Closed whedon closed 2 years ago
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
PDF failed to compile for issue #4116 with the following error:
Can't find any papers to compile :-(
Software report (experimental):
github.com/AlDanial/cloc v 1.88 T=0.24 s (238.0 files/s, 67327.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
XML 9 0 0 7642
Python 36 1410 1607 4910
Markdown 8 70 0 182
YAML 1 1 0 172
Bourne Shell 3 26 15 90
-------------------------------------------------------------------------------
SUM: 57 1507 1622 12996
-------------------------------------------------------------------------------
Statistical information for the repository 'f841f8a3fe7a1563639de96d' was
gathered on 2022/02/01.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
ISDementyev 95 486 303 2.60
InfluenceFunctional 30 16125 9003 82.90
Tao Liu 70 2448 1945 14.49
siminegroup 1 1 1 0.01
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
ISDementyev 129 26.5 5.5 4.65
InfluenceFunctional 6252 38.8 3.8 9.77
Tao Liu 1546 63.2 2.2 22.45
@whedon generate pdf from branch JOSS
Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon invite @will-rowe as editor
@will-rowe has been invited to edit this submission.
@taoliu032 I have just waitlisted
this submission since none of the editors in the bioinformatics domain are currently available. We will assign an editor once one becomes available.
@whedon invite @csoneson as editor
@csoneson do you think you'd be able to help edit this submission?
@csoneson has been invited to edit this submission.
@Kevin-Mattheus-Moerman Thank you very much! I was just wondering today if I should follow up :)
ππ» @taoliu032 - I had a quick look at the submission, and I was wondering if you could perhaps quickly clarify a couple of things before we move on:
macos_installation.sh
in the repo - do you expect it to work also for other operating systems, or is there an inherent restriction to macOS? I suspect the provided environment yml file will not be portable. Thanks!
Hello @csoneson - Thank you very much for questions!
Thank you! Feel free to let us know if there are other questions :D π
@whedon assign @csoneson as editor
OK, the editor is @csoneson
@taoliu032 Thanks! I'll start by looking for a couple of suitable reviewers for this submission - if you have any suggestions (e.g. from the list in the first comment above), feel free to mention them here.
ππ» @ayush9pandey, @ayaanhossain - would you be interested in reviewing this submission for JOSS?
E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands
I don't think I have the right expertise to be a reviewer for this submission, so I'll pass.
@csoneson thank you so much! After going through the list looking for reviewers in computational chemistry/molecular dynamics simulation particularly, here are two suggestions: JoaoRodrigues and rvhonorato - both are GitHub handles. However, I do not know about either of them and there are so many experts under the same categories. Therefore, feel free to select any reviewers as you see fit :) Have a wonderful week!
@ayush9pandey - no problem, thanks for responding!
ππ» @JoaoRodrigues, @rvhonorato - would you be interested in reviewing this submission for JOSS?
E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands
Thanks for the invite @csoneson and for the suggestion @taoliu032.
Yes I'd like to review this one!
Brilliant, thanks @rvhonorato! Once we have one more reviewer we'll start the actual review issue where you'll have your checklist etc.
@csoneson May I ask to slightly modify the code? One of the toggles was not perfectly set up but it does not affect the backbone or main features of the code at all. I literally just need to edit one line and delete a few.
This is my first ever submission to JOSS (very exciting experience!), so I am not sure if I could make changes to the code at the moment or if I should wait till the official review starts to bring up this request. I wonder if you could point out what action would be deemed to be most appropriate?
My apologies for any inconvenience! Thank you very much!
@taoliu032 - yes, feel free to go ahead and make this change. Once the review has started, it may be good to refrain from making major changes at the very same time that the reviewers are going through the code, just because it may become very confusing which version should be checked :)
@csoneson Thank you for clarification! I have just made the change to the JOSS branch. Yes exactly, I do not intend to confuse any reviewers therefore the JOSS branch will become off limits once the review starts π
Pinging @JoaoRodrigues and @ayaanhossain - would one of you be interested in reviewing this submission for JOSS?
E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands
Hi @csoneson, happy to review. Sorry for the delay in replying!
Thank you @JoaoRodrigues! With two reviewers on board, I'm gonna start the review issue, I'll provide more information over there.
@whedon assign @JoaoRodrigues as reviewer
OK, @JoaoRodrigues is now a reviewer
@whedon add @rvhonorato as reviewer
OK, @rvhonorato is now a reviewer
@whedon start review
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4182.
Submitting author: @taoliu032 (Tao Liu) Repository: https://github.com/siminegroup/E2EDNA2 Version: v1.0 Editor: @csoneson Reviewers: @JoaoRodrigues, @rvhonorato 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.
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Thanks for submitting your paper to JOSS @taoliu032. Currently, there isn't an JOSS editor assigned to your paper.
@taoliu032 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).
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