[REVIEW]: pulse #1539

whedon · Jul 1, 2019

Submitting author: @finsberg (Henrik Nicolay Topnes Finsberg)
Repository: https://github.com/finsberg/pulse
Version: 2019.0
Editor: @trallard
Reviewer: @melund, @trallard
Archive: 10.5281/zenodo.3376811

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/9abee735e6abadabe9252d5fcc84fd40"><img src="http://joss.theoj.org/papers/9abee735e6abadabe9252d5fcc84fd40/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/9abee735e6abadabe9252d5fcc84fd40/status.svg)](http://joss.theoj.org/papers/9abee735e6abadabe9252d5fcc84fd40)

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

@melund & @trallard , 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/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @trallard know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @melund

Conflict of interest

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

Code of Conduct

I confirm that I read and will adhere to the JOSS 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: 2019.0
Authorship: Has the submitting author (@finsberg) 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 @trallard

Conflict of interest

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

Code of Conduct

I confirm that I read and will adhere to the JOSS 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: 2019.0
Authorship: Has the submitting author (@finsberg) 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)?

whedon · Jul 1, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @melund, @trallard 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:

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

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

For a list of things I can do to help you, just type:

@whedon commands

whedon · Jul 1, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 1, 2019

👉 Check article proof 📄 👈

trallard · Jul 1, 2019

Hi @melund your reviewer checklist is at the top 👆🏼 thanks a lot for your time and effort.
Let's use this issue to keep the review alive and use the submitting repo for any longer reviews/discussions.

As per usual if you run into any problems feel free to ping me here!

melund · Jul 1, 2019

Thanks, @trallard. I may be a little while before I can get to this. I am going on sommer holiday on Friday. And I will most likely be away from my computer for at least two weeks.

I am sorry, but I am just too busy before I leave to get this done. I will look at it when I get back :)

trallard · Jul 16, 2019

Hi @melund just checking how you are doing? I am planning to move this forward this week - early the next

melund · Jul 17, 2019

@trallard I am traveling in Asia and I only have my phone. I am back in a week and then I will try to get look at this.

trallard · Jul 19, 2019

@whedon remind @melund in 2 weeks

whedon · Jul 19, 2019

Reminder set for @melund in 2 weeks

finsberg · Jul 24, 2019

@whedon generate pdf

whedon · Jul 24, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 24, 2019

👉 Check article proof 📄 👈

finsberg · Jul 24, 2019

@whedon generate pdf

whedon · Jul 24, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 24, 2019

👉 Check article proof 📄 👈

trallard · Jul 25, 2019

/ooo July 25 to August 19

ooo · Jul 25, 2019

👍 Marked @trallard as OOO from Thursday, July 25th 2019 to Monday, August 19th 2019. 📆

whedon · Aug 2, 2019

👋 @melund, please update us on how your review is going.

melund · Aug 5, 2019

I am done with my review. I think pulse more than qualifies for JOSS. It is a really good example of how to structure an open-source software project. With the recent addition of conda-forge package, I am also sure that the library will continue to work in the future.

All in all, nice work @finsberg 👍

trallard · Aug 25, 2019

Thanks @melund
I just noticed that the item for the license has not been checked on your list but I just double checked and this is in compliance. So @finsberg I am going to move to the following editorial activites.

Can you please make sure to perform the following actions:

Generate a new DOI for the software and past it here
Make sure that the package version is up to date and report here: if needed make a new release and report it here
Do a last review of the paper

trallard · Aug 25, 2019

@whedon generate pdf

whedon · Aug 25, 2019

Attempting PDF compilation. Reticulating splines etc...

trallard · Sep 24, 2019

@whedon check references

whedon · Sep 24, 2019

Attempting to check references...

whedon · Sep 24, 2019


OK DOIs

- 10.1007/s10439-012-0593-5 is OK
- 10.1016/j.jocs.2017.07.013  is OK
- 10.1002/cnm.2982 is OK
- 10.1016/j.cam.2012.10.034 is OK
- 10.1098/rspa.2015.0641 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · Sep 24, 2019

👉 Check article proof 📄 👈

trallard · Sep 24, 2019

@whedon set 10.5281/zenodo.3376811 as archive

whedon · Sep 24, 2019

OK. 10.5281/zenodo.3376811 is the archive.

trallard · Sep 24, 2019

@whedon set 2019.0 as version

whedon · Sep 24, 2019

OK. 2019.0 is the version.

trallard · Sep 24, 2019

@finsberg I have completed my editorial checks and I am willing to recommend this for publication 🎉

@melund thanks for your contribution as a reviewer 🙌🏼

@openjournals/jose-eics I am passing this submission to you for acceptance

danielskatz · Sep 24, 2019

@whedon accept

whedon · Sep 24, 2019

Attempting dry run of processing paper acceptance...

whedon · Sep 24, 2019

Check final proof 👉 openjournals/joss-papers#978

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#978, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · Sep 24, 2019

👋 @trallard - fwiw, the accepted label will be automatically attached during the final processing

trallard · Sep 24, 2019

Thanks for the heads up @danielskatz. I have been following the instructions at https://joss.readthedocs.io/en/latest/editing.html#after-acceptance where it says the editor should add the accepted label

danielskatz · Sep 24, 2019

👋 @finsberg - please merge in the changes in finsberg/pulse#8 and finsberg/pulse#9 or let me know what you disagree with

finsberg · Sep 24, 2019

@danielskatz Done

danielskatz · Sep 24, 2019

@whedon generate pdf

whedon · Sep 24, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Sep 24, 2019

👉 Check article proof 📄 👈

danielskatz · Sep 24, 2019

@whedon accept

whedon · Sep 24, 2019

Attempting dry run of processing paper acceptance...

whedon · Sep 24, 2019

Check final proof 👉 openjournals/joss-papers#979

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#979, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · Sep 24, 2019

@whedon accept deposit=true

whedon · Sep 24, 2019

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

whedon · Sep 24, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · Sep 24, 2019

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#980
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01539
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

danielskatz · Sep 24, 2019

Thanks to @melund for reviewing and @trallard for both reviewing and editing.
And congratulations to @finsberg

whedon · Sep 24, 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](https://joss.theoj.org/papers/10.21105/joss.01539/status.svg)](https://doi.org/10.21105/joss.01539)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01539">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01539/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01539/status.svg
   :target: https://doi.org/10.21105/joss.01539

This is how it will look in your documentation:

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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whedon assigned trallard Jul 1, 2019

whedon added the review label Jul 1, 2019

whedon referenced this issue Jul 1, 2019

[PRE REVIEW]: pulse #1475

Closed

whedon assigned melund Jul 2, 2019

This was referenced Jul 25, 2019

[REVIEW]: AutoClassWrapper: a Python wrapper for AutoClass C classification #1390

Closed

[REVIEW]: mLEARn: An Implementation of Multi-layer Perceptron in C++ openjournals/jose-reviews#59

Open

ooo bot referenced this issue Aug 4, 2019

[REVIEW]: lifelines: survival analysis in Python #1317

Closed

36 of 36 tasks complete

ooo bot referenced this issue Aug 12, 2019

[PRE REVIEW]: thurstonianIRT: Thurstonian IRT Models in R #1641

Closed

trallard added the accepted label Sep 24, 2019

danielskatz closed this Sep 24, 2019

openjournals/joss-reviews

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[REVIEW]: pulse #1539

Comments

whedon commented Jul 1, 2019 • edited

Status

Reviewer instructions & questions

Review checklist for @melund

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @trallard

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon assigned trallard Jul 1, 2019

whedon added the review label Jul 1, 2019

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whedon commented Jul 1, 2019 •

edited

trallard commented Sep 24, 2019 •

edited