Closed whedon closed 3 years ago
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1093/bioinformatics/btl647 is OK
- 10.1093/bioinformatics/btp324 is OK
- 10.1093/nar/gky1015 is OK
- 10.1016/j.cell.2017.09.004 is OK
- 10.1093/nar/gkz966 is OK
- 10.1038/s41587-019-0074-6 is OK
- 10.1038/nbt.2835 is OK
- 10.1101/201178 is OK
- 10.1002/humu.22981 is OK
- 10.1186/s13059-017-1248-5 is OK
- 10.1016/j.cell.2020.07.017 is OK
- 10.7287/peerj.preprints.970v1 is OK
- 10.1093/bioinformatics/bts635 is OK
- 10.21105/joss.00085 is OK
MISSING DOIs
- 10.25080/majora-ebaa42b7-00d may be a valid DOI for title: Building a framework for predictive science
INVALID DOIs
- arXiv:1207.3907v2 is INVALID
PDF failed to compile for issue #2432 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:77:in doi_citation': undefined method
encode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:64:in make_citation' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:50:in
block in generate_citations'
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in
each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/bibtex_parser.rb:43:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/compilers.rb:246:in
crossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/lib/whedon/processor.rb:95:in
compile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-364ded062842/bin/whedon:82:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in
run'
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:in
dispatch'
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-364ded062842/bin/whedon:119: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
@lincoln-harris I am helping to process the acceptance of this work in JOSS. Can you work on the points below?
[x] You have one invalid DOI :point_up:, this is because you link to an arXiv preprint link rather than a valid DOI. Can you change the doi entry in the bib file to be of the url
type instead? I believe this involves replacing:
doi={arXiv:1207.3907v2}
with
url={https://arxiv.org/abs/1207.3907}
[x] Please add a country to your affiliation(s) (please do not use acronyms for countries)
[x] The hyperlink to ENSEMBL in Protein variants are converted to ENSEMBL protein IDs,...
, appears not to work, please check and update.
@openjournals/dev I identified the invalid DOI but am unsure if this is the reason the paper does not compile for @whedon accept
, can you confirm what the issue is here? Thanks
@Kevin-Mattheus-Moerman done, hopefully that takes care of it.
@whedon accept
Attempting dry run of processing paper acceptance...
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1770
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1770, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@whedon accept deposit=true
Doing it live! Attempting automated processing of paper acceptance...
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? Notify your editorial technical team...
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02432/status.svg)](https://doi.org/10.21105/joss.02432)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02432">
<img src="https://joss.theoj.org/papers/10.21105/joss.02432/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02432/status.svg
:target: https://doi.org/10.21105/joss.02432
This is how it will look in your documentation:
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Congratulations @lincoln-harris!
Thanks for your review efforts @betteridiot, @afrubin, also thank you @lpantano for editing!
awesome!! thanks @betteridiot, @afrubin and @lpantano!! I learned a ton through the review process
Submitting author: @lincoln-harris (Lincoln Harris) Repository: https://github.com/czbiohub/cerebra Version: v1.2.0 Editor: @lpantano Reviewer: @betteridiot, @afrubin Archive: 10.5281/zenodo.4050557
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