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[PRE REVIEW]: bfit: A Python Application For Beta-Detected NMR #3405

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @dfujim (Derek Fujimoto) Repository: https://github.com/dfujim/bfit Version: v4.9.1 Editor: @lucydot Reviewers: @nicksisco1932 Managing EiC: Kyle Niemeyer

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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.

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Author instructions

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

@dfujim 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 commented 3 years ago

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 commented 3 years ago

PDF failed to compile for issue #3405 with the following error: 

 /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse': (66d36d9d04c0274c38dccbc8/paper/paper.md): mapping values are not allowed in this context at line 4 column 26 (Psych::SyntaxError)
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/psych.rb:456:in `parse_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:in `load'
    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:in `open'
    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-b63fc70cc085/lib/whedon.rb:127:in `load_yaml'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon.rb:87: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>'
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.15 s (534.8 files/s, 130843.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          66           3649           3579          10681
C/C++ Header                     3             42            120            514
Markdown                         5             73              0            245
TeX                              2             33              6            153
Cython                           1             28             56             64
C++                              1              9             12             34
YAML                             1              5              2             24
-------------------------------------------------------------------------------
SUM:                            79           3839           3775          11715
-------------------------------------------------------------------------------

Statistical information for the repository 'b7d2154d09d333d8518ff347' was
gathered on 2021/06/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Derek Fujimoto                 869         30005          11785           98.69
Ryan M. L. McFadden              4           136             12            0.35
Ξ²-NMR Group                      4           351             55            0.96

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
Derek Fujimoto            18246           60.8         15.2               15.10
Ryan M. L. McFadden         120           88.2          3.6               20.83
Ξ²-NMR Group                 274           78.1          8.5               17.15
kyleniemeyer commented 3 years ago

Hi @dfujim, thanks for your submission to JOSS.

Unfortunately, we have extremely limited editor availability to handle submissions right now, and so we need to put your submission on our waitlist untill an appropriate editor becomes available. Thanks for your patience!

kyleniemeyer commented 3 years ago

In the meantime, it looks like your paper ran into some compilation errors. I think you might need to remove the comments from the file, I don't know if our parser can handle those.

dfujim commented 3 years ago

@whedon generate pdf

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:

dfujim commented 3 years ago

@kyleniemeyer ok strange it was the comments thing. The preview service handles them just fine.

kthyng commented 3 years ago

Is this close enough to your wheelhouse @pdebuyl?

kthyng commented 3 years ago

@whedon invite @pdebuyl as editor

whedon commented 3 years ago

@pdebuyl has been invited to edit this submission.

pdebuyl commented 3 years ago

Hi @kthyng I'll be off until begin august. I also fear that it will be difficult for me to find reviewers, as it is out of my typical areas, so I'd prefer to skip this submission if someone else is available. Else, I can pick it up in august.

kthyng commented 3 years ago

Fair enough @pdebuyl. I think I saw another submission you'd be a good fit for in which case I'll invite you there. You could put up an ooo for the time you'll be out if you'd like to, also.

kthyng commented 3 years ago

Hi @rkurchin and welcome to JOSS! Are you interested in taking on this submission?

kthyng commented 3 years ago

@whedon invite @rkurchin as editor

whedon commented 3 years ago

@rkurchin has been invited to edit this submission.

rkurchin commented 3 years ago

Willing to give it a go, but I don't really know anything about NMR or that particular characterization community, so I wouldn't be able to do a great job of suggesting reviewers if obvious candidates from the list can't do it. I'll leave it up to you, feel free to assign me if you think it's the best fit.

kthyng commented 3 years ago

Ok understandable! We will keep this submission on the waitlist for now. Thanks @rkurchin.

danielskatz commented 3 years ago

πŸ‘‹ @meg-simula - would you be able to edit this submission?

danielskatz commented 3 years ago

@whedon invite @meg-simula as editor

whedon commented 3 years ago

@meg-simula has been invited to edit this submission.

danielskatz commented 3 years ago

πŸ‘‹ @lucydot - Would this be something you could edit as your first JOSS editing assignment?

danielskatz commented 3 years ago

@whedon invite @lucydot as editor

If so, you can use @whedon assign me as editor to assign yourself, or let us know if not

whedon commented 3 years ago

@lucydot has been invited to edit this submission.

lucydot commented 3 years ago

Hi @danielskatz I'm happy to try, though I am not familiar with subject area. Looking at the conversation above it may not fit neatly into any editors area of expertise - if this is the case I'm happy to take it on and do my best to find suitable reviewers.

danielskatz commented 3 years ago

@lucydot - great - please go ahead, and feel free to chat with me and others on slack if you need help with reviewers

lucydot commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

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

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon recommend-accept

# 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

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true
lucydot commented 3 years ago

@whedon assign @lucydot as editor

whedon commented 3 years ago

OK, the editor is @lucydot

lucydot commented 3 years ago

@whedon check repository

lucydot commented 3 years ago

Hi @dfujim I'll be your editor for this submission πŸ‘‹

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).

danielskatz commented 3 years ago

@lucydot - FYI, when we have a paper on the waiting list, it has a waitlisted label. When you get a paper that has such a label, you can remove it, which I will do this time

whedon commented 3 years ago

Wordcount for paper.md is 876

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.24 s (325.5 files/s, 80929.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          66           3722           3624          10887
C/C++ Header                     3             42            120            514
Markdown                         5             70              0            238
TeX                              2             33              6            153
Cython                           1             28             56             64
C++                              1              9             12             34
YAML                             1              5              2             24
-------------------------------------------------------------------------------
SUM:                            79           3909           3820          11914
-------------------------------------------------------------------------------

Statistical information for the repository 'fd6a5214b58d0c10d56958c4' was
gathered on 2021/07/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Derek Fujimoto                 905         30523          11979           98.71
Ryan M. L. McFadden              4           136             12            0.34
Ξ²-NMR Group                      4           351             55            0.94

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
Derek Fujimoto            18570           60.8         16.1               15.04
Ryan M. L. McFadden         120           88.2          5.1               20.83
Ξ²-NMR Group                 274           78.1         10.0               17.15
lucydot commented 3 years ago

Hi πŸ‘‹ @nicksisco1932 would you be able to review this paper given your experience working in NMR? @jpata would you be able to review given your experience with data pipelines for large experimental collaborations?

@dfujim if you can also suggest potential reviewer(s) this will help to expediate the review process.

nicksisco1932 commented 3 years ago

Yes, looks interesting.

dfujim commented 3 years ago

@lucydot Standouts from the end of the list include villaa (Nuclear Physics, Particle Physics) and benjaminbolling (materials chemistry, physics).

Our experiment is somewhat unique in that we are investigating material properties with an NMR probe, but we do so with particle/nuclear physics methods. The technique is similar to muon spin rotation, but much less common. Apart from our lab, I think only ISOLDE is actively conducting implanted-ion beta-NMR experiments.

That being said, I don't think you actually need all too much topic-specific knowledge to review the software. Since our experiments cover a wide range of topics (superconductivity, soft matter, biological processes, battery materials, heterostructures, etc), the software is very general purpose to accommodate each experiment and is mostly concerned with basic data analysis.

jpata commented 3 years ago

@jpata would you be able to review given your experience with data pipelines for large experimental collaborations?

@lucydot I can review this paper, I will look at it this week.

lucydot commented 3 years ago

Hi @dfujim thanks for adding some useful context to the discussion. @jpata and @nicksisco1932 thanks for accepting the invitation to review 🎈

lucydot commented 3 years ago

@whedon assign @jpata as reviewer

whedon commented 3 years ago

OK, @jpata is now a reviewer

lucydot commented 3 years ago

@whedon assign @nicksisco1932 as reviewer

whedon commented 3 years ago

OK, @nicksisco1932 is now a reviewer

lucydot commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3598.