠️

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

The author's suggestion for the handling editor is @pdebuyl.

@glyg 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.

⚠️ JOSS reduced service mode ⚠️

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]

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

OK DOIs

- 10.1038/s41467-019-10720-0 is OK
- 10.1101/704932 is OK
- 10.1038/s41467-018-06497-3 is OK
- 10.1242/dev.146761 is OK
- 10.1098/rstb.2015.0520 is OK
- 10.1038/nphys3471 is OK
- 10.1038/nature14152 is OK
- 10.1007/s10237-015-0724-7 is OK
- 10.1007/s10237-012-0430-7 is OK
- 10.1016/J.CUB.2010.06.075 is OK
- 10.1016/J.CUB.2007.11.049 is OK
- 10.1016/S0021-9290(02)00006-4 is OK

MISSING DOIs

- 10.1242/prelights.16742 may be a valid DOI for title: Mechanical control of morphogenesis robustness

INVALID DOIs

- https://doi.org/10.1016/S0074-7696(08)62339-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/0022-5193(78)90315-6 is INVALID because of 'https://doi.org/' prefix

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.65 s (336.0 files/s, 90043.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             21             19             21          34334
Python                         127           3302           3033          11078
TeX                              2            218              0           3340
Markdown                         6            267              0            503
JSON                            18              1              0            392
reStructuredText                31            320            527            338
CMake                            4             56            184            226
make                             2             35              6            197
C++                              2             36             10            128
YAML                             4             12              2             76
Bourne Shell                     1              5              0             14
INI                              1              0              0              4
-------------------------------------------------------------------------------
SUM:                           219           4271           3783          50630
-------------------------------------------------------------------------------


Statistical information for the repository '3a5dd3b96214f400298ce323' was
gathered on 2020/12/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Bertrand Caré                   12          1088             90            1.55
George C                         2           259              6            0.35
Guillaume Gay                  464         33828          20693           71.62
Hadrien Mary                     5            87             86            0.23
Sophie THEIS                   109         12092           7879           26.24
btbest                           1             2              1            0.00
felixquinton                     1             7              1            0.01
kc lee                           1             2              0            0.00

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
Bertrand Caré                 1            0.1         50.5                0.00
George C                    256           98.8          9.9                7.03
Guillaume Gay             14309           42.3         27.9                6.63
Hadrien Mary                 21           24.1         65.4                0.00
Sophie THEIS               2996           24.8         19.2                7.04
felixquinton                  4           57.1         20.2                0.00

[whedon]

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

[kyleniemeyer]

Hi @pdebuyl, can you edit this submission?

[kyleniemeyer]

@whedon invite @pdebuyl as editor

[whedon]

@pdebuyl has been invited to edit this submission.

[glyg]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[glyg]

@whedon check references

[whedon]

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

OK DOIs

- 10.1101/2020.01.06.896266 is OK
- 10.1038/s41467-019-10720-0 is OK
- 10.1101/704932 is OK
- 10.1038/s41467-018-06497-3 is OK
- 10.1242/dev.146761 is OK
- 10.1098/rstb.2015.0520 is OK
- 10.1038/nphys3471 is OK
- 10.1038/nature14152 is OK
- 10.1007/s10237-015-0724-7 is OK
- 10.1007/s10237-012-0430-7 is OK
- 10.1016/J.CUB.2010.06.075 is OK
- 10.1016/J.CUB.2007.11.049 is OK
- 10.1016/S0021-9290(02)00006-4 is OK
- 10.1016/S0074-7696(08)62339-6 is OK
- 10.1016/0022-5193(78)90315-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[glyg]

@whedon generate pdf

[whedon]

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

[pdebuyl]

@whedon assign me as editor

[whedon]

OK, the editor is @pdebuyl

[pdebuyl]

@smsaladi can you review the article "Tyssue, en Epithelium simulation library" for JOSS?

[smsaladi]

@pdebuyl Thanks for thinking of me, but it's not a great time for me right now (wouldn't be able to respond within the next month). Hope I can help in the future though...

[pdebuyl]

Thank you @smsaladi for your prompt reply! You remain in the list of reviewers, no worry.

[pdebuyl]

PS @smsaladi you might want to unsubscribe to this github issue else you will keep on receiving notifications.

[pdebuyl]

Hi @glyg I am still looking for reviewers. Our pool of volunteers has few matches for the topic here, I will expand the search.

You can suggest reviewers as well, I will then consider including one from that list.

[pdebuyl]

@shriyaamittal can you review the article "Tyssue, en Epithelium simulation library" for the Journal of Open Source Software?

[glyg]

Hi @pdebuyl , thank you,

If you talk about reviewers outside of the volunteers, I can think of Guillaume Salbreux or people in the teams of Lisa Manning, Alexander Fletcher or Frank Jüllicher

[pdebuyl]

@Paijmans can you review the article "Tyssue, en Epithelium simulation library" for the Journal of Open Source Software?

[shriyaamittal]

Sorry, I have no competence in cell biology to review this work.

[pdebuyl]

Thank you for the reply @shriyaamittal . You might want to unsubscribe to this github issue else you will keep on receiving notifications.

[pdebuyl]

@salbreux can you review the article "Tyssue, en Epithelium simulation library" for the Journal of Open Source Software? (please check our COI policy https://joss.readthedocs.io/en/latest/reviewer_guidelines.html#joss-conflict-of-interest-policy ).

[glyg]

Hi @pdebuyl happy new year!

I'm tagging @sophietheis here so she can follow the process
Best

Guillaume

[pdebuyl]

Happy new year @glyg :-)

I have proceeded with email invitations, I'll let you know of course when there is an update. Sorry that this is taking so long.

[glyg]

No worries, there's no rush

[pdebuyl]

@whedon assign @fcooper8472 as reviewer

[whedon]

OK, @fcooper8472 is now a reviewer

[pdebuyl]

@whedon add @SergeDmi as reviewer

[whedon]

OK, @SergeDmi is now a reviewer

[pdebuyl]

@whedon start review

[whedon]

OK, I've started the review over in #2973.