[PRE REVIEW]: BIDSonym - a BIDSapp for the pseudo-anonymization of neuroimaging datasets

[whedon]

Submitting author: @PeerHerholz (Peer Herholz)
Repository: https://github.com/PeerHerholz/BIDSonym/
Version: v0.0.4
Editor: @oliviaguest
Reviewers: @deep-introspection, @chrisgorgo, @neuromusic
Managing EiC: Arfon Smith

⚠️ JOSS reduced service mode ⚠️

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.

Author instructions

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

@PeerHerholz 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]

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

⚠️ JOSS reduced service mode ⚠️

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

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.13 s (295.1 files/s, 47003.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            617           1352           1843
reStructuredText                17            285            164            594
TeX                              2             31              0            450
Dockerfile                       1             25              8            211
Bourne Shell                     1              6              7             92
Markdown                         3             30              0             82
YAML                             2              3              4             33
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                            37           1009           1542           3342
-------------------------------------------------------------------------------


Statistical information for the repository '97165b8a3059e64c054c30f8' was
gathered on 2021/03/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Peer Herholz                    16           981             43            8.59
PeerHerholz                     67          6880           4006           91.34
rxqx                             1             4              4            0.07

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
PeerHerholz                3812           55.4         16.5               13.93

[whedon]

PDF failed to compile for issue #3106 with the following error:

/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/orcid_validator.rb:12:in initialize': undefined method strip' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in block in check_orcids'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in each' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in check_orcids'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:90:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in new'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in prepare'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

[arfon]

@PeerHerholz - please remove the line with the missing orcid for your author entry. Also, the editors in your area are a little overloaded right now so I'm going to put your submission into the backlog.

[PeerHerholz]

Hi @arfon,

thx for the pointer and update.
Sorry for the obvious error...I compiled it locally via the docker image and also the web version, but overlooked my missing orcid both times. I updated the paper.md and added my orcid.
Re editors: of course, I understand, thx for letting me know.

Cheers, Peer

[arfon]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3106 with the following error:

pandoc: Bidsonym.bib: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF

[arfon]

pandoc: Bidsonym.bib: openBinaryFile: does not exist (No such file or directory)

@PeerHerholz - Pandoc is case sensitive for filenames your BibTeX file has a different case from how you're referencing it in the paper.md.

[danielskatz]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3106 with the following error:

pandoc: BidSonym.bib: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF

[danielskatz]

@PeerHerholz - this is waiting for your fix as described by @arfon above - #3106 (comment)

[PeerHerholz]

Hi @danielskatz,

thanks for the ping, I'm sorry for the delay.
I addressed the issue and based on the compiled preview I tested, things should work now.

Thanks again.

Cheers, Peer

[danielskatz]

Thanks - the commands to whedon are generally usable by anyone, such as the following

[danielskatz]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[danielskatz]

@PeerHerholz - now back to the waitlist...

[PeerHerholz]

Hi @danielskatz,

ok, thanks for the notice, I wasn't sure if I should go ahead and try again.
I'll do that going forward.

Thanks again.

Cheers, Peer

[oliviaguest]

I am happy to edit this, if it's not been assigned yet and at that stage. 😊

[danielskatz]

@whedon assign @oliviaguest as editor

Thanks!!

[whedon]

OK, the editor is @oliviaguest

[oliviaguest]

@whedon add @deep-introspection as reviewer

[whedon]

OK, @deep-introspection is now a reviewer

[PeerHerholz]

Thanks so much @oliviaguest!

[oliviaguest]

@whedon add @chrisgorgo as reviewer

[whedon]

OK, @chrisgorgo is now a reviewer

[oliviaguest]

@whedon add @neuromusic as reviewer

[whedon]

OK, @neuromusic is now a reviewer

[oliviaguest]

@whedon start review

[whedon]

OK, I've started the review over in #3169.