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[PRE REVIEW]: taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. #2142

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @joaomcteixeira (João M.C. Teixeira) Repository: https://github.com/joaomcteixeira/taurenmd Version: v0.8.9 Editor: @richardjgowers Reviewers: @amritagos, @luthaf Managing EiC: Kevin M. Moerman

Author instructions

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

@joaomcteixeira 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 commented 4 years ago

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

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 commented 4 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.14 s (590.2 files/s, 59733.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          36           1272           1397           3162
SVG                              2              1              1           1059
reStructuredText                32            258            150            431
INI                              1             15              0            169
TeX                              1             15              0            140
YAML                             4             14             17            136
Markdown                         6             41              0            118
TOML                             1              0              0              5
-------------------------------------------------------------------------------
SUM:                            83           1616           1565           5220
-------------------------------------------------------------------------------

Statistical information for the repository '2142' was gathered on 2020/03/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Joao MC Teixeira               131          7350           3006           77.51
joaomcteixeira                  72          2245            760           22.49

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
Joao MC Teixeira           5831           79.3          2.3                8.03
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1038/267585a0 is OK
- 10.1002/wcms.1449 is OK
- 10.1021/ct400341p is OK
- 10.1002/jcc.21787 is OK
-  10.25080/Majora-629e541a-00e  is OK
- 10.1016/j.bpj.2015.08.015 is OK
- 10.1002/jcc.23753 is OK
- 10.12688/f1000research.17456.1 is OK
- 10.1371/journal.pcbi.1005659 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

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

Kevin-Mattheus-Moerman commented 4 years ago

@majensen @will-rowe @csoneson are you able to edit this submission?

arfon commented 4 years ago

@Kevin-Mattheus-Moerman - we have a new editor joining imminently who this would be perfect for. Can we hold off on this for a few days until I've had a chance to add them to the editorial team?

Kevin-Mattheus-Moerman commented 4 years ago

@arfon, yes sure that sounds good.

arfon commented 4 years ago

:wave: @richardjgowers - I think this also be an excellent paper for you to take on. What do you think?

/ cc @jedbrown

richardjgowers commented 4 years ago

@arfon yep

Kevin-Mattheus-Moerman commented 4 years ago

@whedon assign @richardjgowers as editor

whedon commented 4 years ago

OK, the editor is @richardjgowers

richardjgowers commented 4 years ago

@luthaf any chance you can help review this?

richardjgowers commented 4 years ago

@amritagos are you free to review this?

Kevin-Mattheus-Moerman commented 4 years ago

@richardjgowers a colleague of mine from NUIG @MahdiTavakol (a PhD student in our lab who works on molecular dynamics simulations) is keen to join this review. Add him if you can use an additional reviewer.

amritagos commented 4 years ago

@richardjgowers I would be happy to review this.

Luthaf commented 4 years ago

@richardjgowers I can do it, or leave it MahdiTavakol if they want to do this!

richardjgowers commented 4 years ago

@whedon add @amritagos as reviewer

whedon commented 4 years ago

OK, @amritagos is now a reviewer

richardjgowers commented 4 years ago

@whedon add @luthaf as reviewer

whedon commented 4 years ago

OK, @luthaf is now a reviewer

richardjgowers commented 4 years ago

@mahditavakol are you free to review this?

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

joaomcteixeira commented 4 years ago

Dear editor and reviewers,

Is there any news regarding restarting operations at JOSS after the suspension announced by @arfon referring to COVID-19? These are difficult times and I most deeply hope all you are in safe conditions.

A simple question: in parallel to this submission, I have continued developing the software. Should I update any data on the manuscript if a new PR is merged?

Thanks in advance,

arfon commented 4 years ago

A simple question: in parallel to this submission, I have continued developing the software. Should I update any data on the manuscript if a new PR is merged?

Given that the software has yet to go out for review I think it's fine to make small changes to the submission paper. Once the reviewers are working on the review I think it would be good to keep things stable.

joaomcteixeira commented 4 years ago

Thanks @arfon, I look forward to the continuation of the review process. Kind Regards,

arfon commented 4 years ago

:wave: @richardjgowers - given there are two reviewers identified already I am going to move this forward to review. If you decide we need a third reviewer then we can add them during the review process later.

arfon commented 4 years ago

@whedon start review

whedon commented 4 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2175.

arfon commented 4 years ago

@amritagos, @Luthaf, @joaomcteixeira - see you all over in #2175 where the actual review will take place.