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Reviews for the Journal of Open Source Education (JOSE)
http://jose.theoj.org
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[PRE REVIEW]: Virtual training on virtual environments: an online open-source introduction to conda #126

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @marisalim (Marisa Lim) Repository: https://github.com/nih-cfde/training-and-engagement Version: n/a Editor: @allisonhorst Reviewers: @colbrydi, @shanamatthews Managing EiC: Jordan Gorzalski

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e"><img src="https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e/status.svg)](https://jose.theoj.org/papers/17eef7276bb7ca1229556b8c0f44014e)

Author instructions

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

@marisalim 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 JOSE and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSE 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 commented 3 years ago

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

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE 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 commented 3 years ago

PDF failed to compile for issue #126 with the following error: 

 Can't find any papers to compile :-(
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (1091.3 files/s, 154524.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                       143           4853              0           9750
CSS                              4            854             71           6424
JavaScript                       4             31             52           1141
HTML                             5              1             14            375
YAML                            11             35             69            199
R                                2             72             51            157
Python                           1             13              5             30
reStructuredText                 1              5              7              3
-------------------------------------------------------------------------------
SUM:                           171           5864            269          18079
-------------------------------------------------------------------------------

Statistical information for the repository '612f9aeda623bb677e6a53fc' was
gathered on 2021/08/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Amanda Charbonneau              10         20107          20108           96.85
Jeremy Walter                   12             8              8            0.04
Marisa Lim                       2            49              1            0.12
Saranya Canchi                   4          1234              0            2.97
abhijna                          1             5              4            0.02

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
Marisa Lim                   48           98.0          9.8               10.42
Saranya Canchi             1224           99.2          8.4                4.25
labarba commented 3 years ago

@whedon generate pdf from branch JOSE-conda-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSE-conda-paper. Reticulating splines etc...
whedon commented 3 years ago

PDF failed to compile for issue #126 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/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-b63fc70cc085/lib/whedon.rb:155:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:155:in `block in check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/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-b63fc70cc085/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 `<main>'
labarba commented 3 years ago

hi @marisalim — our bot is not able to compile your paper; I don't know why, but I saw you have the string ^[co-first author] after an author name. Could you try deleting that, just in case this is causing the problem?

labarba commented 3 years ago

ping @openjournals/dev — we're having some issues with compiling a paper here. S.O.S.

labarba commented 3 years ago

I tried compiling the paper in our test site: https://whedon.theoj.org ...and it works there!!! What is going on? Help!

labarba commented 3 years ago

@whedon invite @allisonhorst

whedon commented 3 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
labarba commented 3 years ago

@whedon invite @allisonhorst as editor

whedon commented 3 years ago

@allisonhorst has been invited to edit this submission.

marisalim commented 3 years ago

hi @labarba - yes, i can try deleting the ^[co-first author]. is it a problem to have the paper on a github branch?

marisalim commented 3 years ago

@whedon generate pdf from branch JOSE-conda-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSE-conda-paper. Reticulating splines etc...
whedon commented 3 years ago

PDF failed to compile for issue #126 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/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-b63fc70cc085/lib/whedon.rb:155:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:155:in `block in check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:153:in `check_orcids'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:90:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/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-b63fc70cc085/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 `<main>'
marisalim commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
labarba commented 3 years ago

@openjournals/dev — We see an error on compile time coming from orcid_validator.rb

marisalim commented 3 years ago

@whedon generate pdf from branch JOSE-conda-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSE-conda-paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

marisalim commented 3 years ago

@labarba i think it worked this time! there was an accidental empty key/pair in the yaml header. oops, i want to try adding the co-first author back

marisalim commented 3 years ago

@whedon generate pdf from branch JOSE-conda-paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch JOSE-conda-paper. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

allisonhorst commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @allisonhorst

allisonhorst commented 3 years ago

Hi @shanamatthews, thank you for signing up to review for the Journal of Open Source Education! Would you like to contribute a review for this submission, "Virtual training on virtual environments: an online open-source introduction to conda"? Please let me know if you're available and willing to review this submission. Thank you!

allisonhorst commented 3 years ago

Hi @colbrydi, thank you for signing up to review for the Journal of Open Source Education! Would you like to contribute a review for this submission, "Virtual training on virtual environments: an online open-source introduction to conda"? Please let me know if you're available and willing to review this submission. Thank you!

colbrydi commented 3 years ago

Hi @allisonhorst, I should be able to do this review. Please note that I am new to this git centered review process so it may take me some time to figure out.

allisonhorst commented 3 years ago

Thank you @colbrydi, we really appreciate your willingness to review for JOSE! No worries at all about learning the review process. I am new to it, too, and here to help (with the support of the JOSE editorial board). I'll go ahead and add you as a reviewer for this paper and kick off the review process. Please reach out any time with questions, and I'll follow up with some information within the next two days.

allisonhorst commented 3 years ago

@whedon assign @colbrydi as reviewer

whedon commented 3 years ago

OK, @colbrydi is now a reviewer

shanamatthews commented 3 years ago

Hi @shanamatthews, thank you for signing up to review for the Journal of Open Source Education! Would you like to contribute a review for this submission, "Virtual training on virtual environments: an online open-source introduction to conda"? Please let me know if you're available and willing to review this submission. Thank you!

Hi @allisonhorst! I’m happy to review as well.

allisonhorst commented 3 years ago

Wonderful, thank you @shanamatthews! I'll add you as a reviewer then kick-off the review, & follow up with a bit more information.

allisonhorst commented 3 years ago

@whedon add @shanamatthews as reviewer

whedon commented 3 years ago

OK, @shanamatthews is now a reviewer

allisonhorst commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/jose-reviews/issues/130.