[PRE REVIEW]: SeqTools: A python package for easy transformation, combination and evaluation of large datasets

[whedon]

Submitting author: @nlgranger (Nicolas Granger)
Repository: https://github.com/nlgranger/SeqTools
Version: v0.9.0
Editor: @pjotrp
Reviewers: @Benjamin-Lee

Author instructions

Thanks for submitting your paper to JOSS @nlgranger. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.

@nlgranger 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

[Benjamin-Lee]

This looks really cool! @arfon I'd be happy to help out in the review of this.

[arfon]

@mgymrek @pjotrp - would either if you be willing to edit this submission for JOSS?

[pjotrp]

Yes, I am happy to help out. Unless Melissa feels she should do this one.

[pjotrp]

@whedon assign @pjotrp as editor

[whedon]

OK, the editor is @pjotrp

[pjotrp]

@whedon assign @Benjamin-Lee as reviewer

[whedon]

OK, the reviewer is @Benjamin-Lee

[pjotrp]

@whedon start review magic-word=bananas

[whedon]

OK, I've started the review over in #1006. Feel free to close this issue now!

[pjotrp]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #998 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: bibliography (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:69:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:99:in <top (required)>'
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

'

[pjotrp]

@nlgranger please fix the PDF. You can generate it yourself with `@whedon generate pdf'

[nlgranger]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #998 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:91:in block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Mounîm A. El Yacoubi (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:89:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:89:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:70:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:99:in <top (required)>'
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

'

[nlgranger]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈