[PRE REVIEW]: Pychron: Automated Data Collection and Reduction for Noble Gas and Ar/Ar Geochronology

[whedon]

Submitting author: @jirhiker (Jake Ross) Repository: https://github.com/NMGRL/pychron_joss_manuscript Version: v20.1 Editor: Pending Reviewer: Pending Managing EiC: Kristen Thyng

: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.

Author instructions

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

The author's suggestion for the handling editor is @Kevin-Mattheus-Moerman.

@jirhiker 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.

: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

[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (44.7 files/s, 1729.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         2             14              0             51
TeX                              1              2              0             49
-------------------------------------------------------------------------------
SUM:                             3             16              0            100
-------------------------------------------------------------------------------

Statistical information for the repository 'c76ab0aebc2f9ac1b1db7b8a' was
gathered on 2020/12/16.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #2912 with the following error:

/app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in parse': (59c8350a95e4b8a1487240f5/paper.md): mapping values are not allowed in this context at line 2 column 15 (Psych::SyntaxError) from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:inparse_stream' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:390:in parse' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:277:inload' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:578:in block in load_file' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:inopen' from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:577:in load_file' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-a0b7af7c4770/lib/whedon.rb:127:inload_yaml' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-a0b7af7c4770/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-a0b7af7c4770/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-a0b7af7c4770/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-a0b7af7c4770/bin/whedon:58:inprepare' 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:ininvoke_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:instart' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-a0b7af7c4770/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

[kthyng]

Hi @jirhiker, is the software you are submitting for review with JOSS at: https://github.com/NMGRL/pychron?

[jirhiker]

Yes that is correct https://github.com/NMGRL/pychron

On Wed, Dec 16, 2020 at 11:29 AM Kristen Thyng notifications@github.com wrote:

Hi @jirhiker https://github.com/jirhiker, is the software you are submitting for review with JOSS at: https://github.com/NMGRL/pychron?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2912#issuecomment-746782574, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAPQ64GLFTCHQ5KFQR2RNH3SVD37ZANCNFSM4U6M5DNA .

-- Jake Ross, Ph.D Research Scientist II New Mexico Tech New Mexico Bureau of Geology New Mexico Geochronology Research Laboratory Pychron Labs jake.ross@nmt.edu jirhiker@nmt.edu jirhiker@gmail.com 575-835-5994 (office)

[kthyng]

@jirhiker We need the JOSS paper to be in the same repo as the software that is to be reviewed. It can be in a branch if you prefer. As per the docs:

Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository together with your software (although they may be in a short-lived branch which is never merged with the default).

Because of this, I am going to close this issue. Please resubmit your software but move the paper to the same repository as the software, and then that link is what you should associate with the submission (presumably this will be https://github.com/NMGRL/pychron).

Also it looks like the paper isn't compiling correctly yet. You can test run the compilation. More info: https://joss.readthedocs.io/en/latest/submitting.html#checking-that-your-paper-compiles.

[kthyng]

@whedon withdraw

[whedon]

Paper withdrawn.