[REVIEW]: Biosiglive: an Open Sources python package for real-time biosignals processing.

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@aceglia@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @finsberg, @marcoghislieri Archive: 10.5281/zenodo.7703146

Status

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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

@finsberg & @marcoghislieri, 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 @Kevin-Mattheus-Moerman 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 @finsberg

📝 Checklist for @marcoghislieri

editorialbot commented 1 year ago

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 commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (215.3 files/s, 256314.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                             16              0              0          57346
Python                          34            458           1379           3559
Markdown                         2             55              0            242
TeX                              1              6              0             65
-------------------------------------------------------------------------------
SUM:                            53            519           1379          61212
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 966

editorialbot commented 1 year ago

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

OK DOIs

- None

MISSING DOIs

- 10.21105/joss.03714 may be a valid DOI for title: Kinetics toolkit: An open-source Python package to facilitate research in biomechanics
- 10.1016/j.cmpb.2016.11.007 may be a valid DOI for title: biomechZoo: An open-source toolbox for the processing, analysis, and visualization of biomechanical movement data
- 10.21105/joss.02431 may be a valid DOI for title: Pyomeca: an open-source framework for biomechanical analysis
- 10.21428/92fbeb44.3ce22588 may be a valid DOI for title: Feeling the Effort of Classical Musicians - A Pipeline from Electromyography to Smartphone Vibration for Live Music Performance
- 10.1016/j.cmpb.2014.01.012 may be a valid DOI for title: Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data

INVALID DOIs

- None

editorialbot commented 1 year ago

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

finsberg commented 1 year ago

Review checklist for @finsberg

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 https://github.com/pyomeca/biosiglive?
[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 (@aceglia) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

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

Kevin-Mattheus-Moerman commented 1 year ago

@marcoghislieri thanks for your help here. Are you able to provide an update on review progress? Thanks!

marcoghislieri commented 1 year ago

@marcoghislieri thanks for your help here. Are you able to provide an update on review progress? Thanks!

Dear @Kevin-Mattheus-Moerman, By the beginning of the next week I'll provide my review! My apologies for the late response. All the best, Marco

finsberg commented 1 year ago

@Kevin-Mattheus-Moerman I am done with my review and can recommend biosiglive for publication in JOSS.

Kevin-Mattheus-Moerman commented 1 year ago

@marcoghislieri I hope you are getting on okay. Let me know if I can help.

marcoghislieri commented 1 year ago

Review checklist for @marcoghislieri

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 https://github.com/pyomeca/biosiglive?
[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 (@aceglia) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

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

Kevin-Mattheus-Moerman commented 1 year ago

@marcoghislieri great to see you've started to review this submission. I see some boxes are not ticked. Please let the authors know if there are any issues that need work. You can open issues on their software repository and link to them here.

marcoghislieri commented 1 year ago

Dear @Kevin-Mattheus-Moerman, I've just completed my review of biosiglive python package. Green light for me for publication in JOSS. All the best

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

aceglia commented 1 year ago

Thanks a lot @finsberg and @marcoghislieri for the time spent in reviewing my library and paper in a such short notice!

aceglia commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

aceglia commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

aceglia commented 1 year ago

Dear @Kevin-Mattheus-Moerman I fixed some issues in the code of the paper draft (lines too long) and passed Biosiglive to the version 2.0.2 after the reviewers comments. Thanks.

finsberg commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- None

MISSING DOIs

- 10.21105/joss.03714 may be a valid DOI for title: Kinetics toolkit: An open-source Python package to facilitate research in biomechanics
- 10.1016/j.cmpb.2016.11.007 may be a valid DOI for title: biomechZoo: An open-source toolbox for the processing, analysis, and visualization of biomechanical movement data
- 10.21105/joss.02431 may be a valid DOI for title: Pyomeca: an open-source framework for biomechanical analysis
- 10.21428/92fbeb44.3ce22588 may be a valid DOI for title: Feeling the Effort of Classical Musicians - A Pipeline from Electromyography to Smartphone Vibration for Live Music Performance
- 10.1016/j.cmpb.2014.01.012 may be a valid DOI for title: Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data

INVALID DOIs

- None

aceglia commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1016/j.cmpb.2014.01.012 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.21105/joss.03714 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cmpb.2016.11.007 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.21105/joss.02431 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.21428/92fbeb44.3ce22588 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1186/1743-0003-10-60 is INVALID because of 'https://doi.org/' prefix

aceglia commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.21105/joss.03714 is OK
- 10.1016/j.cmpb.2016.11.007 is OK
- 10.21105/joss.02431 is OK
- 10.21428/92fbeb44.3ce22588 is OK
- 10.1016/j.cmpb.2014.01.012 is OK
- 10.1186/1743-0003-10-60 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 1 year ago

@aceglia I've spotted a single typo:

[x] Please fix platfroms to be platforms

After you've completed the above ☝️ , Please work on the following:

[x] Please archive a copy of the software on ZENODO. You can do this manually, or you may follow these automated steps: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
[ ] Once you have the above archive, please report back here with the archive DOI.
[ ] Please ensure that the ZENODO archive has the same title and author list (and order) as the paper, and the same license (it might list "Other(open)" by default) as your software. You may need to manually edit these aspects.
[ ] Please let me know if v2.0.0 is still the current version tag for the JOSS publication. It may have altered during review or be incremented during archiving. Note that the version listed on ZENODO, should match the version listed here, and should also be a release tag on your repository.

aceglia commented 1 year ago

@Kevin-Mattheus-Moerman

I fixed the typo in the paper
The DOI on Zenodo is : 10.5281/zenodo.7703146
The version is now 2.0.2

Thanks

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.7703146 as archive

editorialbot commented 1 year ago

Done! Archive is now [ 10.5281/zenodo.7703146](https://doi.org/ 10.5281/zenodo.7703146)

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.7703146 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7703146

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set v2.0.2 s version

editorialbot commented 1 year ago

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

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Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set v2.0.2 as version

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set version as v2.0.2

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set version as v2.0.2

editorialbot commented 1 year ago

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

@editorialbot commands

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set v2.0.2 as version

editorialbot commented 1 year ago

Done! version is now v2.0.2

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.21105/joss.03714 is OK
- 10.1016/j.cmpb.2016.11.007 is OK
- 10.21105/joss.02431 is OK
- 10.21428/92fbeb44.3ce22588 is OK
- 10.1016/j.cmpb.2014.01.012 is OK
- 10.1186/1743-0003-10-60 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4019, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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