[REVIEW]: WaveletsExt.jl: Extending the boundaries of wavelets in Julia

[whedon]

Submitting author: @ShozenD (Shozen Dan)
Repository: https://github.com/UCD4IDS/WaveletsExt.jl
Version: v0.1.17
Editor: @bmcfee
Reviewer: @lostanlen, @malmaud
Archive: 10.5281/zenodo.5893843

⚠️ JOSS reduced service mode ⚠️

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 badge code:

HTML: <a href="https://joss.theoj.org/papers/af5f6558736b9c3ec2bd3cf36b0cdf40"><img src="https://joss.theoj.org/papers/af5f6558736b9c3ec2bd3cf36b0cdf40/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/af5f6558736b9c3ec2bd3cf36b0cdf40/status.svg)](https://joss.theoj.org/papers/af5f6558736b9c3ec2bd3cf36b0cdf40)

Reviewers and authors:

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Reviewer instructions & questions

@lostanlen & @malmaud, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @lostanlen

✨ 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

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
• Contribution and authorship: Has the submitting author (@ShozenD) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @malmaud

✨ 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

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
• Contribution and authorship: Has the submitting author (@ShozenD) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lostanlen, @malmaud it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

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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]

Wordcount for paper.md is 1310

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (668.4 files/s, 145034.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           31           1509           1381           7656
Markdown                        17            192              0            974
TeX                              1             17              0            244
YAML                             4              0              1            120
TOML                             3              4              0             53
-------------------------------------------------------------------------------
SUM:                            56           1722           1382           9047
-------------------------------------------------------------------------------


Statistical information for the repository 'cd689c006c37304b3a8af5dd' was
gathered on 2021/11/19.
No commited files with the specified extensions were found.

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF01250288 is OK
- 10.1007/978-1-4612-2544-7_17 is OK
- 10.1109/78.258102 is OK
- 10.1109/ICASSP.1995.480422 is OK
- 10.1093/biomet/81.3.425 is OK
- 10.2307/2291512 is OK
- 10.1109/TSIPN.2016.2632039 is OK
- 10.1137/1.9781611970104 is OK
- 10.1016/B978-0-12-374370-1.50001-9 is OK
- 10.1201/9781439863619 is OK
- 10.1007/978-1-4612-2544-7_5 is OK
- 10.1016/S0031-3203(00)00116-3 is OK
- 10.1016/S0031-3203(02)00019-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[whedon]

👋 @lostanlen, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @malmaud, please update us on how your review is going (this is an automated reminder).

[lostanlen]

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

LICENSE is MIT but not recognized by GitHub as such
UCD4IDS/WaveletsExt.jl#39

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

Necessary vs. recommended dependencies
UCD4IDS/WaveletsExt.jl#40

[bmcfee]

Checking in on this as there hasn't been much action in the past week. @malmaud and @lostanlen . Any updates here?

I know we're going into holidays and it's a busy time of year, but I'd like to know where this one stands and whether we should expect to pause until the new year.

[lostanlen]

both issues i raised two weeks ago are now closed (39 and 40)

[bmcfee]

Checking back in to see how things are going on this one. Any updates?

[lostanlen]

I have raised one issue regarding community guidelines (the last before approval)
UCD4IDS/WaveletsExt.jl#42

[lostanlen]

Update: the issue above has been closed, thanks to @zengfung. At this stage i approve publication in JOSS.

[malmaud]

I completed my review and recommend acceptance.

• This package is using all the latest best-practices for Julia packages (eg the Project.toml dependency system, CI based on Github actions, modular code organization under the src directory).
• The documentation is thorough.
• I was able to locally install the package and run the unit tests without error.
• As far as I know, there is no other native Julia package offering a similarly robust implementation of these wavelet methods.

[bmcfee]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[bmcfee]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF01250288 is OK
- 10.1007/978-1-4612-2544-7_17 is OK
- 10.1109/78.258102 is OK
- 10.1109/ICASSP.1995.480422 is OK
- 10.1093/biomet/81.3.425 is OK
- 10.2307/2291512 is OK
- 10.1109/TSIPN.2016.2632039 is OK
- 10.1137/1.9781611970104 is OK
- 10.1016/B978-0-12-374370-1.50001-9 is OK
- 10.1201/9781439863619 is OK
- 10.1007/978-1-4612-2544-7_5 is OK
- 10.1016/S0031-3203(00)00116-3 is OK
- 10.1016/S0031-3203(02)00019-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[bmcfee]

Thanks @lostanlen and @malmaud !

I'm proof-reading the paper now, and have the following comments / suggestions:

• line 43/44: I think this would be a bit easier to read if you changed the order of "acdwt" and "sdwt" to agree with the order of presentation in the previous sentence.
• Only your first example is numbered, the rest are unnumbered subsections. I think they should be either all numbered, or none of them should be.

Everything else looks good to me so far.

[zengfung]

Thanks @bmcfee for your suggestions! I’ve updated the paper in the most recent commit to the master branch.

[bmcfee]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[bmcfee]

Great, thanks @zengfung ! Next steps for you:

1. Create and tag release of the package (unless the most recent release already addresses all reviewer comments)
2. Archive the release (eg at zenodo or figshare)
3. Report back here with the version number and DOI for the archive

[zengfung]

Hi @bmcfee, I have completed the steps you mentioned.

1. Package has been tagged to v0.1.16.
2. Release is archived at Zenodo with DOI: 10.5281/zenodo.5889625

[bmcfee]

@whedon set 10.5281/zenodo.5889625 as archive

[whedon]

OK. 10.5281/zenodo.5889625 is the archive.

[bmcfee]

@whedon set v0.1.16 as version

[whedon]

OK. v0.1.16 is the version.

[bmcfee]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF01250288 is OK
- 10.1007/978-1-4612-2544-7_17 is OK
- 10.1109/78.258102 is OK
- 10.1109/ICASSP.1995.480422 is OK
- 10.1093/biomet/81.3.425 is OK
- 10.2307/2291512 is OK
- 10.1109/TSIPN.2016.2632039 is OK
- 10.1137/1.9781611970104 is OK
- 10.1016/B978-0-12-374370-1.50001-9 is OK
- 10.1201/9781439863619 is OK
- 10.1007/978-1-4612-2544-7_5 is OK
- 10.1016/S0031-3203(00)00116-3 is OK
- 10.1016/S0031-3203(02)00019-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2901

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2901, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[zengfung]

Hi @bmcfee I was just proof-reading our work for one last time, and I found that some of the code snippets contain lines of codes that are too long. I made the necessary fixes, and the updates are:

VERSION: v0.1.17
DOI: 10.5281/zenodo.5893843

I hope this isn't too late for changes. Apologies for the inconvenience caused.

[arfon]

@whedon set v0.1.17 as version

[whedon]

OK. v0.1.17 is the version.

[arfon]

@whedon set 10.5281/zenodo.5893843 as archive

[whedon]

OK. 10.5281/zenodo.5893843 is the archive.

[arfon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/BF01250288 is OK
- 10.1007/978-1-4612-2544-7_17 is OK
- 10.1109/78.258102 is OK
- 10.1109/ICASSP.1995.480422 is OK
- 10.1093/biomet/81.3.425 is OK
- 10.2307/2291512 is OK
- 10.1109/TSIPN.2016.2632039 is OK
- 10.1137/1.9781611970104 is OK
- 10.1016/B978-0-12-374370-1.50001-9 is OK
- 10.1201/9781439863619 is OK
- 10.1007/978-1-4612-2544-7_5 is OK
- 10.1016/S0031-3203(00)00116-3 is OK
- 10.1016/S0031-3203(02)00019-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2902

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2902, 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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03937 joss-papers#2903
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03937
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@lostanlen, @malmaud – many thanks for your reviews here and to @bmcfee for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@ShozenD – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 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.03937/status.svg)](https://doi.org/10.21105/joss.03937)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03937">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03937/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03937/status.svg
   :target: https://doi.org/10.21105/joss.03937

This is how it will look in your documentation:

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