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[REVIEW]: sluRm: A lightweight wrapper for HPC with Slurm #1493

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whedon opened this issue Jun 6, 2019 · 58 comments

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commented Jun 6, 2019

Submitting author: @gvegayon (George Vega Yon)
Repository: https://github.com/USCbiostats/sluRm
Version: v0.2-0
Editor: @karthik
Reviewer: @mschubert, @mllg
Archive: 10.5281/zenodo.3272773

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/5e1564ca907e4b47accc722ab2913826"><img src="http://joss.theoj.org/papers/5e1564ca907e4b47accc722ab2913826/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/5e1564ca907e4b47accc722ab2913826/status.svg)](http://joss.theoj.org/papers/5e1564ca907e4b47accc722ab2913826)

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

@mschubert & @mllg, 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 @karthik know.

Please try and complete your review in the next two weeks

Review checklist for @mschubert

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: v0.2-0
  • Authorship: Has the submitting author (@gvegayon) 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 @mllg

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: v0.2-0
  • Authorship: Has the submitting author (@gvegayon) 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 6, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @mschubert, @mllg 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 6, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jun 6, 2019

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commented Jun 6, 2019

@whedon check references

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commented Jun 6, 2019

Attempting to check references...
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commented Jun 6, 2019


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1007/10968987_3 may be missing for title: SLURM: Simple Linux Utility for Resource Management

INVALID DOIs

- None
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commented Jun 10, 2019

I finished my first 2 passes. Nice work @gvegayon and @pmarjora!

I'm happy for this to be accepted if the following issues are addressed: #5, #6, #7, #8, #13 (others are optional, but would be nice to have)

edit: forgot to link number 5

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commented Jun 10, 2019

@mschubert this is great, we really appreciate it! We will address those (and the optional issues) ASAP. Thanks!

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commented Jun 17, 2019

I've also finished my first pass. Issues are referenced here, USCbiostats/sluRm#14 and USCbiostats/sluRm#15 are mandatory.

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commented Jun 22, 2019

@gvegayon Please update us once you've addressed these issues.

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commented Jun 25, 2019

OK @mschubert @mllg, I've worked on the issues you created on the project's repo. Addressed all of the required ones plus some of those which were not mandatory (thanks!). LMK if you are OK with the changes, and if so, please close the issues that you consider complete.

Also, following recent changes on how to list contributions on R packages (if you are OK with it) I've added both of you in the list of authors with the role of "rev" (see here).

PS: A thing that I'm not sure whether JOSS does but I think is worthy is to keep track of how much projects change after submission. I am proud to say that my git diff --stat is (+)917 (-)269 lines since the package was submitted (on R/Rmd/md files), so yes, this review has required me to make significant changes towards I think is an improved version of the package, in other words, I think the review process works!

gvegayon added a commit to USCbiostats/sluRm that referenced this issue Jul 8, 2019

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commented Jul 8, 2019

Hey @labarba , the DOI is 10.5281/zenodo.3272773 Thanks!

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commented Jul 8, 2019

Please report the version number here, so we can updated the metadata.

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commented Jul 8, 2019

And the DOI unfortunately does not resolve http://doi.org/10.5281/zenodo.3272773

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commented Jul 8, 2019

I found the tag of the version https://github.com/USCbiostats/sluRm/releases

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commented Jul 8, 2019

@whedon set v0.2-0 as version

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commented Jul 8, 2019

OK. v0.2-0 is the version.

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commented Jul 8, 2019

And the DOI unfortunately does not resolve http://doi.org/10.5281/zenodo.3272773

Now it does :)

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commented Jul 8, 2019

Please check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.

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commented Jul 8, 2019

Please check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.

Just did: Authors (with ORCID), title and description (as provided in the R package). Question: On the upload type field, should I check Publication or Software?

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commented Jul 8, 2019

Software. The Zenodo deposit is an archive of the software.

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commented Jul 8, 2019

@whedon set 10.5281/zenodo.3272773 as archive

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commented Jul 8, 2019

OK. 10.5281/zenodo.3272773 is the archive.

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commented Jul 8, 2019

@whedon accept

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commented Jul 8, 2019

Attempting dry run of processing paper acceptance...
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commented Jul 8, 2019


OK DOIs

- 10.1007/10968987_3 is OK
- 10.21105/joss.00135 is OK
- 10.1093/bioinformatics/btz284 is OK
- 10.21105/joss.00550 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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commented Jul 8, 2019

Check final proof 👉 openjournals/joss-papers#826

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#826, 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 8, 2019

@whedon accept deposit=true

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commented Jul 8, 2019

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

@whedon whedon added the accepted label Jul 8, 2019

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commented Jul 8, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Jul 8, 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#827
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01493
  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 8, 2019

Congratulations, @gvegayon, your JOSS paper is published! 🚀

Big thanks to our editor: @karthik, and reviewers: @mschubert, @mllg —JOSS runs on your contribution 🙏

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commented Jul 8, 2019

👋 Hey @labarba...

Letting you know, @karthik is currently OOO until Friday, August 30th 2019. ❤️

@labarba labarba closed this Jul 8, 2019

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commented Jul 8, 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.01493/status.svg)](https://doi.org/10.21105/joss.01493)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01493">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01493/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01493/status.svg
   :target: https://doi.org/10.21105/joss.01493

This is how it will look in your documentation:

DOI

We need your help!

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 8, 2019

Great! Thanks :)! one small problem! my last name is "Vega Yon", not "Yon" (see here)

@gvegayon gvegayon referenced this issue Jul 8, 2019

Closed

[REVIEW]: fmcmc: A friendly MCMC framework #1427

18 of 18 tasks complete
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commented Jul 8, 2019

Ping @arfon for this ☝️

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commented Jul 8, 2019

Ping @arfon for this ☝️

This should be fixed now. The PDF on the JOSS site can take a while to refresh as it's cached.

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