[REVIEW]: MNELAB: a graphical user interface for MNE-Python

[editorialbot]

Submitting author: @cbrnr (Clemens Brunner) Repository: https://github.com/cbrnr/mnelab Branch with paper.md (empty if default branch): joss Version: v0.8.4 Editor: @Kevin-Mattheus-Moerman Reviewers: @vahid-sb, @tuliofalmeida Archive: Pending

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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

@sappelhoff & @vahid-sb & @tuliofalmeida, 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 @vahid-sb

📝 Checklist for @tuliofalmeida

[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]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "--21" (NAME) ["@", #<BibTeX::Entry >, {:author=>["Delorme, A. and Makeig, S."], :title=>["{EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis}"], :journal=>["Journal of Neuroscience Methods"], :volume=>"134", :number=>"1", :year=>"2004", :pages=>"9"}]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (1053.6 files/s, 84180.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          46            752            634           4311
Markdown                        10            165              0            509
SVG                             22              2              2            444
YAML                             5             15              3            156
TeX                              1              3              0             37
DOS Batch                        1              8              1             26
CSS                              1              4              0             15
make                             1              3              3              9
HTML                             1              1              0              6
TOML                             1              0              0              2
-------------------------------------------------------------------------------
SUM:                            89            953            643           5515
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 820

[editorialbot]

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

[sappelhoff]

@Kevin-Mattheus-Moerman reading the conflict of interest guidelines I realize that I do have a paper with @cbrnr from 2019 (also published in JOSS). Furthermore, we both contribute to several repositories together, such as mne-python or pybv.

However, I am sure that this will not impact my ability to make an impartial scientific judgment/evaluation of the submitted work.

Do you think you can waive these concerns? Or should I step down as a reviewer? Sorry that I only bring this up now ... the checklist reminded me.

[Kevin-Mattheus-Moerman]

@sappelhoff this would qualify as a COI so I'll remove you as reviewer for now. This is no problem at this stage and we still have two other reviewers. Thanks for letting us know and thanks for volunteering in principle.

[Kevin-Mattheus-Moerman]

@editorialbot remove @sappelhoff as reviewer

[editorialbot]

@sappelhoff removed from the reviewers list!

[sappelhoff]

this would qualify as a COI so I'll remove you as reviewer for now. This is no problem at this stage and we still have two other reviewers.

Understood :+1:

Thanks for letting us know and thanks for volunteering in principle.

I'll be happy to join for another paper where I don't have a COI.

[vahid-sb]

Review checklist for @vahid-sb

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/cbrnr/mnelab?
• [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 (@cbrnr) 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

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?

[tuliofalmeida]

Review checklist for @tuliofalmeida

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/cbrnr/mnelab?
• [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 (@cbrnr) 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

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]

@vahid-sb thank again for your help here. Can you pick up this review again. I see you several boxes unticked. Can you summarise to @cbrnr what actions you expect for these?

@tuliofalmeida looks like all your boxes are ticked. Would you be happy to formally recommend acceptance? Thanks again for your help!

[tuliofalmeida]

Hi @Kevin-Mattheus-Moerman, sorry for not doing this sooner. I recommend acceptance, the interface worked well in my tests and has good documentation. I understand that the features of the MNE will be implemented in the future, and they met what they proposed.

[vahid-sb]

@vahid-sb thank again for your help here. Can you pick up this review again. I see you several boxes unticked. Can you summarise to @cbrnr what actions you expect for these?

@Kevin-Mattheus-Moerman I have opened an Issue in the MNELAB repo two weeks ago, currently includes two issues needs resolving, and have been waiting for the authors to resolve those issues. When done I can continue with the review.

[cbrnr]

I'm back from vacation today and I will start working on the open issues! I'll also comment here once they have been resolved.

[cbrnr]

Relevant issue is https://github.com/cbrnr/mnelab/issues/359.

[cbrnr]

Just a heads up, the issues raised by @vahid-sb have been resolved. Looking forward for your review.

[vahid-sb]

@Kevin-Mattheus-Moerman I am done with the review, and I can recommend MNELAB to be published in JOSS.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@cbrnr I have read you paper and it mostly looks like, I just have the following minor final comments:

• [x] Check ...specific use cases: I recommend just using ...specific use cases.
• [x] Check ... involve (1) specifying... this should likely read ... involves (1) specifying...
• [x] Check how these steps might look like it is better to say what these steps might look like
• [x] Check which does not feature a GUI though, although correct I would recommend although it does not feature a GUI.

Once you've looked at these, and if you've made changes, please call @editorialbot generate pdf to update the paper.

[cbrnr]

@editorialbot generate pdf

[editorialbot]

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

[cbrnr]

@editorialbot generate pdf

[editorialbot]

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

[cbrnr]

@editorialbot generate pdf

[editorialbot]

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

[cbrnr]

Thanks @Kevin-Mattheus-Moerman, I applied your suggestions. I also added a figure, which I completely forgot in the first draft, but I think it's pretty important for a paper about a GUI. I hope that this is OK. The first page is a bit empty now, I tried moving some text, but it seems like I cannot change the figure position.

[Kevin-Mattheus-Moerman]

@cbrnr I checked the changes and all looks good. I will now process this work for acceptance in JOSS. At this point can you work on the following:

• [x] Please archive a copy of the reviewed software on ZENODO you can do this manually, or some find these automated steps useful: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
• [x] Once the ZENODO archive is created please check the meta-data and amend it where needed. For instance the title should match the title of the paper, and that the author list should match as well (the list should only be for the paper authors, remove other contributors if they are listed). Furthermore you can add ORCID for authors if you like.
• [x] Once the ZENODO archive is complete please report back here with the ZENODO DOI.
• [x] Please can you inform me what the version tag for the published version should be? This review currently lists v0.8.4, but please let me know if that has changed in the mean time.