[REVIEW]: EMGFlow: A Python package for pre-processing and feature extraction of electromyographic signals

[editorialbot]

Submitting author: @WiIIson (D. William Lawrence Conley)
Repository: https://github.com/WiIIson/EMGFlow-Python-Package
Branch with paper.md (empty if default branch):
Version: v1.0.16
Editor: @faroit
Reviewers: @wbaccinelli, @samiralavi
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d63dac2393dede4adb8ebc6910f3b65c/status.svg)](https://joss.theoj.org/papers/d63dac2393dede4adb8ebc6910f3b65c)

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

@wbaccinelli & @samiralavi, 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 @faroit 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 @wbaccinelli

📝 Checklist for @samiralavi

[editorialbot]

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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]

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

✅ OK DOIs

- 10.1109/TAFFC.2015.2392932 is OK
- 10.1016/j.softx.2024.101712 is OK
- 10.1109/ACCESS.2022.3146729 is OK
- 10.1109/TAFFC.2015.2457417 is OK
- 10.1111/j.1469-8986.1986.tb00676.x is OK
- 10.5281/zenodo.6403363 is OK
- 10.1007/s12253-019-00668-3 is OK
- 10.1109/T-AFFC.2011.15 is OK
- 10.3389/fpsyg.2016.00780 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.3389/fneur.2020.576729 is OK
- 10.1038/s41598-021-85163-z is OK
- 10.1145/3242969.3242985 is OK
- 10.1038/s41597-019-0209-0 is OK
- 10.3389/fict.2017.00001 is OK
- 10.1044/1092-4388(2011/11-0214) is OK
- 10.1073/pnas.0908994106 is OK
- 10.1186/1743-0003-7-21 is OK
- 10.1109/SSCI.2016.7849931 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A practicum on the use of sEMG signals in movement...
- No DOI given, and none found for title: An electromyographic index for localized muscle fa...
- No DOI given, and none found for title: A novel feature extraction for robust EMG pattern ...
- No DOI given, and none found for title: PhysioData Toolbox

❌ MISSING DOIs

- 10.1152/jappl.1983.54.1.51 may be a valid DOI for title: Changes in electromyogram power spectra of facial ...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.04 s (846.2 files/s, 190262.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        11           1210              0           2176
Python                          11            668           1550           1249
TeX                              1             24              0            342
YAML                             2             17              0             92
TOML                             1              2              0             28
JSON                             4              0              0             24
INI                              1              3              0             19
Text                             2              0              0             16
-------------------------------------------------------------------------------
SUM:                            33           1924           1550           3946
-------------------------------------------------------------------------------

Commit count by author:

   143	WiIIson

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1653

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[faroit]

@wbaccinelli @samiralavi 👋 Hi and thanks again for agreeing to review this paper. You can start the review now. Please use issues in the package repository to discuss with @WiIIson about the submission and refer to these issues here to keep this thread lightweight.

If you have any further questions, let me know

[wbaccinelli]

Review checklist for @wbaccinelli

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/WiIIson/EMGFlow-Python-Package?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@WiIIson) 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?

[samiralavi]

Review checklist for @samiralavi

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/WiIIson/EMGFlow-Python-Package?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@WiIIson) 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?

[faroit]

@samiralavi @wbaccinelli can you update us on how the review is going, please? Also please let me know if you need any additional help or input from me or the authors

[wbaccinelli]

@faroit unfortunately I'm more busy now than when I accepted the review a few months ago, so I will need another couple of weeks to perform the review. I'm sorry for the inconvenience.

[wbaccinelli]

General checks

Contribution and authorship: Has the submitting author (@WiIIson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I see that two author are listed, but @WiIIson is the only contributor to the software. Can the contribution of the second author be explicitly explained?

[srlivingstone]

I see that two author are listed, but @WiIIson is the only contributor to the software. Can the contribution of the second author be explicitly explained?

Hi Dr Baccinelli. @WiIIson) is the lead author of the EMGFlow package code. As his thesis supervisor, I am the senior author on the paper, which I co-wrote with Mr Conley. I supervised the development of EMGFlow. However, Mr Conley was responsible for writing the code and making all commits. If you like, we could add an "author contributions" section to our manuscript to make this explicit.

[wbaccinelli]

Hi Dr Baccinelli. @WiIIson) is the lead author of the EMGFlow package code. As his thesis supervisor, I am the senior author on the paper, which I co-wrote with Mr Conley. I supervised the development of EMGFlow. However, Mr Conley was responsible for writing the code and making all commits. If you like, we could add an "author contributions" section to our manuscript to make this explicit.

Thank you for the explanation @srlivingstone. I think that the "author contributions" section would be a fair addition, even though is not needed. I suggest, on the other hand, splitting the names of the authors in the pyproject.toml.

[WiIIson]

Hi there,

Just confirming that I've updated the documentation to include the author contributions section:
https://github.com/WiIIson/EMGFlow-Python-Package/blob/main/papers/JOSS/paper.pdf

[faroit]

@WiIIson @srlivingstone the author contributions section look good to me. Thank you for addressing this.

[faroit]

@samiralavi can you update us on the status of your review please?

[samiralavi]

@faroit I have finished my review. Only two items in the checklist are remaining, which I will update once the authors address the issues that I have created on the software repository. Here are the links to the issues:
WiIIson/EMGFlow-Python-Package#1
WiIIson/EMGFlow-Python-Package#2

@WiIIson please let me know if you think those issues are not valid. Thanks.

[WiIIson]

@editorialbot generate pdf

[editorialbot]

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

[WiIIson]

Hi Dr Baccinelli. @WiIIson) is the lead author of the EMGFlow package code. As his thesis supervisor, I am the senior author on the paper, which I co-wrote with Mr Conley. I supervised the development of EMGFlow. However, Mr Conley was responsible for writing the code and making all commits. If you like, we could add an "author contributions" section to our manuscript to make this explicit.

Thank you for the explanation @srlivingstone. I think that the "author contributions" section would be a fair addition, even though is not needed. I suggest, on the other hand, splitting the names of the authors in the pyproject.toml.

Thank you for the comment. I have updated the pyproject.toml per your suggestion.
https://github.com/WiIIson/EMGFlow-Python-Package/blob/main/EMGFlow-Package/pyproject.toml

[WiIIson]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1109/TAFFC.2015.2392932 is OK
- 10.1016/j.softx.2024.101712 is OK
- 10.1109/ACCESS.2022.3146729 is OK
- 10.1109/TAFFC.2015.2457417 is OK
- 10.1111/j.1469-8986.1986.tb00676.x is OK
- 10.5281/zenodo.6403363 is OK
- 10.1007/s12253-019-00668-3 is OK
- 10.1109/T-AFFC.2011.15 is OK
- 10.1152/jappl.1977.43.4.750 is OK
- 10.3389/fpsyg.2016.00780 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.3389/fneur.2020.576729 is OK
- 10.48550/arXiv.0912.3973 is OK
- 10.1038/s41598-021-85163-z is OK
- 10.1145/3242969.3242985 is OK
- 10.1038/s41597-019-0209-0 is OK
- 10.3389/fict.2017.00001 is OK
- 10.1044/1092-4388(2011/11-0214) is OK
- 10.1073/pnas.0908994106 is OK
- 10.1186/1743-0003-7-21 is OK
- 10.1152/jappl.1983.54.1.51 is OK
- 10.1109/SSCI.2016.7849931 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: A practicum on the use of sEMG signals in movement...
- No DOI given, and none found for title: PhysioData Toolbox

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[wbaccinelli]

@faroit @WiIIson @srlivingstone, I completed my review.
The package is well organized and documented, thank you for your work. I have some points that I raised. I think that some of them would need to be addressed before ticking all the boxes, while others are suggestions that might help you.

The issues that should be addressed for this publication are:

• Fix the errors found when running the examples ( see this and this issue)
• Add specifications about the data format (see this issue)
• Add documentation about running tests (see this issue)
• I also agree with the issues opened by @samiralavi. In particular this one. While a dataset is indicated in the text of the paper, it should be also indicated in the package documentation to let the users work with the code.

Optional issues:

• Move the documentation to GitHub pages and automatize its release (see this issue)
• Add a separate file for the community guidelines, and expand them with more information (see this issue)

I hope that the inputs will help in improving the overall package usability.

[faroit]

@wbaccinelli thank you already for your reviews!

[srlivingstone]

Hi @samiralavi and @wbaccinelli thank you both for your supportive feedback and helpful suggestions. We're actively revising the docs and toolbox to address your concerns, and are aiming to provide detailed responses in the next few weeks.

[WiIIson]

@WiIIson please let me know if you think those issues are not valid. Thanks.

Hi @samiralavi,

Thank you for those helpful suggestions. As we detail in the individual Issue threads [1, 2], we've added sample data to the package, updated the example docs, and updated the .gitignore to remove unwanted files.

[faroit]

@WiIIson please let me know if you think those issues are not valid. Thanks.

Hi @samiralavi,

Thank you for those helpful suggestions. As we detail in the individual Issue threads [1, 2], we've added sample data to the package, updated the example docs, and updated the .gitignore to remove unwanted files.

@WiIIson @wbaccinelli please take a look at the open issues and update/close them if the recent changes have addressed them already

[srlivingstone]

@WiIIson please let me know if you think those issues are not valid. Thanks.

Hi @samiralavi,
Thank you for those helpful suggestions. As we detail in the individual Issue threads [1, 2], we've added sample data to the package, updated the example docs, and updated the .gitignore to remove unwanted files.

@WiIIson @wbaccinelli please take a look at the open issues and update/close them if the recent changes have addressed them already

Hi @faroit - thanks for checking in. Following @wbaccinelli and @samiralavi's suggestions, @WiIIson and I have recently made extensive revisions to site documentation, transitioned to the docs generator VitePress, and further revised our examples with an eye towards simplicity and consistency. Once these are complete, we'll update the respective open issues.

@faroit For our knowledge, should we close issues, or should this be left to the reviewers?

[faroit]

@faroit For our knowledge, should we close issues, or should this be left to the reviewers?

@wbaccinelli For most issues it is clear to see when they were are addressed (ideally when links to PR are provided) so closing from either side is ok. For some others, feedback might be required (eg. WiIIson/EMGFlow-Python-Package#8), so its best if the reviewer can confirm that this was addressed and then close. Hope that helps

[faroit]

@srlivingstone can you update us on how the revision of the code is going and whether you need more time or help to address them?

[srlivingstone]

@srlivingstone can you update us on how the revision of the code is going and whether you need more time or help to address them?

Hi @faroit thanks for checking in. We have nearly completed our revisions, and will post the changes shortly.

[faroit]

@srlivingstone do you have some updates or do you need more time?

[srlivingstone]

@srlivingstone do you have some updates or do you need more time?

Hi @faroit Thanks for checking in again, we are actively continuing revisions and hope to get update you in the next two weeks. The updates are substantial and we're aiming to push them in one release. Thank you for your patience.