[PRE REVIEW]: Science Capsule - Capturing the Data Life Cycle #2401

whedon · 2020-06-28T14:34:33Z

Submitting author: @dghoshal-lbl (Devarshi Ghoshal)
Repository: https://bitbucket.org/sciencecapsule/sciencecapsule
Version: v0.1.0
Editor: Pending
Reviewer: Pending
Managing EiC: Arfon Smith

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whedon · 2020-06-28T14:34:37Z

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 · 2020-06-28T14:34:54Z

PDF failed to compile for issue #2401 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2401 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:50:in prepare' 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-446a0298a33b/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

'

whedon · 2020-06-28T14:34:58Z

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

arfon · 2020-06-28T14:36:49Z

@whedon generate pdf

whedon · 2020-06-28T14:37:04Z

PDF failed to compile for issue #2401 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/orcid_validator.rb:12:in initialize': undefined method strip' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:153:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:153:in block in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:151:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:151:in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon.rb:88:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-446a0298a33b/bin/whedon:55:in prepare'
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-446a0298a33b/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 `

'

arfon · 2020-06-28T14:38:36Z

@dghoshal-lbl - please remove the blank orcid entries for the two authors:

 - name: Abdelilah Essiari
   orcid: 
   affiliation: 1
 - name: Michael Beach
   orcid: 
   affiliation: "1, 2"

arfon · 2020-06-28T14:38:46Z

@whedon check repository

whedon · 2020-06-28T14:39:02Z

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.18 s (353.0 files/s, 52135.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          41           1446            410           3861
JSON                             5              0              0           1143
JavaScript                       3            140             36            621
Markdown                         4            233              0            512
HTML                             1             60              4            360
CSS                              2             32              2            132
Ruby                             1             28             12            106
Dockerfile                       2             43             13             85
Bourne Shell                     1             18              7             65
YAML                             3              2              8             63
TeX                              1              1              0             10
-------------------------------------------------------------------------------
SUM:                            64           2003            492           6958
-------------------------------------------------------------------------------


Statistical information for the repository '2401' was gathered on 2020/06/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ludovico Bianchi               173         11901           9046           68.58
Michael Beach                    3           867              0            2.84
abessiari                        2             7              0            0.02
dghoshal-lbl                    31          5781           2920           28.49
unknown                          2            16              5            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
Abdelilah Essiari             7          100.0          0.8                0.00
Ludovico Bianchi           5652           47.5          1.8                5.68
dghoshal-lbl                855           14.8         13.4                7.84

arfon · 2020-06-28T14:41:02Z

@whedon invite @pibion as editor

👋 @pibion - would you be willing to edit this submission for JOSS?

whedon · 2020-06-28T14:41:05Z

@pibion has been invited to edit this submission.

dghoshal-lbl · 2020-06-28T19:31:01Z

@dghoshal-lbl - please remove the blank orcid entries for the two authors:
 - name: Abdelilah Essiari
   orcid: 
   affiliation: 1
 - name: Michael Beach
   orcid: 
   affiliation: "1, 2"

@arfon I have removed the blank orcid entries.

danielskatz · 2020-06-28T19:56:35Z

@whedon generate pdf

whedon · 2020-06-28T19:57:18Z

👉 Check article proof 📄 👈

danielskatz · 2020-06-28T19:58:15Z

@whedon check references

whedon · 2020-06-28T19:58:34Z

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz · 2020-06-28T20:01:05Z

👋 @dghoshal-lbl - can you explain how this is research software that will be cited by users, as opposed to infrastructure software (like operating systems and compilers) that is important to research but is not research software?

whedon added the pre-review label Jun 28, 2020

openjournals deleted a comment from whedon Jun 28, 2020

whedon added Groovy Python Shell labels Jun 28, 2020

openjournals / joss-reviews

[PRE REVIEW]: Science Capsule - Capturing the Data Life Cycle #2401

[PRE REVIEW]: Science Capsule - Capturing the Data Life Cycle #2401

whedon commented Jun 28, 2020 •

edited by arfon

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[PRE REVIEW]: Science Capsule - Capturing the Data Life Cycle #2401

[PRE REVIEW]: Science Capsule - Capturing the Data Life Cycle #2401

Comments

whedon commented Jun 28, 2020 • edited by arfon

whedon commented Jun 28, 2020

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whedon commented Jun 28, 2020 •

edited by arfon