[REVIEW]: libfmp: A Python Package for Fundamentals of Music Processing

[whedon]

Submitting author: @fzalkow (Frank Zalkow)
Repository: https://github.com/meinardmueller/libfmp
Version: v1.2.1
Editor: @arfon
Reviewer: @brunaw, @expectopatronum
Archive: 10.5281/zenodo.5113869

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/47b595f5a3d0259d9ae5574e0d4a09b7/status.svg)](https://joss.theoj.org/papers/47b595f5a3d0259d9ae5574e0d4a09b7)

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

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✨ 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 @brunaw

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 (@fzalkow) 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 @expectopatronum

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 (@fzalkow) 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? #3415
• 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. @brunaw, @expectopatronum it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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[whedon]

PDF failed to compile for issue #3326 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.36 s (423.6 files/s, 164540.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            59           8855            174          21375
JavaScript                      14           2404           2467           9203
Python                          55           1880           3643           4641
SVG                              1              0              0           2671
CSS                              4            181             33            726
reStructuredText                13             47            181             66
DOS Batch                        1              8              1             26
Markdown                         2             18              0             22
make                             1              4              7              9
YAML                             1              0              2              6
-------------------------------------------------------------------------------
SUM:                           151          13397           6508          38745
-------------------------------------------------------------------------------


Statistical information for the repository '9f562e921fc63288d9416627' was
gathered on 2021/06/01.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Frank Zalkow                     6         16413           1871           65.33
Meinard Müller                   3          9700              4           34.67

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Frank Zalkow              16405          100.0          0.6               15.56
Meinard Müller             7833           80.8          0.1               10.29

[arfon]

@brunaw, @expectopatronum – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/3326 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[arfon]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[whedon]

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

[whedon]

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

[brunaw]

@whedon I will start the review next week

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[expectopatronum]

This is a more general question about how to understand "Substantial scholarly effort". If I would follow the list here, I would have to say no because:

"positive" answers:

• Total lines of code (LOC). Submissions under 1000 LOC will usually be flagged, those under 300 LOC will be desk rejected.: many :)
• Whether the software is sufficiently useful that it is likely to be cited by your peer group.: probably yes. It has lots of useful functions and reference implementations.

"negative" answers (leading to saying no):

• Age of software (is this a well-established software project) / length of commit history.: according to the git history it's 6 month old
• Number of commits.: 12
• Number of authors.: 2
• Whether the software has already been cited in academic papers.: My search for "libfmp" in Google Scholar only returned other work by the same group.

The two "positive" answers might outweigh some of the negatives. I don't think that the age of the software / the number of commits / number of authors should have much to say, as I would say that also one person could create a very useful software package, and 10 people might not; and additionally, the age of the git repository and the number of commits might not reflect the actual development effort as many software packages start in a private repository.

This leaves me with the last question (according to my reordered list), which is actually important. As mentioned above "libfmp" is only mentioned in papers by the same group. Since libfmp has only been available via pip for a couple of months, and was not promoted before (I think), this seems reasonable. So I also checked the papers citing the FMP notebooks paper which I would expect people to cite if they were using the code and it looks like the FMP notebooks paper is exclusively cited by work from the same group.

Maybe @arfon can clarify how this question should be answered given the information I provided. Thanks!

[expectopatronum]

I created an issue for almost all the things I noticed. There are two other things that I am not sure about and might be interesting to discuss with the other reviewer or the editor:

• The "Statement of Need" in the paper is quite long. From the sentence starting at line 58 onward it feels more like a description of the actual package rather than a statement of need, maybe this could be moved to a separate section.
• There are some design choices I am not completely happy with:
  • The paper claims to integrated and build upon the librosa package, but many variable are named differently, and unfortunately some are harder to understand, such as H instead of hop_length, N instead of n_fft.
  • Naming of the sub packages. I understand that the reason for naming the sub packages b, c1, ... c8 is to follow the FMP notebooks, and the book they are based on but for me as a user it is a bit cumbersome to remember or look up the sub package everytime instead of remembering a meaningful package name. I think it might be possible to keep the structure as it is and add some imports to the __init__.py files, to "rename" how the sub packages could be imported.

Would be interesting to hear other people's opinion about those two things.

Best regards
Verena

[fzalkow]

Many thanks for the thorough review process. I just want to clarify two of the mentioned points.

Age of software: The development of libfmp went hand in hand with developing the FMP notebooks, which have been developed internally before releasing libfmp on GitHub. This development process preceded the first GitHub release by a few years. Furthermore, some of the algorithms are based on previously unpublished internal MATLAB implementations, which predate FMP by several years.

Variable names: The deviations of the variable names compared to librosa is intentional. An essential aspect of the FMP notebooks and libfmp is to establish a close connection to the FMP book. This connection enables students to study fundamental MIR concepts in-depth by reading a textbook along with implementations of the concepts explained in the book. Thus, the variable names reflect the mathematical notation used in the book.

Best,

Frank

[expectopatronum]

Age of software ...

That's what I assumed! (and also doesn't have an impact on my review) The first comment was more of a question for the editor, since it is not clear to me what is expected from me for answering the "Substantial scholarly effort" question, although I am inclined to answer it with yes.

Variable names ...

Thanks for the clarification, makes sense!

If you can take care of the minor issues I raised here I can tick all the missing boxes and can finish my review.

[arfon]

Maybe @arfon can clarify how this question should be answered given the information I provided. Thanks!

Thanks for raising these questions about scholarly effort @expectopatronum – the 'signals' we suggest are just pointers you might be able to use to guide your thinking. We also say that the work should represent three or more months of effort which is sound like it does?

After reading the README in a little more detail myself I did have one question for the authors – could you clarify @fzalkow if this is software designed for addressing research challenges or is a teaching tool? JOSS doesn't publish software designed for teaching (we encourage authors to submit to our sister journal JOSE for submissions that fall into this category).

[fzalkow]

Dear arfon,

Many thanks for your question.

Indeed libfmp covers both teaching and research aspects. This combination is due to the origin of libfmp. The starting point is Müller's FMP book, where fundamental music information retrieval (MIR) algorithms are presented in a didactically prepared textbook. These algorithms summarize the essence from the research of many years. Then, we developed the FMP notebooks, which expand and complement the FMP book. Here, the aim is more on the teaching side. During the development of the FMP notebooks, many research-related algorithms have been collected in the libfmp package, which we now made available independent of the FMP notebooks. Thus, compared to the FMP notebooks, the research aspect is more dominant in libfmp. Due to this development, we consider libfmp an ideal tool to transition from studying (using the FMP notebooks and the FMP book) to research. The package is intended for research purposes and contains (similar to librosa) many implementations of core algorithms and advanced methods for MIR.

Concerning three or more months of effort: This holds undoubtedly. The development of libfmp started a few years ago. Considering the origins in the FMP book, it even can be traced back more than a decade.

Best,

Frank

[arfon]

The package is intended for research purposes and contains (similar to librosa) many implementations of core algorithms and advanced methods for MIR.

Got it. Thanks for the additional context and background.

@brunaw – do you think you might be able to complete your review soon?

[brunaw]

Dear @arfon,

I will complete my review next week, my apologies for the delay. Is that okay?

[brunaw]

@expectopatronum Just my two cents of the previous discussion. It's a little strange to me that the FMP notebooks paper isn't cited much because, at least from my experience, the notebooks are widely known in the ISMIR community. I know a few people who have used it in their research so they might have missed it when writing their references. This also leads to the age question, the first time I got to know the FMP notebooks was about ~3 years ago, and they were already very well developed/organized by them, so the software is certainly older than 6 months. I hope this helps with something.

[arfon]

I will complete my review next week, my apologies for the delay. Is that okay?

Absolutely! Thanks for the update.

[whedon]

OK. 10.5281/zenodo.5113869 is the archive.

[arfon]

@whedon set v1.2.1 as version

[whedon]

OK. v1.2.1 is the version.

[arfon]

@whedon recommend-accept from branch paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3326 with the following error:

 /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:50:in `read': No such file or directory @ rb_sysopen - 5c6867af5266b997a2e1f6c4/paper/["references.bib"] (Errno::ENOENT)
	from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/bibliography.rb:50:in `open'
	from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-6.0.0/lib/bibtex/utilities.rb:25:in `open'
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	from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

[arfon]

@fzalkow – could you please merge this PR which fixes your paper: meinardmueller/libfmp#5

[fzalkow]

@fzalkow – could you please merge this PR which fixes your paper: meinardmueller/libfmp#5

Done!

[arfon]

@whedon recommend-accept from branch paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.25080/Majora-7b98e3ed-003 is OK
- 10.1109/MSP.2018.2876190 is OK
- 10.5281/zenodo.1415016 is OK
- 10.1145/2964284.2973795 is OK
- 10.1145/1631272.1631459 is OK
- 10.5281/zenodo.1417145 is OK
- 10.5281/zenodo.3527872 is OK
- 10.1109/TASL.2010.2096216 is OK
- 10.1109/ICASSP.2010.5495219 is OK
- 10.1109/TASL.2012.2227732 is OK
- 10.5281/zenodo.1416024 is OK
- 10.5281/zenodo.1416800 is OK
- 10.5281/zenodo.1415226 is OK
- 10.1109/ICASSP.2012.6287834 is OK

MISSING DOIs

- 10.1007/978-3-319-21945-5 may be a valid DOI for title: Fundamentals of Music Processing

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2467

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2467, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper 

[arfon]

@whedon accept deposit=true from branch paper

[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.03326 joss-papers#2468
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03326
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]

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

@fzalkow – 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.03326/status.svg)](https://doi.org/10.21105/joss.03326)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03326">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03326/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03326/status.svg
   :target: https://doi.org/10.21105/joss.03326

This is how it will look in your documentation:

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[fzalkow]

Awesome! Many thanks, @arfon, @brunaw, and @expectopatronum for the fantastic review process! 🥳

[expectopatronum]

@fzalkow Thanks as well, it was nice working with you! Congrats on your paper!

[brunaw]

@fzalkow No problem at all, it was a pleasure, congrats on the excellent work 😊