[REVIEW]: treesiftr: An R package and server for viewing phylogenetic trees and data

whedon commented 6 years ago

Submitting author: @wrightaprilm (April Wright) Repository: https://github.com/wrightaprilm/treesiftr Version: v1.0.0 Editor: @juanklopper Reviewer: @ethanwhite, @rachelss Archive: 10.5281/zenodo.2541824

Status

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Markdown: [![status](http://jose.theoj.org/papers/82b5b8c6223ec0735602bbf927045913/status.svg)](http://jose.theoj.org/papers/82b5b8c6223ec0735602bbf927045913)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ethanwhite & @rachelss, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/jose-reviews/invitations

The reviewer guidelines are available here: https://jose.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @juanklopper know.

Review checklist for @ethanwhite

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: Does the release version given match the repository release (v1.0.0)?
[x] Authorship: Has the submitting author (@wrightaprilm) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @rachelss

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

[x] Repository: Is the source for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: Does the release version given match the repository release (v1.0.0)?
[x] Authorship: Has the submitting author (@wrightaprilm) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

wrightaprilm commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

wrightaprilm commented 5 years ago

All right, got 'em. I also fixed a couple title case issues - R as a solo letter in an article title needs to be {R} to escape auto-format.

arfon commented 5 years ago

@labarba @wrightaprilm - the margin bug should also now be fixed because of the changes in https://github.com/openjournals/whedon/pull/39.

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

PDF failed to compile for issue #35 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 14 0 14 0 0 23 0 --:--:-- --:--:-- --:--:-- 23 /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/lib/whedon/bibtex.rb:44:in make_citation': undefined methodhas_field?' for # (NoMethodError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/lib/whedon/bibtex.rb:31:in block in generate_citations' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:ineach' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/lib/whedon/bibtex.rb:29:ingenerate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/lib/whedon/processor.rb:214:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/lib/whedon/processor.rb:91:incompile' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/bin/whedon:76:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a8346675b421/bin/whedon:113: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

'

labarba commented 5 years ago

I just tried to compile locally with whedon download then whedon compile, and I get a similar error message. Strange that @whedon generate pdf on here works, but whedon compile fails. Aren't they supposed to be doing the same thing, @arfon?

labarba commented 5 years ago

My error message:

bundler: failed to load command: whedon (/Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/bin/whedon)
NoMethodError: undefined method `has_field?' for #<BibTeX::String an = "The American Naturalist">
Did you mean?  has_type?
  /Users/labarba/GitHub/whedon/lib/whedon/bibtex.rb:44:in `make_citation'
  /Users/labarba/GitHub/whedon/lib/whedon/bibtex.rb:31:in `block in generate_citations'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:in `each'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/bibtex-ruby-4.4.7/lib/bibtex/bibliography.rb:150:in `each'
  /Users/labarba/GitHub/whedon/lib/whedon/bibtex.rb:29:in `generate_citations'
  /Users/labarba/GitHub/whedon/lib/whedon/processor.rb:214:in `generate_crossref'
  /Users/labarba/GitHub/whedon/lib/whedon/processor.rb:91:in `compile'
  /Users/labarba/GitHub/whedon/bin/whedon:76:in `compile'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
  /Users/labarba/GitHub/whedon/bin/whedon:113:in `<top (required)>'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/bin/whedon:23:in `load'
  /Users/labarba/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/bin/whedon:23:in `<top (required)>'
electra:whedon labarba$

labarba commented 5 years ago

@wrightaprilm — I see that you are using a long file bibliography.bib as the source of citations. Would it be too annoying to copy and paste just the BibTeX entries you are citing in the paper into a paper.bib and use that instead?

wrightaprilm commented 5 years ago

Let's try it!

wrightaprilm commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

wrightaprilm commented 5 years ago

OK, had to fix one citation to R core, but looks fine. Fingers crossed!

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/24

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/24, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

wrightaprilm commented 5 years ago

OK, looks good!

labarba commented 5 years ago

Nope ... some DOI links are broken. See screenshot.

arfon commented 5 years ago

I think bibtex expects doi fields in paper.bib to be of the form

10.1662/0002-7685(2007)69[71:csmaet]2.0.co;2 

not 

https://doi.org/10.1662/0002-7685(2007)69[71:csmaet]2.0.co;2

Entries like this one need updating: https://github.com/wrightaprilm/treesiftr/blob/master/paper.bib#L181

wrightaprilm commented 5 years ago

Right, just went ahead and stripped off the `https' wrappers. Will re-render.

wrightaprilm commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

labarba commented 5 years ago

Checking all the links and ... http://ggplot2.org shows "not found"?

labarba commented 5 years ago

Did you want this URL instead? https://ggplot2.tidyverse.org

wrightaprilm commented 5 years ago

I changed the link in my .bib. That's from the maintainer's own bibtex entry on their site. I should probably make a pull request and let them know its broken. Good catch!

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/25

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/25, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

labarba commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 5 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSE! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/jose-papers/pull/26
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/jose.00035
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba commented 5 years ago

Congratuations, @wrightaprilm, your paper is published! 🎉 (you made us work hard for this one, phew!)

Big thank you to your handling editor, @juanklopper and your reviewers, @ethanwhite and @rachelss 🙏

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://jose.theoj.org/papers/10.21105/jose.00035/status.svg)](https://doi.org/10.21105/jose.00035)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00035">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00035/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00035/status.svg
   :target: https://doi.org/10.21105/jose.00035

This is how it will look in your documentation:

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wrightaprilm commented 5 years ago

Thanks so much @juanklopper, @rachelss, @ethanwhite and @labarba!

labarba commented 5 years ago

https://twitter.com/JOSE_TheOJ/status/1086026521846996994

juanklopper commented 5 years ago

Well done @wrightaprilm and thank you to everyone for their input.

openjournals / jose-reviews