[REVIEW]: pyheartlib: A Python package for processing electrocardiogram signals

[editorialbot]

Submitting author: @devnums (Sadegh Mohammadi)
Repository: https://github.com/devnums/pyheartlib
Branch with paper.md (empty if default branch): paper
Version: 1.22.0
Editor: @britta-wstnr
Reviewers: @cudmore, @LegrandNico, @Bsingstad
Archive: 10.5281/zenodo.10730468

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4c9af4eef164d4647174e8a225a416e8"><img src="https://joss.theoj.org/papers/4c9af4eef164d4647174e8a225a416e8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4c9af4eef164d4647174e8a225a416e8/status.svg)](https://joss.theoj.org/papers/4c9af4eef164d4647174e8a225a416e8)

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

@cudmore & @LegrandNico, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @britta-wstnr 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 ✨

Checklists

📝 Checklist for @cudmore

📝 Checklist for @Bsingstad

📝 Checklist for @LegrandNico

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1057.2 files/s, 102360.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          32            646           1323           2512
Markdown                         9            113              0            187
YAML                             6             39             23            153
Jupyter Notebook                 4              0            535            140
TeX                              1              6              0            122
TOML                             1              5              0             45
DOS Batch                        1              8              1             27
reStructuredText                 6             25             35             22
Bourne Shell                     1              5              2             10
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            62            851           1924           3228
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1109/51.932724 is OK
- 10.1161/01.CIR.101.23.e215 is OK
- 10.13026/9njx-6322 is OK
- 10.13026/zzpx-h016 is OK
- 10.3758/s13428-020-01516-y is OK

MISSING DOIs

- 10.1163/1574-9347_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 487

[britta-wstnr]

Hello again! 👋

@LegrandNico and @cudmore
FYI @devnums

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).
✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.
💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #5792 so that a link is created to this thread. That will also help me to keep track!
❓ Please also feel free to comment and ask questions on this thread.
🎯 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.

[editorialbot]

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

[britta-wstnr]

@editorialbot add @Bsingstad as reviewer

[editorialbot]

@Bsingstad added to the reviewers list!

[britta-wstnr]

Hi @cudmore, @LegrandNico, @Bsingstad,

let me know if you have any questions or anything is unclear regarding the next steps!
It would be great if you could just generate your checklist so I can see that everything is in order 😄

[cudmore]

Review checklist for @cudmore

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 https://github.com/devnums/pyheartlib?
• 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 (@devnums) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[Bsingstad]

Review checklist for @Bsingstad

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 https://github.com/devnums/pyheartlib?
• 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 (@devnums) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[Bsingstad]

Hi. What is meant by "please mention the link to LINK.."

[britta-wstnr]

Good catch @Bsingstad - that was to be replace with this issue's number before posting. I updated the comment - thanks!

[LegrandNico]

Review checklist for @LegrandNico

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 https://github.com/devnums/pyheartlib?
• 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 (@devnums) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[LegrandNico]

Hi @britta-wstnr , I have now completed my review and asked for changes in the 3 issues opened above.

[devnums]

Hi @LegrandNico, @britta-wstnr,

I have answered those issues, and have made some changes to the paper.
Please let me know if there are any other issues.

Thank you🙏

[britta-wstnr]

@devnums and @LegrandNico: looks like things are going smoothly for you, I will of course leave it to @LegrandNico to say if the comments are fully answered.

Looks like @Bsingstad is also making progress already, and how are you doing @cudmore ? Don't hesitate to contact me if you have any questions or are stuck in the process! 🙂

[LegrandNico]

Thank you @devnums for your work on this. I have commented on some of the issues. Currently, the paper is still missing a side-by-side comparison between the deep learning methods that can be used and the most traditional peak detection algorithm that can be found in other packages. I think that is the main question that a potential user would have: why use a more complicated model if not for better performance/accuracy? But JOSS is not intended to host a method paper that would go too deep in such a comparison so I will let @britta-wstnr decide whether this is something that should be added to the paper or not.

[britta-wstnr]

Thanks for flagging this @LegrandNico - I will have a detailed look at this and let you know my decision.

Ping @Bsingstad and @cudmore, how are your reviews coming along?

[britta-wstnr]

@LegrandNico and @devnums, I looked into it and it seems to me like there is a motivation in the paper on which gap this toolbox is filling as compared to other toolboxes (i.e., there is no other toolboxes allowing deep learning models to be utilized). Such a "statement of need" is necessary, but to show that a toolbox is performing better in comparison to other toolboxes is not. As you already suspected, @LegrandNico, this is beyond the scope of the JOSS paper (but can still be a good idea to show e.g. in the documentation or a separate paper as users indeed might ask this question).
So I guess the question then is: do you agree that there is a statement of need/statement of relation towards existing toolboxes in the paper? @LegrandNico
Also curious what the other reviewers will say @Bsingstad and @cudmore!

[britta-wstnr]

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1109/51.932724 is OK
- 10.1161/01.CIR.101.23.e215 is OK
- 10.13026/9njx-6322 is OK
- 10.13026/zzpx-h016 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.21105/joss.05411 is OK
- 10.1109/TBME.1985.325532 is OK
- 10.1109/CIC.2002.1166717 is OK

MISSING DOIs

- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...
- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

[editorialbot]

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

[britta-wstnr]

@editorialbot set 10.5281/zenodo.10730468 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10730468

[britta-wstnr]

@editorialbot set 1.22.0 as version

[editorialbot]

Done! version is now 1.22.0

[britta-wstnr]

@editorialbot generate pdf

[editorialbot]

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

[britta-wstnr]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/51.932724 is OK
- 10.1161/01.CIR.101.23.e215 is OK
- 10.13026/9njx-6322 is OK
- 10.13026/zzpx-h016 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.21105/joss.05411 is OK
- 10.1109/TBME.1985.325532 is OK
- 10.1109/CIC.2002.1166717 is OK

MISSING DOIs

- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...
- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

[britta-wstnr]

Okay! Everything in order here as far as I can see 🎉 @devnums I will hand this off to our EiC now for acceptance.

A big thank you to the reviewers @cudmore @LegrandNico and @Bsingstad - we deeply appreciate your review work for JOSS! 🙏 🌷

A quick note to the EiC taking this over: I checked the two missing DOIs that the editorialbot flags and both Keras and Tensorflow are cited as the homepages for the softwares request as far as I can see.

[britta-wstnr]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1109/51.932724 is OK
- 10.1161/01.CIR.101.23.e215 is OK
- 10.13026/9njx-6322 is OK
- 10.13026/zzpx-h016 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.21105/joss.05411 is OK
- 10.1109/TBME.1985.325532 is OK
- 10.1109/CIC.2002.1166717 is OK

MISSING DOIs

- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...
- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5104, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

👋 @devnums - I've now proofread this as the track editor, and it all looks fine

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Mohammadi
  given-names: Sadegh
  orcid: "https://orcid.org/0000-0001-9763-4963"
doi: 10.5281/zenodo.10730468
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Mohammadi
    given-names: Sadegh
    orcid: "https://orcid.org/0000-0001-9763-4963"
  date-published: 2024-03-09
  doi: 10.21105/joss.05792
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5792
  title: "Pyheartlib: A Python package for processing electrocardiogram
    signals"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05792"
  volume: 9
title: "Pyheartlib: A Python package for processing electrocardiogram
  signals"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.05792 joss-papers#5111
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05792
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...

[danielskatz]

Congratulations to @devnums (Sadegh Mohammadi) on your publication!!

And thanks to @cudmore, @LegrandNico, and @Bsingstad for reviewing, and to @britta-wstnr for editing!
JOSS depends on volunteers and we couldn't do this without you

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.05792/status.svg)](https://doi.org/10.21105/joss.05792)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05792/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05792/status.svg
   :target: https://doi.org/10.21105/joss.05792

This is how it will look in your documentation:

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[devnums]

Great, thank you all 🙏