[REVIEW]: ReSurfEMG: A Python library for preprocessing and analysis of respiratory EMG.

[editorialbot]

Submitting author: @drcandacemakedamoore (Candace Makeda Moore)
Repository: https://github.com/ReSurfEMG/ReSurfEMG
Branch with paper.md (empty if default branch):
Version: v0.1.3
Editor: @AJQuinn
Reviewers: @ixjlyons, @ajbaird
Archive: 10.5281/zenodo.8429265

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5f08d1f2bb717b7d05762296e37ded3d"><img src="https://joss.theoj.org/papers/5f08d1f2bb717b7d05762296e37ded3d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5f08d1f2bb717b7d05762296e37ded3d/status.svg)](https://joss.theoj.org/papers/5f08d1f2bb717b7d05762296e37ded3d)

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

@marcoghislieri & @ixjlyons, 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 @AJQuinn 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 @ixjlyons

📝 Checklist for @ajbaird

[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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.82 s (100.3 files/s, 258079.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                38              0         195457           8679
Python                          12            690           1139           2616
CSS                              1            192             32            685
Markdown                         7            226              0            522
YAML                             6             36             23            233
TeX                              1             10              0            143
reStructuredText                12             84             66            128
Dockerfile                       1              2              0              4
JSON                             1              1              0              4
Bourne Shell                     1              0              0              3
DOS Batch                        1              0              0              2
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            82           1241         196717          13020
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 871

[editorialbot]

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

OK DOIs

- 10.1016/S0921-884X(96)95190-5 is OK
- 10.1109/10.661154 is OK
- 10.1016/0013-4694(86)90163-X is OK
- 10.1046/j.1365-2842.1998.00242.x is OK
- 10.1007/s00421-010-1521-8 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.21105/joss.04156 is OK

MISSING DOIs

- 10.1007/978-3-642-34546-3_71 may be a valid DOI for title: Towards Improving the Usability of Electromyographic Interfaces

INVALID DOIs

- None

[editorialbot]

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

[AJQuinn]

👋🏼 @drcandacemakedamoore @marcoghislieri @ixjlyons this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 openjournals/joss-reviews#5251 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@AJQuinn) if you have any questions/concerns.

[AJQuinn]

Hi @marcoghislieri @ixjlyons - its been around a week so I'd like to check in and make sure all is in place for you to get started on the review?

You can create a list of key points to assess for the review by commenting @editorialbot generate my checklist in this thread. Then the main review can take place over in ReSurfEMG's issues board - don't forget to tag this thread in any issues that you open so we can keep track.

Let me know if you have face any issues or have any questions.

Cheers

[ixjlyons]

Thanks @AJQuinn, no issues for me so far, just a delayed start.

@editorialbot generate my checklist

[ixjlyons]

Review checklist for @ixjlyons

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/ReSurfEMG/ReSurfEMG?
• 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 (@drcandacemakedamoore) 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?

[AJQuinn]

Hi @marcoghislieri - have you been able to get started on the checklist and the review? We're hoping to get the reviews in place over the next couple of weeks.

No problem if you'll need a bit more time, just let me know here or via and email.

[AJQuinn]

Hi @ixjlyons Thanks for filling out the review checklist.

Are there specific issues to be resolved before you can sign-off on the 'Installation' and 'Functionality' sections? Could you add a link to this thread in the relevant github issues so I can keep a track of them from here?

Cheers

[ixjlyons]

No particular issues so far, I just wasn't able to finish reviewing in one pass and I had to step away for a couple weeks. I should be able to revisit and finish up in the next few days.

[AJQuinn]

Hello @behinger, @ajbaird and @peterakirk!

This is a review thread for a Python package "ReSurfEMG: A Python library for preprocessing and analysis of respiratory EMG" at the Journal of Open Source Software. More details in the links in the top comment.

Review has started - but we need to find another reviewer to join us at short notice. Would any of you be willing to contribute a review for this submission for JOSS? We'd ideally like to find someone who could get started soon as the review has been going for a while now.

JOSS carries out checklist-driven reviews here in GitHub issues. Reviews follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

If you have any questions or queries before committing to a review please just let me know!

[behinger]

hi! unfortunately I am swamped right now - it will be better in 3-4 weeks only

[ajbaird]

I'm happy to help but what does the timeline look like. I can possibly finish a review in 2 weeks? If that timeline works let me know!

[AJQuinn]

Thank you both,

Around two weeks for the review would be great if that's possible @ajbaird - let me know and I'll set things up.

No problem @behinger, thanks for letting me know!

[AJQuinn]

@editorialbot remove @marcoghislieri from reviewers

[editorialbot]

@marcoghislieri removed from the reviewers list!

[peterakirk]

I'm swamped and just finished another JOSS review yesterday, so unfortunately I must decline. Best of luck!

[AJQuinn]

No problem, thanks for letting me know @peterakirk

@ajbaird - quick clarification! two weeks would be great, but fine if you need a bit longer as long as we have a broad idea in advance.

Thanks all

[ajbaird]

ok great, well lets say June 10th deadline and I should be able to reach that goal. Happy to help out!

[AJQuinn]

@editorialbot add @ajbaird as reviewer

[editorialbot]

@ajbaird added to the reviewers list!

[editorialbot]

Done! archive is now 10.5281/zenodo.8429265

[AJQuinn]

@editorialbot set v0.1.3 as version

[editorialbot]

Done! version is now v0.1.3

[AJQuinn]

@editorialbot generate pdf

[editorialbot]

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

[AJQuinn]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/S0921-884X(96)95190-5 is OK
- 10.1109/10.661154 is OK
- 10.1016/0013-4694(86)90163-X is OK
- 10.1046/j.1365-2842.1998.00242.x is OK
- 10.1007/s00421-010-1521-8 is OK
- 10.1007/978-3-642-34546-3_71 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.21105/joss.04156 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[AJQuinn]

This all looks good from my side. An Editor-in-Chief will do a final check to make sure I've not missed anything.

[AJQuinn]

@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

- 10.1016/S0921-884X(96)95190-5 is OK
- 10.1109/10.661154 is OK
- 10.1016/0013-4694(86)90163-X is OK
- 10.1046/j.1365-2842.1998.00242.x is OK
- 10.1007/s00421-010-1521-8 is OK
- 10.1007/978-3-642-34546-3_71 is OK
- 10.3758/s13428-020-01516-y is OK
- 10.21105/joss.04156 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-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#4696, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[AJQuinn]

Hi @drcandacemakedamoore - I'm happy to recommend this paper to be accepted, pending a final Editor-in-Chief check. We can make any fix-ups they recommend if required.

Thanks for your submission to JOSS, and thanks to @ixjlyons and @ajbaird for reviews!

[Kevin-Mattheus-Moerman]

@drcandacemakedamoore I am the EiC on this track and here to help with final steps. I have checked this review, the paper, the repository, and the archive. Most seems in order. I do have the below points which needs your attention.

• Please amend the archive title as it still does not match the paper title
• If you can, please add a town/city name to the second affiliation.
• Recommendation: The citation Londral et al. does not have a DOI, but perhaps you can consider adding the URL by adding this to the big entry: url = "https://www.raco.cat/index.php/JACCES/article/view/315915"

[ElineOppersma]

@editorialbot generate pdf

[editorialbot]

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

[ElineOppersma]

@Kevin-Mattheus-Moerman All 3 tasks have been adjusted according to the checklist, but I am not able to check the boxes. Please let me know if there is anything else we need to do to proceed.

[Kevin-Mattheus-Moerman]

@ElineOppersma @drcandacemakedamoore great thanks. All looks good now.

[Kevin-Mattheus-Moerman]

@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: Moore
  given-names: Candace Makeda
  orcid: "https://orcid.org/0000-0003-1672-7565"
- family-names: Baccinelli
  given-names: Walter
  orcid: "https://orcid.org/0000-0001-8888-4792"
- family-names: Sivokon
  given-names: Oleg
- family-names: Warnaar
  given-names: Robertus Simon Petrus
  orcid: "https://orcid.org/0000-0001-9443-4069"
- family-names: Oppersma
  given-names: Eline
  orcid: "https://orcid.org/0000-0002-0150-306X"
doi: 10.5281/zenodo.8429265
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Moore
    given-names: Candace Makeda
    orcid: "https://orcid.org/0000-0003-1672-7565"
  - family-names: Baccinelli
    given-names: Walter
    orcid: "https://orcid.org/0000-0001-8888-4792"
  - family-names: Sivokon
    given-names: Oleg
  - family-names: Warnaar
    given-names: Robertus Simon Petrus
    orcid: "https://orcid.org/0000-0001-9443-4069"
  - family-names: Oppersma
    given-names: Eline
    orcid: "https://orcid.org/0000-0002-0150-306X"
  date-published: 2023-10-23
  doi: 10.21105/joss.05251
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5251
  title: "ReSurfEMG: A Python library for preprocessing and analysis of
    respiratory EMG."
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05251"
  volume: 8
title: "ReSurfEMG: A Python library for preprocessing and analysis of
  respiratory EMG."

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.05251 joss-papers#4715
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05251
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...

[Kevin-Mattheus-Moerman]

@drcandacemakedamoore congratulations on this JOSS publication!

Thanks for editing @AJQuinn!

And a special thank you to the reviewers: @ixjlyons, @ajbaird

[editorialbot]

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

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HTML:
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</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.05251

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