Joss-reviews: [REVIEW]: EMViz (Early Music Visualization): MATLAB runtime application

[whedon]

Submitting author: @carterenyi (Aaron Carter-Enyi)
Repository: https://github.com/carterenyi/emviz
Version: v1.0.1
Editor: @Kevin-Mattheus-Moerman
Reviewers: @ybayle
Archive: 10.5281/zenodo.3051781

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/a9752eb882eefa9e3ec06e3c4aa6a50d/status.svg)](http://joss.theoj.org/papers/a9752eb882eefa9e3ec06e3c4aa6a50d)

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 instructions & questions

@ybayle, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

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

Review checklist for @ybayle

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: v1.0.1
• [x] Authorship:
  
  
  
  • [x] Has the submitting author (@carterenyi) made major contributions to the software?
  
  
  • [x] Does the full list of paper authors seem appropriate and complete?
  
  

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
  
  
  
  • [x] Works on Windows 7
  
  
• [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)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ybayle, it looks like you're currently assigned as the reviewer for 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:

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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:

[Kevin-Mattheus-Moerman]

@ybayle, @gwynethbradbury, thanks for agreeing to review this submission for JOSS! :tada:
This is where the review process takes place. There are instructions and check boxes at the top of this issue that guide you through the process. Feel free to open issues you have on the project repository, and please refer to them here as well e.g. by making a checkbox list (using - [ ]):

Minor comment

• [ ] I have this minor issue [LINK TO ISSUE 1]

Major issues:

• [ ] and this one [LINK TO ISSUE 2]

Let me know if you have any questions.

[ybayle]

[First part of the review]

- Version: Does the release version given match the GitHub release (v1.0.0)?

There is no release currently (cf https://github.com/carterenyi/emviz/releases). Would it be possible to have a released version or is it preferable to wait for the end of the review process?

- Authorship: Does the full list of paper authors seem appropriate and complete?

There is no clear context about the work done. There are no references to William S. Dula that is mentioned on the pdf on the windows download link nor to Khalif Ali that is mentioned as the proprietary of the repository where the installer and pdf are stored. Would it be possible to have more details about them as they are not mentioned in the list of authors?

- Installation instructions.

The installation procedure works fine on Windows 7. I haven't tested it yet on Mac nor Windows 10 but I will soon. For a direct git clone, there was a missing Matlab addpath that seems to have been resolved with the latest commit https://github.com/carterenyi/emviz/commit/74a60b6d49042d4cf0618d97599a7f70ba78c52d
I have to retry from scratch the install process to double check this.
Yet, there is still a problem with the program when cloned and launch from scratch. The GUI can handle the loading of a MIDI file and plot correctly but after the first plot, there are multiple error messages and no buttons react at all. This is a behaviour that I did not observe with the windows installer. Do you have the same problem on your side? Could you provide a detailed procedure to launch the GUI from a git clone in a Matlab environment?

[carterenyi]

Response to @ybayle https://github.com/ybayle:

First of all, thank you!

Version:
I will work on that, if @Kevin-Mattheus-Moerman
https://github.com/Kevin-Mattheus-Moerman has any insight on the standard
for JOSS, it would be appreciated
Authorship:
I am the sole author of the MATLAB code. Mr. Dula and Mr. Ali were
undergrad students hired to translate the existing MATLAB code into Python.
Mr. Ali dropped from the project without completing any translations, Mr.
Dula is still working with me on the Python translation and when that is
released will be credited as a coauthor.
Installation instructions:
Deploying the functions as a MATLAB Runtime application for Mac with MATLAB
Compiler SDK has been a consistent issue and that version (which was the
best after many tries) only works on about 50% of Mac systems. I have
contacted Mathworks repeatedly but they don't have great support for Mac,
their only suggestion was to zip the application. Perhaps this should be a
Windows only release. Mac users that have MATLAB can run it in MATLAB
without having to use the MATLAB Runtime version.

@Kevin-Mattheus-Moerman https://github.com/Kevin-Mattheus-Moerman what's
the next step?

Aaron

On Sun, Dec 2, 2018 at 2:34 PM Yann Bayle [e-mail] wrote:

[First part of the review]

• Version: Does the release version given match the GitHub release
  (v1.0.0)?

There is no release currently (cf
https://github.com/carterenyi/emviz/releases). Would it be possible to
have a released version or is it preferable to wait for the end of the
review process?

• Authorship: Does the full list of paper authors seem appropriate and
  complete?

There is no clear context about the work done. There are no references to William
S. Dula that is mentioned on the pdf on the windows download link nor to Khalif
Ali that is mentioned as the proprietary of the repository where the
installer and pdf are stored. Would it be possible to have more details
about them as they are not mentioned in the list of authors?

• Installation instructions.

The installation procedure works fine on Windows 7. I haven't tested it
yet on Mac nor Windows 10 but I will soon. For a direct git clone, there
was a missing Matlab addpath that seems to have been resolved with the
latest commit carterenyi/emviz@74a60b6
https://github.com/carterenyi/emviz/commit/74a60b6d49042d4cf0618d97599a7f70ba78c52d
I have to retry from scratch the install process to double check this.
Yet, there is still a problem with the program when cloned and launch from
scratch. The GUI can handle the loading of a MIDI file and plot correctly
but after the first plot, there are multiple error messages and no buttons
react at all. This is a behaviour that I did not observe with the windows
installer. Do you have the same problem on your side? Could you provide a
detailed procedure to launch the GUI from a git clone in a Matlab
environment?

—
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.

--
Aaron Carter-Ényì, PhD, CAGO

[Kevin-Mattheus-Moerman]

@gwynethbradbury thanks again for helping with this review. When can we expect your review contribution?

[Kevin-Mattheus-Moerman]

@carterenyi about the version issue. Yes you can create a release and let us know about the version number after the review process is complete.
Rebranding this as a Windows only release sounds like a good plan for now. Perhaps make changes to the readme/documentation to reflect this. Are you able to continue the review process on a Windows system? Thanks.
@ybayle thanks for your review efforts so far! Would you be able to focus on evaluation for Windows? Thanks.

[ybayle]

@Kevin-Mattheus-Moerman
I will focus on the Windows releases.

References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Could you clarify, which check do you expect from that question?

@carterenyi
Thank you for the details you provided.

Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?

There are no minimial test suite to check for regression or functionnality. Do you think you could do that?

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

There are no documentation. However, you already have documented some functions and some files in your project. Do you think you could refactor your comments and use a documentation generator (e.g. Sphinx, Doxygen, ...)?

Functionality: Have the functional claims of the software been confirmed?

The GUI seems broken in Windows 7 and does not looks like the Mac version displayed in https://github.com/carterenyi/emviz/blob/master/EMViz_Manual.pdf. So far the program seems to work correctly even with this GUI's text misplacements.

[Kevin-Mattheus-Moerman]

@ybayle thanks for these comments.

In relation to DOI's I've opened an issue on this (https://github.com/carterenyi/emviz/issues/4) whenever DOI's are available they need to be added. @carterenyi can you work on adding those?

[carterenyi]

@Kevin-Mattheus-Moerman Yes, I will work on adding the DOIs

On Wed, Dec 19, 2018 at 5:30 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@ybayle https://github.com/ybayle thanks for these comments.

In relation to DOI's I've opened an issue on this (carterenyi/emviz#4
https://github.com/carterenyi/emviz/issues/4) whenever DOI's are
available they need to be added. @carterenyi
https://github.com/carterenyi can you work on adding those?

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.

--
Aaron Carter-Ényì, PhD, CAGO

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

Happy 2019 everybody.

@carterenyi how are you getting on? Did you manage to check those DOI's in the paper?

@ybayle, @gwynethbradbury can you provide an update on the review process? What are the major issues @carterenyi should work on? Thanks.

[ybayle]

Happy 2019 everybody.

Thank you and best wishes to you too.

@ybayle can you provide an update on the review process?

There are still comments to be processed by the author from here: https://github.com/openjournals/joss-reviews/issues/1094#issuecomment-448377467

What are the major issues @carterenyi should work on? Thanks.

The GUI does not display properly on Windows and the Github cloned version only works once.

[carterenyi]

Hello All,

Thanks for checking in. I am in Nigeria without a strong internet
connection so it is not easy for me to work on the article right now. I
hope to complete the DOIs, GUI display and cloning issues by the end of the
month.

Aaron

On Fri, Jan 4, 2019 at 1:49 PM Yann Bayle [e-mail] wrote:

Happy 2019 everybody.

Thank you and best wishes to you too.

@ybayle https://github.com/ybayle can you provide an update on the
review process?

There are still comments to be processed by the author from here: #1094
(comment)
https://github.com/openjournals/joss-reviews/issues/1094#issuecomment-448377467

What are the major issues @carterenyi https://github.com/carterenyi
should work on? Thanks.

The GUI does not display properly on Windows and the Github cloned version
only works once.

—
You are receiving this because you were mentioned.
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.

--
Aaron Carter-Ényì, PhD, CAGO

[Kevin-Mattheus-Moerman]

@carterenyi how are you getting on? Have you been able to resume work on this?

[carterenyi]

Hi Kevin,

Thanks so much for following up. Just got back to US and resumed teaching,
hope to complete the revisions by next week.

Aaron

On Thu, Jan 31, 2019 at 9:15 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi how are you getting on? Have
you been able to resume work on this?

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.

--
Aaron Carter-Ényì, PhD, CAGO

[Kevin-Mattheus-Moerman]

@carterenyi Thanks, looking forward to seeing your comments.

[Kevin-Mattheus-Moerman]

@carterenyi any updates on the review process? Thanks!

[carterenyi]

Hi Kevin,

I've updated my matlab to 2018b on my mac and am now working on the
revisions. I've ordered a pc so that I can deploy the windows version. I
hope to have an update within a week.

On Sun, Feb 10, 2019 at 3:35 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi any updates on the review
process? Thanks!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1094#issuecomment-462114035,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AXim6gwCZUYL8Kd3yGcqCTap3eQvA9U0ks5vL9nfgaJpZM4YtePz
.

--
Aaron Carter-Ényì, PhD, CAGO

[carterenyi]

@Kevin-Mattheus-Moerman DOIs, urls and/or ISBNs have been added to all
references where applicable. The windows laptop I ordered arrived yesterday
so I should be able to fix the GUI display issue for Windows 10 this week.

On Thu, Feb 21, 2019 at 2:41 PM Aaron Carter-Enyi [e-mail]
wrote:

Hi Kevin,

I've updated my matlab to 2018b on my mac and am now working on the
revisions. I've ordered a pc so that I can deploy the windows version. I
hope to have an update within a week.

On Sun, Feb 10, 2019 at 3:35 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi any updates on the review
process? Thanks!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1094#issuecomment-462114035,
or mute the thread
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.

--
Aaron Carter-Ényì, PhD, CAGO

--
Aaron Carter-Ényì, PhD, CAGO

[carterenyi]

@whedon https://github.com/whedon generate pdf

On Sun, Feb 24, 2019 at 7:47 PM Aaron Carter-Enyi [e-mail]
wrote:

@Kevin-Mattheus-Moerman DOIs, urls and/or ISBNs have been added to all
references where applicable. The windows laptop I ordered arrived yesterday
so I should be able to fix the GUI display issue for Windows 10 this week.

On Thu, Feb 21, 2019 at 2:41 PM Aaron Carter-Enyi [e-mail]
wrote:

Hi Kevin,

I've updated my matlab to 2018b on my mac and am now working on the
revisions. I've ordered a pc so that I can deploy the windows version. I
hope to have an update within a week.

On Sun, Feb 10, 2019 at 3:35 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi any updates on the review
process? Thanks!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1094#issuecomment-462114035,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AXim6gwCZUYL8Kd3yGcqCTap3eQvA9U0ks5vL9nfgaJpZM4YtePz
.

--
Aaron Carter-Ényì, PhD, CAGO

--
Aaron Carter-Ényì, PhD, CAGO

--
Aaron Carter-Ényì, PhD, CAGO

[carterenyi]

@whedon https://github.com/whedon generate pdf

On Tue, Feb 26, 2019 at 12:49 PM Aaron Carter-Enyi [e-mail]
wrote:

@whedon https://github.com/whedon generate pdf

On Sun, Feb 24, 2019 at 7:47 PM Aaron Carter-Enyi [e-mail]
wrote:

@Kevin-Mattheus-Moerman DOIs, urls and/or ISBNs have been added to all
references where applicable. The windows laptop I ordered arrived yesterday
so I should be able to fix the GUI display issue for Windows 10 this week.

On Thu, Feb 21, 2019 at 2:41 PM Aaron Carter-Enyi [e-mail]
wrote:

Hi Kevin,

I've updated my matlab to 2018b on my mac and am now working on the
revisions. I've ordered a pc so that I can deploy the windows version. I
hope to have an update within a week.

On Sun, Feb 10, 2019 at 3:35 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi any updates on the review
process? Thanks!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1094#issuecomment-462114035,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AXim6gwCZUYL8Kd3yGcqCTap3eQvA9U0ks5vL9nfgaJpZM4YtePz
.

--
Aaron Carter-Ényì, PhD, CAGO

--
Aaron Carter-Ényì, PhD, CAGO

--
Aaron Carter-Ényì, PhD, CAGO

--
Aaron Carter-Ényì, PhD, CAGO

[carterenyi]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

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

[carterenyi]

@whedon check references

[whedon]

Attempting to check references...

[carterenyi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1094 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 15 0 15 0 0 248 0 --:--:-- --:--:-- --:--:-- 250
Error reading bibliography ./paper.bib (line 66, column 4):
unexpected "t"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[whedon]

```Reference check summary:

OK DOIs

• http://doi.org/doi.org/10.30535/mto.22.1.1 is OK
• http://doi.org/10.2307/745755 is OK
• http://doi.org/10.1121/1.387814 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[carterenyi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[carterenyi]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• http://doi.org/10.30535/mto.22.1.1 is OK
• http://doi.org/10.2307/745755 is OK
• http://doi.org/10.1121/1.387814 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[carterenyi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1094 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Aaron Carter-Ényì, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/author.rb:57:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/author.rb:17:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:109:inblock in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:106:inparse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/bin/whedon:55:inprepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[carterenyi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[carterenyi]

@Kevin-Mattheus-Moerman, @ybayle, I've redeployed the software with MATLAB 2018b on Windows 10 and tested it. I've also added functionality testing instructions in the readme, generated documentation with m2html and updated information about windows only release in the paper and pdf. I did a v1.0 release on GitHub, but not sure if I did that right.

[Kevin-Mattheus-Moerman]

@ybayle, @gwynethbradbury are you able to pick up the review process.

@ybayle are you a happy with the revisions proposed by @carterenyi?

[Kevin-Mattheus-Moerman]

@ybayle, @gwynethbradbury :wave: :point_up:

[ybayle]

The revised version works fine for me.
As the computation process may take some time, it would be nice to have a little text message indicating to wait (or better to have a progress bar). Currently, I don't know if the program has crashed or is running.

Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
This is the last check remaining. There are no automated tests implemented currently for the 3 parts of the algo (namely Data Preparation, Pattern Recognition and Visualization). How critical is this assertion for the review process?

Minor typos in the pdf:

• There are extra parenthesis for some citations (e.g. ([@Wattenberg:2002]) instead of [@Wattenberg:2002])
• currently being developing Python

[carterenyi]

@Kevin-Mattheus-Moerman, @ybayle,

Manual steps are provided to verify functionality of the Pattern
Recognition and Visualization (with the csv output and arc diagram),
neither of which will be correct without the data preparation working. Is
that satisfactory?

I'll fix the minor typos.

On Wed, Mar 20, 2019 at 3:23 PM Yann Bayle [e-mail] wrote:

The revised version works fine for me.

Automated tests: Are there automated tests or manual steps described so
that the function of the software can be verified?
This is the last check remaining. There are no automated tests implemented
currently for the 3 parts of the algo (namely Data Preparation, Pattern
Recognition and Visualization). How critical is this assertion for the
review process?

Minor typos in the pdf:

• There are extra parenthesis for some citations (e.g.
  ([@Wattenberg:2002]) instead of [@Wattenberg:2002])
• currently being developing Python

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[carterenyi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1094 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Aaron Carter-Ényì, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/author.rb:17:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:109:inblock in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:106:inparse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon.rb:73:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:innew'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:32:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:55:inprepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[carterenyi]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[carterenyi]

@Kevin-Mattheus-Moerman, @ybayle,

I've fixed the typos, are we good to go?

[Kevin-Mattheus-Moerman]

@whedon remove @gwynethbradbury as reviewer

[whedon]

OK, @gwynethbradbury is no longer a reviewer

[Kevin-Mattheus-Moerman]

Manual steps are provided to verify functionality of the Pattern Recognition and Visualization (with the csv output and arc diagram), neither of which will be correct without the data preparation working. Is that satisfactory?

@carterenyi would it be easy to add a basic script to automate these manual steps?

[Kevin-Mattheus-Moerman]

@carterenyi some comments on the paper:

• [x] "is brilliant" can you rephrase this more professionally? e.g. perhaps you mean to say something like: innovative and useful?
• [x] Missing ) bracket in: "(now available in MATLAB Runtime[)], and ATAVizM (currently being developed in Python)"
• [x] Should "C+" be written as "C++"?
• [x] Are there any references/links (Zenodo, Github, website,...) for "ATAVizM" since there are currently none (and I cannot find it through a quick Google), should the comparison to "ATAVizM" (which is listed as in development) perhaps be removed? Instead, perhaps mention it as future work at the end?
• [x] Table 1 lists "Add ..." for the ATAVizM components. Does this mean these features are to be added? So this is a work in progress? Again perhaps remove all references to this package here.
• [x] Consider removing "—instead of just a pretty picture.", to me the nice summary given is enough and this statement feels out of place.

[carterenyi]

@whedon generate pdf

On Mon, Apr 8, 2019 at 4:46 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi some comments on the paper:

• "is brilliant" can you rephrase this more professionally? e.g.
  perhaps you mean to say something like: innovative and useful?
• Missing ) bracket in: "(now available in MATLAB Runtime[)], and
  ATAVizM (currently being developed in Python)"
• Should "C+" be written as "C++"?
• Are there any references/links (Zenodo, Github, website,...) for
  "ATAVizM" since there are currently none (and I cannot find it through a
  quick Google), should the comparison to "ATAVizM" (which is listed as in
  development) perhaps be removed? Instead, perhaps mention it as future work
  at the end?
• Table 1 lists "Add ..." for the ATAVizM components. Does this mean
  these features are to be added? So this is a work in progress? Again
  perhaps remove all references to this package here.
• Consider removing "—instead of just a pretty picture.", to me the
  nice summary given is enough and this statement feels out of place.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[carterenyi]

Hi @Kevin-Mattheus-Moerman,

Thanks for the suggested revisions and all your help through this process.

I have responded to all:
-revised wording as you suggested
-the check is basically is automated, the short CSV file and visualization
are the output of running the test file and the user can just briefly
compare it to those printed in the manual, I'm not sure how I would make it
more automated
-I did not remove ATAVizM, because that is the funded project of which this
is a basic version, I instead added some elaboration and links to the
website and a GitHub repository where those materials will be available in
the near future.

On Mon, Apr 8, 2019 at 2:24 PM whedon [e-mail] wrote:

👉 Check article proof 📄 👈
https://github.com/openjournals/joss-papers/blob/joss.01094/joss.01094/10.21105.joss.01094.pdf

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[Kevin-Mattheus-Moerman]

@ybayle If you can confirm the somewhat automated tests @carterenyi describes then this is sufficient. If so, are you able to tick the last box? Thanks!

[Kevin-Mattheus-Moerman]

@ybayle :point_up:

[ybayle]

@carterenyi The provided test works for me.

However, this is not an automated test nor a suite of unit tests.
If I refer to this: Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?, yes there is one manual test that can check the output of the whole program but no there are not test verfying the output of each function.
@Kevin-Mattheus-Moerman How do you handle this? If you think this is enough, I can check the box, otherwise tell me if I need to re-check something!

[carterenyi]

Thanks @ybayle and @Kevin-Mattheus-Moerman for your patience with me. While
I know signal processing, I don't know much about software development
standards--and I'm learning a lot with this process!

Unfortunately, while I am understanding better the nature of an automated
test, it is not possible for me to redeploy the windows version of the
software right now (I bought a used windows machine but it stopped working
and I returned it). Is it possible to go with the manual tests?

Thanks,
Aaron

On Wed, May 1, 2019 at 7:42 AM Yann Bayle [e-mail] wrote:

@carterenyi https://github.com/carterenyi The provided test works for
me.

However, this is not an automated test nor a suite of unit tests.
If I refer to this: Automated tests: Are there automated tests or manual
steps described so that the function of the software can be verified?,
yes there is one manual test that can check the output of the whole program
but no there are not test verfying the output of each function.
@Kevin-Mattheus-Moerman https://github.com/Kevin-Mattheus-Moerman How
do you handle this? If you think this is enough, I can check the box,
otherwise tell me if I need to re-check something!

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[Kevin-Mattheus-Moerman]

@ybayle since you confirmed the tests work I believe this is fine, so yes please go ahead and tick that last box. Thanks @carterenyi for the explanation.

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.30535/mto.22.1.1 is OK
• 10.7551/mitpress/6575.001.0001 is OK
• 10.2307/j.ctt1xp3ss4 is OK
• 10.2307/745755 is OK
• 10.1121/1.387814 is OK
• 10.1109/INFVIS.2002.1173155 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[Kevin-Mattheus-Moerman]

@carterenyi at this point can you:

• [ ] Please archive a copy of the reviewed software on Zenodo (some find the steps defining this automated process useful). Once you've done that can you provide us with the DOI of the archived version?
• [ ] Can you please list the final version label for the reviewed software?

[carterenyi]

@Kevin-Mattheus-Moerman Zenodo is down, but I will take care of that as
soon as it is up.

What do you mean by final version label (is it e.g. "1.0") and where should
I list it?

Thanks,
Aaron

On Wed, May 15, 2019 at 4:14 AM Kevin Mattheus Moerman <
[email protected]> wrote:

@carterenyi https://github.com/carterenyi at this point can you:

• Please archive a copy of the reviewed software on Zenodo
  http://about.zenodo.org/ (some find the steps defining this
  https://guides.github.com/activities/citable-code/ automated process
  useful). Once you've done that can you provide us with the DOI of the
  archived version?
• Can you please list the final version label for the reviewed
  software?

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[carterenyi]

@Kevin-Mattheus-Moerman I have taken care of the Zenodo DOI and listed the Version Release

[carterenyi]

@carterenyi at this point can you:

• [x] Please archive a copy of the reviewed software on Zenodo (some find the steps defining this automated process useful). Once you've done that can you provide us with the DOI of the archived version?
• [x] Can you please list the final version label for the reviewed software?

[Kevin-Mattheus-Moerman]

@whedon set 10.5281/zenodo.2919897 as archive

[whedon]

OK. 10.5281/zenodo.2919897 is the archive.

[Kevin-Mattheus-Moerman]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[Kevin-Mattheus-Moerman]

@openjournals/joss-eics this submission is ready to be accepted. Can you confirm the title of this archived version is okay or does it need to be amended to match this submission? https://zenodo.org/record/2919897

[labarba]

We prefer that the Zenodo deposit match the title of the paper. Also, note that here the author list needs editing, too. On editing the Zenodo metadata, I suggest that the author also add their ORCID.

[carterenyi]

@openjournals/joss-eics
https://github.com/orgs/openjournals/teams/joss-eics I've made the
changes to Zenodo deposit and metadata

On Sat, May 18, 2019 at 1:27 PM Lorena A. Barba [e-mail]
wrote:

We prefer that the Zenodo deposit match the title of the paper. Also, note
that here the author list needs editing, too. On editing the Zenodo
metadata, I suggest that the author also add their ORCID.

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[labarba]

Is @arfon a co-author??

[arfon]

Is @arfon a co-author??

Looks like I fixed the paper for the author: https://github.com/carterenyi/emviz/commits?author=arfon

@carterenyi - you should probably remove me from the authors on Zenodo :-)

Also, @labarba - please could I process the acceptance of this paper? I've been making some changes to Whedon I'd like to test when accepting this paper.

[carterenyi]

Hello @labarba https://github.com/labarba and @arfon
https://github.com/arfon,

The only way I could figure out how to remove Arfon is to submit a new
version (v1.0.1) to zenodo.

Here is the new Zenodo DOI:
10.5281/zenodo.3051781 https://doi.org/10.5281/zenodo.3051781

Thank you @Kevin-Mattheus-Moerman and @ybayle https://github.com/ybayle for
all your time on this submission!

On Sat, May 18, 2019 at 3:09 PM Arfon Smith [e-mail]
wrote:

Is @arfon https://github.com/arfon a co-author??

Looks like I fixed the paper for the author:
https://github.com/carterenyi/emviz/commits?author=arfon

@carterenyi https://github.com/carterenyi - you should probably remove
me from the authors on Zenodo :-)

Also, @labarba https://github.com/labarba - please could I process the
acceptance of this paper? I've been making some changes to Whedon I'd like
to test when accepting this paper.

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[arfon]

@whedon set 10.5281/zenodo.3051781 as archive

[whedon]

OK. 10.5281/zenodo.3051781 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.30535/mto.22.1.1 is OK
• 10.7551/mitpress/6575.001.0001 is OK
• 10.2307/j.ctt1xp3ss4 is OK
• 10.2307/745755 is OK
• 10.1121/1.387814 is OK
• 10.1109/INFVIS.2002.1173155 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/706

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/706, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@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/707
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01094
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...

[arfon]

@ybayle - many thanks for your review here and to @Kevin-Mattheus-Moerman for editing this submission ✨

@carterenyi - your paper is now accepted into JOSS :zap::rocket::boom:

[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](http://joss.theoj.org/papers/10.21105/joss.01094/status.svg)](https://doi.org/10.21105/joss.01094)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01094">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01094/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01094/status.svg
   :target: https://doi.org/10.21105/joss.01094

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.salsalabs.org/donate-to-joss

[Kevin-Mattheus-Moerman]

@arfon did you update the version tag to v1.0.1?

[arfon]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.