Joss-reviews: [REVIEW]: pulse

[whedon]

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:

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 @trallard know.

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

Review checklist for @melund

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: 2019.0
• [x] Authorship: Has the submitting author (@finsberg) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

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

Review checklist for @trallard

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: 2019.0
• [x] Authorship: Has the submitting author (@finsberg) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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 :tada:.

:star: Important :star:

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:

1. 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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[trallard]

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]

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]

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

[melund]

@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]

@whedon remind @melund in 2 weeks

[whedon]

Reminder set for @melund in 2 weeks

[finsberg]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[finsberg]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[trallard]

/ooo July 25 to August 19

[ooo[bot]]

:+1: Marked @trallard as OOO from Thursday, July 25th 2019 to Monday, August 19th 2019. :calendar:

[whedon]

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

[melund]

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]

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:

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

[trallard]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[trallard]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.1007/s10439-012-0593-5 may be missing for title: A novel rule-based algorithm for assigning myocardial fiber orientation to computational heart models
• https://doi.org/10.1016/j.jocs.2017.07.013 may be missing for title: Estimating cardiac contraction through high resolution data assimilation of a personalized mechanical model
• https://doi.org/10.1002/cnm.2982 may be missing for title: Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization
• https://doi.org/10.1016/j.cam.2012.10.034 may be missing for title: A computational method to assess the in vivo stresses and unloaded configuration of patient-specific blood vessels

INVALID DOIs

• None
  ```

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[finsberg]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[finsberg]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

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]

:point_right: Check article proof :page_facing_up: :point_left:

[finsberg]

1. @trallard How do you want me do generate a DOI for the software? Zenodo?
2. Package version number 2019.0 is up to date.
3. I have done final review of the paper, and made a few corrections. The last article proof looks good. I also added the DOIs in the bib-file.

[trallard]

Hey @finsberg you can archive the software in Zenodo and add here the DOI for it

[finsberg]

DOI: 10.5281/zenodo.3376811

[melund]

@trallard I forgot to check the license box. Everything is fine now. Good work @finsberg

[arfon]

:wave: @trallard - I think this paper is waiting on you to make your last checks here.

[trallard]

Hi everyone thanks for the ping! I will finalise this today's evening

[trallard]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[trallard]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

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]

:point_right: Check article proof :page_facing_up: :point_left:

[trallard]

@whedon set 10.5281/zenodo.3376811 as archive

[whedon]

OK. 10.5281/zenodo.3376811 is the archive.

[trallard]

@whedon set 2019.0 as version

[whedon]

OK. 2019.0 is the version.

[trallard]

@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]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/978

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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]

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

[trallard]

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]

👋 @finsberg - please merge in the changes in https://github.com/finsberg/pulse/pull/8 and https://github.com/finsberg/pulse/pull/9 or let me know what you disagree with

[finsberg]

@danielskatz Done

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/979

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/980
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01539
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...

[danielskatz]

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

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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:

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