Joss-reviews: [PRE REVIEW]: Cocktail Shaker: An open source drug expansion and enumeration library for peptides

[whedon]

Submitting author: @Sulstice (Suliman Sharif)
Repository: https://github.com/Sulstice/cocktail-shaker
Version: v1.1.0
Editor: @csoneson
Reviewers: @floux, @olivertomic

Author instructions

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

@Sulstice if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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.

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

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1916 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:145:in check_fields': Paper YAML header is missing expected fields: affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon.rb:87:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/lib/whedon/processor.rb:36:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-df8b50fe58b8/bin/whedon:116:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[Kevin-Mattheus-Moerman]

@Sulstice your paper seems to be missing some fields (e.g. affiliations).

Have a look here:
https://joss.readthedocs.io/en/latest/submitting.html#checking-that-your-paper-compiles

You can test compile your paper here:
https://whedon.theoj.org/

[Sulstice]

Hi @Kevin-Mattheus-Moerman I just updated the affiliations to "No affiliations" since I currently have none. Does that suffice or is there another protocol I should follow?

[arfon]

@Sulstice - you can add an affiliation of 'None' but this need to be in the affiliations block as described in the example paper: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

[Kevin-Mattheus-Moerman]

@csoneson @will-rowe @majensen could one of you edit this submission? thanks

[majensen]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[csoneson]

@whedon assign @csoneson as editor

[whedon]

OK, the editor is @csoneson

[csoneson]

Hi @Sulstice - could you check Figure 1 in your paper? It doesn't seem to show up.

[arfon]

@Sulstice - you'll need to link to the image URL like this rather than the relative path you're currently using:

https://raw.githubusercontent.com/Sulstice/cocktail-shaker/master/images/figure_1.png

[Sulstice]

@csoneson @arfon Made the change!

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[arfon]

@Sulstice - Could you move the references you currently have in the paper.md file into a paper.bib file and cite them directly please? (You can read how to do that here)

[Sulstice]

@arfon Done!

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[csoneson]

Thanks @Sulstice. I will take care of your submission, and start by finding suitable reviewers. If you have suggestions (e.g., from the list linked in the first post above), please let me know.

[Sulstice]

@csoneson I looked through the list

Username: mskwark, road2stat, semacu seem most reasonable since they are in the peptide/cheminformatics space.

[Sulstice]

Should I be doing a release of the software so y'all can pip install it? Or should I wait pending on whether you approve or not?

[csoneson]

@Sulstice - yes, I think that would be nice.

[csoneson]

@whedon add @floux as reviewer

[whedon]

OK, @floux is now a reviewer

[csoneson]

@mskwark, @semacu - would one of you be willing to review this submission for JOSS?

[Sulstice]

@csoneson I released the cocktail shaker v1.1.0 and it is labeled as a "pre-release" for now pending the JOSS approval.

You should be able to easily install with this command pip install cocktail-shaker==1.1.0

[csoneson]

Ping @mskwark, @semacu

@mskwark, @semacu - would one of you be willing to review this submission for JOSS?

[csoneson]

@olivertomic, @nanxstats - would one of you be willing to review this submission for JOSS?

[olivertomic]

@csoneson , I will be unavailable until mid-february. Would that be too late?

[nanxstats]

Thanks @csoneson for the invitation but I'm a bit busy with a personal project right now and in the next few months. My apologies. Maybe next time...

[csoneson]

Thanks @olivertomic - I'm hoping to start the review soon, so I will reach out to a couple of more potential reviewers, but I may come back to you :)

[csoneson]

@diegoenry, @matthiaslein - would one of you be willing to review this submission for JOSS?

[csoneson]

@fdroessler, @keipertk - would one of you be interested in reviewing this submission for JOSS?

[csoneson]

:wave: @Sulstice - I suspect we may have more luck finding available reviewers after the holidays and the often hectic end of semester time. If you would be ok with a slight delay, and @olivertomic is still available from mid-February, that is one option. Otherwise I suggest we continue looking for reviewers in early January, after the holidays.

@floux - thanks for your patience! I'll start the actual review issue as soon as we have one more reviewer.

[Sulstice]

@csoneson No worries! I'm not in a rush and can wait! Please let me know if there is anything I can do to help as well.

[csoneson]

👋 @olivertomic - Happy New Year! Would you still be interested and available in mid-February to review this submission for JOSS?

Cocktail Shaker: An open source drug expansion and enumeration library for peptides

[olivertomic]

@csoneson - Happy New Year to you too! Sure, I would be still interested to do it from the proposed time.

[csoneson]

@olivertomic - brilliant, thanks! Then I'll add you as a reviewer and start the review issue. I'll also ask our bot whedon to send an automated reminder in mid-February.

[csoneson]

@whedon add @olivertomic as reviewer

[whedon]

OK, @olivertomic is now a reviewer

[csoneson]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1992. Feel free to close this issue now!