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

whedon commented 2 years ago

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

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Status

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Markdown: [![status](https://joss.theoj.org/papers/af5f6558736b9c3ec2bd3cf36b0cdf40/status.svg)](https://joss.theoj.org/papers/af5f6558736b9c3ec2bd3cf36b0cdf40)

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@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

[x] 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

[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] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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

[x] 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

[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] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

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 :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.

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whedon commented 2 years ago

Wordcount for paper.md is 1310

whedon commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

whedon commented 2 years ago

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

whedon commented 2 years ago

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

lostanlen commented 2 years ago

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 https://github.com/UCD4IDS/WaveletsExt.jl/issues/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 https://github.com/UCD4IDS/WaveletsExt.jl/issues/40

bmcfee commented 2 years ago

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 commented 2 years ago

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

bmcfee commented 2 years ago

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

lostanlen commented 2 years ago

I have raised one issue regarding community guidelines (the last before approval) https://github.com/UCD4IDS/WaveletsExt.jl/issues/42

lostanlen commented 2 years ago

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

malmaud commented 2 years ago

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 commented 2 years ago

@whedon generate pdf

whedon commented 2 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 2 years ago

@whedon check references

whedon commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

bmcfee commented 2 years ago

@whedon generate pdf

whedon commented 2 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 2 years ago

Great, thanks @zengfung ! Next steps for you:

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

zengfung commented 2 years ago

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

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

bmcfee commented 2 years ago

@whedon set 10.5281/zenodo.5889625 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5889625 is the archive.

bmcfee commented 2 years ago

@whedon set v0.1.16 as version

whedon commented 2 years ago

OK. v0.1.16 is the version.

bmcfee commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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 commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2901

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 2 years ago

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 commented 2 years ago

@whedon set v0.1.17 as version

whedon commented 2 years ago

OK. v0.1.17 is the version.

arfon commented 2 years ago

@whedon set 10.5281/zenodo.5893843 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5893843 is the archive.

arfon commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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 commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2902

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

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

whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/2903
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03937
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@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 :zap::rocket::boom:

whedon commented 2 years ago

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

HTML:
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  <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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