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[REVIEW]: SeqTools: A python package for easy transformation, combination and evaluation of large datasets #1006

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whedon opened this Issue Oct 9, 2018 · 9 comments

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whedon commented Oct 9, 2018

Submitting author: @nlgranger (Nicolas Granger)
Repository: https://github.com/nlgranger/SeqTools
Version: v0.9.0
Editor: @pjotrp
Reviewer: @Benjamin-Lee
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/527a3c6e78ef0b31f93bbd29235d5a0b"><img src="http://joss.theoj.org/papers/527a3c6e78ef0b31f93bbd29235d5a0b/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/527a3c6e78ef0b31f93bbd29235d5a0b/status.svg)](http://joss.theoj.org/papers/527a3c6e78ef0b31f93bbd29235d5a0b)

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

@Benjamin-Lee, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

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

Please try and complete your review in the next two weeks

Review checklist for @Benjamin-Lee

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.9.0)?
  • Authorship: Has the submitting author (@nlgranger) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon Oct 9, 2018

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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Benjamin-Lee it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon commented Oct 9, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Benjamin-Lee it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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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whedon commented Oct 9, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon Oct 9, 2018

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PDF failed to compile for issue #1006 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: bibliography (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' 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-dbdd2bfb2d31/bin/whedon:99: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

'

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whedon commented Oct 9, 2018

PDF failed to compile for issue #1006 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: bibliography (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-dbdd2bfb2d31/bin/whedon:37:in prepare' 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-dbdd2bfb2d31/bin/whedon:99: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

'

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pjotrp Oct 9, 2018

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@whedon generate pdf

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pjotrp commented Oct 9, 2018

@whedon generate pdf

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Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 9, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 9, 2018

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@nlgranger to expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.

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pjotrp commented Oct 9, 2018

@nlgranger to expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.

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nlgranger Oct 9, 2018

@pjotrp I have fixed the contribution guideline and checked thee article proof. Should I bump up the version number to include those modifications in the release?

nlgranger commented Oct 9, 2018

@pjotrp I have fixed the contribution guideline and checked thee article proof. Should I bump up the version number to include those modifications in the release?

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Thanks! You can bump before final publishing.

@Benjamin-Lee you can start review. Please read the reviewer guidelines above

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pjotrp commented Oct 9, 2018

Thanks! You can bump before final publishing.

@Benjamin-Lee you can start review. Please read the reviewer guidelines above

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