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[REVIEW]: CGIMP: Real-time exploration and covariate projection for self-organizing map datasets' #1520

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whedon opened this issue Jun 24, 2019 · 40 comments

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commented Jun 24, 2019

Submitting author: @adadiehl (Adam Diehl)
Repository: https://github.com/Boyle-Lab/CGIMP
Version: 1.0.0
Editor: @lpantano
Reviewers: @adriancbondia, @ @arunhpatil, @arunhpatil
Archive: 10.5281/zenodo.3276069

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/e9e7eb0708270dcaae9a2f322d346ff5"><img src="http://joss.theoj.org/papers/e9e7eb0708270dcaae9a2f322d346ff5/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/e9e7eb0708270dcaae9a2f322d346ff5/status.svg)](http://joss.theoj.org/papers/e9e7eb0708270dcaae9a2f322d346ff5)

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) by leaving comments 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

@adriancbondia & @ @arunhpatil, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lpantano know.

Please try and complete your review in the next two weeks

Review checklist for @adriancbondia

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 (1.0.0)?
  • Authorship: Has the submitting author (@adadiehl) 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)?

Review checklist for @ @arunhpatil

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 (1.0.0)?
  • Authorship: Has the submitting author (@adadiehl) 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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commented Jun 24, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @adriancbondia, @ @arunhpatil it looks like you're currently assigned to review 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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commented Jun 24, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 24, 2019

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commented Jun 26, 2019

@whedon add @arunhpatil as reviewer

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commented Jun 26, 2019

OK, @arunhpatil is now a reviewer

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commented Jun 27, 2019

Hi @adadiehl,

Do you have a link for the reference without DOI, or what exactly is that, a chapter in a book, a talk...?

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commented Jun 27, 2019

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commented Jun 27, 2019

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commented Jun 27, 2019

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commented Jun 27, 2019

@whedon commands

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commented Jun 27, 2019

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

# 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

# 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 accept the paper and deposit with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

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commented Jun 27, 2019

@whedon generate pdf

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commented Jun 27, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 27, 2019

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commented Jun 27, 2019

@whedon check references

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commented Jun 27, 2019

Attempting to check references...
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commented Jun 27, 2019


OK DOIs

- 10.18637/jss.v021.i05 is OK
- 10.1016/j.cell.2013.09.043 is OK
- 10.1038/nature13668 is OK
- 10.1109/5.58325 is OK
- 10.1093/bioinformatics/btq033 is OK
- 10.1093/nar/gky018 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 8, 2019

Hi @adriancbondia and @arunhpatil , I think you finished the review but can you confirm here to make it clear? thanks!

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commented Jul 9, 2019

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commented Jul 9, 2019

Yes. The review is complete. The application CGIMP has an interactive browser with lot of features for users to explore, however as mentioned in the documentation, the first few attempts load slowly due to indexing which upon subsequent usage loads faster. This is a minor issue and can be further improvised. I confirm.

@lpantano lpantano added the accepted label Jul 9, 2019

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commented Jul 9, 2019

Hi @adadiehl , can you create a Zenodo archive where the title and authors match the paper version and give me back the doi link?

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commented Jul 9, 2019

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commented Jul 9, 2019

@whedon set 10.5281/zenodo.3276069 as archive

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commented Jul 9, 2019

OK. 10.5281/zenodo.3276069 is the archive.

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commented Jul 9, 2019

Thanks, can you make sure the title is the same? I don't know if you would need a new doi link then, but let me know. Cheers

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commented Jul 9, 2019

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commented Jul 9, 2019

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commented Jul 9, 2019

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commented Jul 9, 2019

@openjournals/joss-eics, I think we are all set, please take a look. Thanks!

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commented Jul 10, 2019

@whedon accept

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commented Jul 10, 2019

Attempting dry run of processing paper acceptance...
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commented Jul 10, 2019


OK DOIs

- 10.18637/jss.v021.i05 is OK
- 10.1016/j.cell.2013.09.043 is OK
- 10.1038/nature13668 is OK
- 10.1109/5.58325 is OK
- 10.1093/bioinformatics/btq033 is OK
- 10.1093/nar/gky018 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 10, 2019

Check final proof 👉 openjournals/joss-papers#830

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#830, 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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commented Jul 10, 2019

@whedon accept deposit=true

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commented Jul 10, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Jul 10, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Jul 10, 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#831
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01520
  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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commented Jul 10, 2019

@adriancbondia, @arunhpatil - many thanks for your reviews and to @lpantano for editing this submission

@adadiehl - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Jul 10, 2019

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commented Jul 10, 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.01520/status.svg)](https://doi.org/10.21105/joss.01520)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01520">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01520/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01520/status.svg
   :target: https://doi.org/10.21105/joss.01520

This is how it will look in your documentation:

DOI

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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commented Jul 10, 2019

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