[PRE REVIEW]: pylj: A teaching tool for classical simulation about jose-reviews HOT 35 CLOSED

@labarba Resolved, sorry again!

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Hello human, I'm @whedon. I'm here to help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

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Attempting PDF compilation. Reticulating splines etc...

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PDF failed to compile for issue #17 with the following error:

Can't find any papers to compile :-(

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Hello, @arm61 -- Your submission is lacking the required paper. Please see the Author Guidelines.

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Hey @labarba, just realised that the paper directory was still in my .gitignore, resolved in arm61/pylj@ef0e4dc

sorry about that.

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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PDF failed to compile for issue #17 with the following error:

/app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse': (tmp/17/paper/paper.md): mapping values are not allowed in this context at line 2 column 12 (Psych::SyntaxError) from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:379:in parse_stream'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:327:in parse' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:254:in load'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:475:in block in load_file' from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in open'
from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/psych.rb:474:in load_file' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon.rb:67:in initialize'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/bin/whedon:37:in prepare' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-195e6d124d0f/bin/whedon:99:in <top (required)>'
from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in load' from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in

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Title of paper wasn't in inverted commas, fingers crossed for arm61/pylj@3ce1332

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@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...

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--> Check article proof 📄 <--

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Possible reviewers from those already agreed to review of JOSE would include @shivupa, @william-pfalzgraff, and @TJFord. Although I am sure there are many other qualified individuals.

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Hi! I'd like to confirm that I am eligible to be a reviewer as I am only a graduate student. I do have publications on related topics.

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@arm61 -- Thanks for fixing that.

Now, I understand that this software implements basic molecular dynamics algorithms. And I see that you have two Jupyter notebooks in the examples folder (molecular dynamics, and Monte Carlo). If you read the Author Guide, you'll see that we are expecting "learning modules"—that is, complete worked examples with narration.

Your software may be useful by itself as a teaching tool, but it will be much more useful with full worked-out examples.

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I had actually hoped to submit pylj as a piece of educational open-source software in its own right. And then once the laboratory exercises that we are developing within the University of Bath (which make use of pylj) are fully baked these would be submitted as full learning modules (indeed examples/ideal_gas_law/ideal_gas_law.ipynb is an example of one of such exercise).

I would be happy to flesh out the MC and MD examples if necessary to enable submission as an educational open-source software

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I realize that. The first submissions to JOSE have turned out to be different than we were anticipating in the founding of the journal: our Call for Papers talks about two kinds of submissions: "learning modules"—which are fully narrated worked examples that use code to teach a technical subject—and "educational software"—which are infrastructure-type software, like auto-graders.

We've started to get submissions that are just software, but not infrastructure software. That is, the "code part" of a learning module that uses coding to teach. It can be acceptable in some cases but, for the most part, narrated worked out examples are necessary for another instructor to be realistically able to adopt the software in their teaching, or for a self-learner to use the software to teach themselves.

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Ahh right, I see now. In hindsight I recognise that wording in the Authors Guide, however, it is not initially crystal clear. 😄

Before the weekend I will endeavour to flesh out the examples such that someone would be able to easily follow them to understand what the software is capable of and let you know when the appropriate commit is there. Would this be acceptable?

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@TJFord You can find the paper PDF via the link provided by our helpful bot, whedon: #17 (comment)

If you agree to review, yes, you are asked to review the software elements in the submission repository. Have a look at the Reviewer Guidelines. Once the review starts (this thread is the "pre-review"), you will have a handy checklist. Maybe look at this recent completed review: #15

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@shivupa We are happy to involve graduate students in JOSE reviews!

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@labarba Yay! Thanks, I'd love to help out.

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I would also be happy to review this, but perhaps there are enough interested reviewers already? If I am needed, just let me know.

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Thanks, @william-pfalzgraff —we've not had confirmation from @TJFord that he accepts the reviewer role. Stay tuned.

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@whedon assign @labarba as editor

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OK, the editor is @labarba

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@whedon assign @shivupa as reviewer

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OK, the reviewer is @shivupa

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@whedon add @TJFord as reviewer

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OK, @TJFord is now a reviewer

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@whedon start review magic-word=bananas

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OK, I've started the review over in #19. Feel free to close this issue now!

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@william-pfalzgraff Thank you for your gracious volunteering! I'll be sure reaching out to you soon with another submission. In any case, if you're curious, the Review issue is open for comments from anyone. (Follow the link above to the Review issue.)

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