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[REVIEW]: CytobankAPIstats: Computes Signaling and Population Statistics for Cytometry Data on Cytobank using 'CytobankAPI' #445

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whedon opened this Issue Oct 30, 2017 · 70 comments

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whedon commented Oct 30, 2017

Submitting author: @athrom (Allison Throm)
Repository: https://github.com/athrom/CytobankAPIstats
Version: v1.0
Editor: @pjotrp
Reviewer: @nelkibs
Archive: 10.5281/zenodo.2583300

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/0f9584c0716270ac91c9384d483dc342"><img src="http://joss.theoj.org/papers/0f9584c0716270ac91c9384d483dc342/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/0f9584c0716270ac91c9384d483dc342/status.svg)](http://joss.theoj.org/papers/0f9584c0716270ac91c9384d483dc342)

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 questions

@nelkibs, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @biorelated know.

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 (v1.0)?
  • Authorship: Has the submitting author (@athrom) 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 commented Oct 30, 2017

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @nelkibs 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 as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS 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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george-githinji commented Nov 7, 2017

@nelkibs just a quick ping on the status of this review?

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arfon commented Dec 10, 2017

👋 @nelkibs are you still able to review this submission for us?

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arfon commented Jan 8, 2018

@biorelated - I think we might need to find a new reviewer...

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arfon commented Feb 12, 2018

@biorelated - could you start looking for a new reviewer for this submission please?

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nelkibs commented Feb 12, 2018

@biorelated and @arfon Sorry for the very slow response. I have been off radar for a while. The checkbox button are inactive on my end? Is there a setting I need to change?

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arfon commented Feb 12, 2018

@nelkibs - you should have permissions to edit the checklist - GitHub requires a pretty modern browser - which are you using?

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arfon commented Mar 19, 2018

@nelkibs - how are you getting along here?

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george-githinji commented Mar 19, 2018

@nelkibs raised some issues in regard to this submission. @athrom has not commented on the issues.
@athrom could you kindly comment on these issues?

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athrom commented Mar 20, 2018

I have addressed the issues raised by adding LICENSE and INSTALLATION INSTRUCTIONS documents to github.

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arfon commented May 6, 2018

👋 @nelkibs - please take another look at this submission when you get a chance.

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arfon commented Jun 15, 2018

👋 @nelkibs - could you please take another look at this submission?

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arfon commented Sep 16, 2018

@george-githinji - could you please chase @nelkibs? This review is currently stuck.

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arfon commented Nov 3, 2018

@pjotrp or @mgymrek - would either of you be able to take over as the editor here?

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pjotrp commented Nov 4, 2018

I am pinging @nelkibs and @george-githinji

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george-githinji commented Nov 5, 2018

@arfon Following up on this.

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nelkibs commented Nov 13, 2018

@arfon Not sure why I didn't get notifications at all on this. My github settings have been on mute apparently. I have checked the app. One final comment.
All check boxes have been ticked. You can however add a little more information on community guidelines (e.g how a user can seek help or extend the package etc). Again, very sorry about all the delay. hadn't notice the changes you made 8 months ago.

@nelkibs nelkibs closed this Nov 13, 2018

@arfon arfon reopened this Nov 13, 2018

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arfon commented Nov 13, 2018

Thanks @nelkibs.

You can however add a little more information on community guidelines (e.g how a user can seek help or extend the package etc).

@athrom - do you think you could do this ☝️

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athrom commented Nov 14, 2018

Hi @nelkibs @arfon
I added the followinglines to the README file:

For help using the package, please see the CRAN repository documentation: https://cran.r-project.org/web/packages/CytobankAPIstats/CytobankAPIstats.pdf.

If interested in extending the package, please cite the original CRAN package: https://cran.r-project.org/web/packages/CytobankAPIstats/index.html

Please let me know if there is anything else I need to address/add to this declaration.

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george-githinji commented Nov 14, 2018

Hi @nelkibs please confirm if this is satisfactory.

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pjotrp commented Dec 28, 2018

@whedon assign @pjotrp as editor

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pjotrp commented Dec 28, 2018

@whedon generate pdf

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whedon commented Dec 28, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Dec 28, 2018

PDF failed to compile for issue #445 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: tags (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon.rb:69:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/lib/whedon/processor.rb:32:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-443822f01563/bin/whedon:52:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:in run'
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:in dispatch'
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-443822f01563/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

'

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kyleniemeyer commented Mar 5, 2019

Hi @athrom @pjotrp I'm going to send this back to you for some more work, because the paper itself does not quite meet our expectations. Right now the article itself is extremely brief and doesn't contain much substance; while we don't expect a full article here, it should be 250–1000 words (currently the main article is <150, which put together is a long paragraph). To me, these items need to be improved:

  • A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience
  • A clear statement of need that illustrates the purpose of the software

Further, I think the article should be improved with more description of how the software works, some examples, and use cases.

Also, the first reference has some issues in the way the DOI is being presented, I think.

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pjotrp commented Mar 5, 2019

@kyleniemeyer I think the paper is fine. It is not meant for a non-specialist audience and I understand it. The purpose is stated too. It is an impressively short paper - which is usually hard to do.

Yes, the first DOI may be wrong, but the system did not catch that.

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arfon commented Mar 5, 2019

@kyleniemeyer I think the paper is fine. It is not meant for a non-specialist audience and I understand it. The purpose is stated too. It is an impressively short paper - which is usually hard to do.

This is incorrect. Quoting directly from https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

JOSS welcomes submissions from broadly diverse research areas. For this reason, we request that authors include in the paper some sentences that would explain the software functionality and domain of use to a non-specialist reader. Your submission should probably be somewhere between 250-1000 words.

Terse papers are acceptable, ones that don't meet our documented submission criteria are not.

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kyleniemeyer commented Mar 5, 2019

@pjotrp Furthermore, the @openjournals/joss-eics have agreed that it's our responsibility to give a final pass over a submission, such that we can give feedback to the author(s), reviewers, and editor (if needed) on the expectations we have agreed on.

If you have issues with that, we can take this offline (... online?) to discuss over email, rather than in the review thread.

Yes, the first DOI may be wrong, but the system did not catch that.

While whedon's superpowers are very helpful, the system isn't perfect, and it's the job of the editor & @openjournals/joss-eics to give a human review. Clearly in this case a minor fix is needed.

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athrom commented Mar 11, 2019

@whedon generate pdf

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whedon commented Mar 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 11, 2019

PDF failed to compile for issue #445 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
100 17 0 17 0 0 190 0 --:--:-- --:--:-- --:--:-- 191
Error reading bibliography ./paper.bib (line 49, column 3):
unexpected "v"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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athrom commented Mar 11, 2019

@whedon generate pdf

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whedon commented Mar 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 11, 2019

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athrom commented Mar 11, 2019

@kyleniemeyer @pjotrp
I have updated the PDF to include more details as outlined in paper requirements and updated the doi with the version in Pubmed. Is there anything else I need to do to move the process forward?

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pjotrp commented Mar 12, 2019

Thanks you @athrom. @kyleniemeyer lgtm.

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kyleniemeyer commented Mar 12, 2019

Hi @athrom, thanks for making those edits! The text looks great now.

I did notice some minor issues with the references, so I went ahead and fixed them (along with a few things in the paper) and submitted as two pull requests: athrom/CytobankAPIstats#4 and athrom/CytobankAPIstats#5

Could you merge those and let me know when?

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athrom commented Mar 13, 2019

@kyleniemeyer Thanks for helping with reference formatting. I have merged the pull requests.

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kyleniemeyer commented Mar 13, 2019

@whedon generate pdf

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whedon commented Mar 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 13, 2019

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kyleniemeyer commented Mar 13, 2019

@athrom thanks, looks all good now!

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kyleniemeyer commented Mar 13, 2019

@whedon accept

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whedon commented Mar 13, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Mar 13, 2019


OK DOIs

- 10.1126/science.1198704 is OK
- 10.1002/0471142956.cy1017s53 is OK
- 10.1172/jci.insight.121544 is OK
- 10.1172/jci.insight.123236 is OK

MISSING DOIs

- https://doi.org/10.1007/978-1-4302-4726-5_7 may be missing for title: CytobankAPI: Cytobank API Wrapper for R

INVALID DOIs

- None
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whedon commented Mar 13, 2019

Check final proof 👉 openjournals/joss-papers#547

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#547, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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kyleniemeyer commented Mar 13, 2019

Looks like that missing DOI is a fluke.

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kyleniemeyer commented Mar 13, 2019

@whedon accept deposit=true

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whedon commented Mar 13, 2019

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

@whedon whedon added the accepted label Mar 13, 2019

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whedon commented Mar 13, 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#550
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00445
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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kyleniemeyer commented Mar 13, 2019

@athrom your paper is now published in JOSS!

Thanks to @nelkibs for reviewing and @pjotrp for editing!

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whedon commented Mar 14, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00445/status.svg)](https://doi.org/10.21105/joss.00445)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00445">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00445/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00445/status.svg
   :target: https://doi.org/10.21105/joss.00445

This is how it will look in your documentation:

DOI

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