search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
722 stars 38 forks source link

[REVIEW]: AuditoryStimuli.jl: A Julia package for generating real-time auditory stimuli #3613

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @rob-luke (Robert Luke) Repository: https://github.com/rob-luke/AuditoryStimuli.jl Version: v0.0.11 Editor: @bmcfee Reviewer: @vahid-sb, @jongwook Archive: 10.5281/zenodo.5525443

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b91a016d27744caa7bce0ad558c177ba"><img src="https://joss.theoj.org/papers/b91a016d27744caa7bce0ad558c177ba/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b91a016d27744caa7bce0ad558c177ba/status.svg)](https://joss.theoj.org/papers/b91a016d27744caa7bce0ad558c177ba)

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

@vahid-sb & @jongwook, 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 @bmcfee know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @vahid-sb

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jongwook

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @vahid-sb, @jongwook it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

: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:

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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.02 s (1535.6 files/s, 109903.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           14            383             79           1135
Markdown                        12            194              0            507
YAML                             7              9              9            143
TOML                             2              4              0             42
-------------------------------------------------------------------------------
SUM:                            35            590             88           1827
-------------------------------------------------------------------------------

Statistical information for the repository '058112c24edfc33faa47f0ec' was
gathered on 2021/08/13.
No commited files with the specified extensions were found.
whedon commented 3 years ago

PDF failed to compile for issue #3613 with the following error: 

 Can't find any papers to compile :-(
rob-luke commented 3 years ago

@whedon generate pdf from branch manuscript

whedon commented 3 years ago 
Attempting PDF compilation from custom branch manuscript. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jongwook commented 3 years ago

@whedon list reviewers

whedon commented 3 years ago

Here's the current list of reviewers: https://bit.ly/joss-reviewers

jongwook commented 3 years ago

Great work @rob-luke! Below are my reviews and suggestions for minor revisions.

rob-luke commented 3 years ago

Thank you for the review and kind words @jongwook. I will briefly respond to your feedback. Please let me know if you want more information or further discussion. I also welcome any additional feedback once the review is done too.

Some of the URLs in the citation stick out of the margin and overflow out of the page. I didn't see this issue in a few of JOSS paper I've checked, but I'm not sure this only happens in the draft mode.

I confirm that I see this too. I looked up the three most recent JOSS papers and I confirm that they do not have this URL formatting problem. I then looked up their .bib files and they look the same as mine (see figure below, the URL string is very long). So I am not sure how to solve this @bmcfee do you have any suggestions as to how this may be solved?

Figure from Vaidya et al., (2021). JPhyloRef: a tool for testing and resolving phyloreferences. Journal of Open Source Software, 6(64), 3374, https://doi.org/10.21105/joss.03374 image

Quite a shameless plug, but being a Julia library on audio, MusicProcessing.jl could be considered as a citation to mention alongside librosa. The publication is not open-access, but happy to share the preprint.

A completely appropriate plug and I should have added this earlier as I am aware of the great package, but didnt know it had an associated article. I have updated the manuscript to include this reference.

40% of which is for tests

Yep, I love tests.

The git repository takes up 200M after the initial clone, which doesn't seem to be used in the HEAD of any of the branches. In case those are taken up by a few large files, stripping them from the Git history using git filter-branch commands would be helpful

Thanks for the tip. It was the documentation taking up all the space. I have cleared that history and now the repository is <800 KiB.

The GitHub repository currently lacks the community guidelines, which is one of the JOSS review criteria. It could be a few sentences in the README.md welcoming contribution, and addition of CONTRIBUTING.md or issue templates would be a great plus, which can show up when someone opens up an issue.

As per your suggestion I have added community guidelines to the README. I have also added a CONTRIBUTING.md file. And I have created issue templates.

Again, thank you @jongwook for the review.

rob-luke commented 3 years ago

@whedon generate pdf from branch manuscript

whedon commented 3 years ago 
Attempting PDF compilation from custom branch manuscript. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

bmcfee commented 3 years ago

So I am not sure how to solve this @bmcfee do you have any suggestions as to how this may be solved?

This is apparently a templating issue on our side -- don't worry about it for now, we'll take care of it when it comes time for the final version.

jongwook commented 3 years ago

@rob-luke Thanks for responding so fast, and I meant "40% of which is for tests" as a totally positive note as well!

I confirm that the git clone size has been reduced, and the community guidelines and the issue templates look great. Thanks!

@bmcfee All checkboxes marked off!

rob-luke commented 3 years ago

Thanks @bmcfee and @jongwook

rob-luke commented 3 years ago

Don't bother about deleting comments. No worries, I understand we are all busy. I don't want to use more of your time than required cleaning a chat thread.

vahid-sb commented 3 years ago

@rob-luke I'd come back to you with my comments as soon as I can.

rob-luke commented 3 years ago

@rob-luke I'd come back to you with my comments as soon as I can.

Thanks @vahid-sb I appreciate your volunteered time.

whedon commented 3 years ago

:wave: @vahid-sb, please update us on how your review is going (this is an automated reminder).

bmcfee commented 3 years ago

Just giving another gentle nudge to @vahid-sb here - any update on when you'll be able to move this forward would be appreciated!

vahid-sb commented 3 years ago

Hi @bmcfee I haVe tested the code, run the example files and looked into the documentation. The code does what the documentation says it does and I find it comprehensive enough to be suitable for JOSS. As somebody who has worked on behavioural studies, I see there are some features that I might have needed and currently not available. But I do not find it reasonable to ask for all the features that various users may or may not need, at least in this stage of development. Hence, I'm ready to approve this software/paper in its current form to be published in JOSS.

rob-luke commented 3 years ago

Wonderful!! Thanks @vahid-sb

Of course feel free to add any wish-list features as an issue on the repo. I plan to keep developing this software and adding more features as required.

rob-luke commented 3 years ago

@vahid-sb i think you need to close off all the tick boxes in the first comment. Thanks

vahid-sb commented 3 years ago

@rob-luke I just ticked all the boxes. You have done a good job and I hope it will be used wildly by experimentalists and hope to see it constantly improving. Although I should add given what I have seen, wouldn't bet on it. But maybe efforts such as yours would help to introduce Julia-based libraries to a wider audience.

vahid-sb commented 3 years ago

@bmcfee Thanks for the invitation for the review. It was an interesting experience.

bmcfee commented 3 years ago

Thanks @vahid-sb ! It does look like you still have an unchecked box (Performance) -- can you resolve that?

vahid-sb commented 3 years ago

@bmcfee done!

bmcfee commented 3 years ago

@rob-luke back to the bib formatting issues, can you try using url={...} instead of howpublished={...}? It may not resolve the issue entirely, but it's the first thing to try.

rob-luke commented 3 years ago

@whedon generate pdf from branch manuscript

whedon commented 3 years ago 
Attempting PDF compilation from custom branch manuscript. Reticulating splines etc...
whedon commented 3 years ago

PDF failed to compile for issue #3613 with the following error: 

 Error producing PDF.
! TeX capacity exceeded, sorry [input stack size=5000].
\reserved@a ->\def \reserved@a 
                               *{\@hspacer }\reserved@a 
l.504 ...}https://github.com/sam81/pychoacoustics}

Looks like we failed to compile the PDF
rob-luke commented 3 years ago

@whedon generate pdf from branch manuscript

whedon commented 3 years ago 
Attempting PDF compilation from custom branch manuscript. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rob-luke commented 3 years ago

Genius @bmcfee!! That seems to have fixed the issue. Anything else I need to do now the reviews are in?

rob-luke commented 3 years ago

Actually I can see that the patent numbers aren't formatting correctly in the bibliography either. Please give me a few hours to try and fix this in the bib file.

rob-luke commented 3 years ago

@whedon generate pdf from branch manuscript

whedon commented 3 years ago 
Attempting PDF compilation from custom branch manuscript. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rob-luke commented 3 years ago

Thanks for your patience @bmcfee. I had to switch from @misc to @patent for the formatting to work. But I think it all looks good now. Let me know if there's anything else I need to do.

bmcfee commented 3 years ago

@whedon check references

rob-luke commented 3 years ago

Maybe I can help out our overworked friend Whedon.

There are no dois for the software references, so I added urls:

There are no dois for the patents, so I added URLs to the google patent pages:

I could not find a doi for:

I dont know much about the doi system, so please correct any misunderstanding I have.

bmcfee commented 3 years ago

Thanks @rob-luke - I think that should be fine from the reference side.

You are right that there does not appear to be a DOI for that particular reference. I think it's okay to leave it as is; citing the entire proceedings would be confusing.

Some last minor comments on the article from my side:

Otherwise, the last steps here are to push an up-to-date version of the software (in case anything has changed in response to the reviews); tag the github repo accordingly, and archive it to zenodo or figshare to get a DOI. When you've done that, comment back with the software's DOI so we can link it to the paper.

rob-luke commented 3 years ago

Thanks for the review @bmcfee. I removed the entire sentence fragment as the same content was addressed in the final paragraph. I changed users responses to participant's responses, and fixed the typo you found. Thanks for the extra set of eyes!

I just released a new version of the software (https://github.com/rob-luke/AuditoryStimuli.jl/releases/tag/v0.1.0). And also created a Zenodo doi 10.5281/zenodo.5525443.

bmcfee commented 3 years ago

@whedon generate pdf from branch manuscript

whedon commented 3 years ago 
Attempting PDF compilation from custom branch manuscript. Reticulating splines etc...
whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

bmcfee commented 3 years ago

@whedon set 10.5281/zenodo.5525443 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5525443 is the archive.