Joss-reviews: [REVIEW]: pyomeca: An Open-Source Framework for Biomechanical Analysis

Created on 3 Jul 2020 · 79Comments · Source: openjournals/joss-reviews

Submitting author: @romainmartinez (Romain Martinez)
Repository: https://github.com/pyomeca/pyomeca/
Version: 2020.0.1
Editor: @Kevin-Mattheus-Moerman
Reviewers: @BKillen05, @mitkof6
Archive: 10.5281/zenodo.4012118

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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

@BKillen05 & @ @mitkof6, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @BKillen05

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 repository url?
[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 (@romainmartinez) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

Review checklist for @mitkof6

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 repository url?
[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 (@romainmartinez) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[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?

accepted published recommend-accept review

Source

whedon

All 79 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @BKillen05, @ @mitkof6 it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon on 3 Jul 2020

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.5334/jors.148 may be missing for title: xarray: N-D labeled Arrays and Datasets in Python
- https://doi.org/10.25080/majora-92bf1922-00a may be missing for title: Data structures for statistical computing in python
- https://doi.org/10.1109/mcse.2007.55 may be missing for title: Matplotlib: A 2D Graphics Environment
- https://doi.org/10.1109/mcse.2011.37 may be missing for title: The NumPy Array: A Structure for Efficient Numerical Computation
- https://doi.org/10.1016/j.cmpb.2016.11.007 may be missing for title: biomechZoo: An open-source toolbox for the processing, analysis, and visualization of biomechanical movement data
- https://doi.org/10.21105/joss.00927 may be missing for title: CusToM: a Matlab toolbox for musculoskeletal simulation
- https://doi.org/10.1007/s00530-019-00633-9 may be missing for title: RMoCap: an R language package for processing and kinematic analyzing motion capture data

INVALID DOIs

- None

whedon on 3 Jul 2020

PDF failed to compile for issue #2431 with the following error:

pandoc-citeproc: reference mitkof6 not found
Error producing PDF.
! TeX capacity exceeded, sorry [input stack size=5000].
\reserved@a ->\def \reserved@a
*{\let \@xs@assign \@xs@expand@and@detokenize...
l.371 }

Looks like we failed to compile the PDF

whedon on 3 Jul 2020

@whedon generate pdf

Kevin-Mattheus-Moerman on 5 Jul 2020

PDF failed to compile for issue #2431 with the following error:

Looks like we failed to compile the PDF

whedon on 5 Jul 2020

@romainmartinez can you check the reference mitkof6 mentioned in this error message? You can run @whedon generate pdf here to check if the paper compiles.

Kevin-Mattheus-Moerman on 5 Jul 2020

@romainmartinez can you check the reference mitkof6 mentioned in this error message? You can run @whedon generate pdf here to check if the paper compiles.

@Kevin-Mattheus-Moerman I don't have any references for mitkof6, which seems to be the reviewer's username.

In the current issue (#2431), @mitkof6 is displayed with two @ while @BKillen05 has only one.
Maybe the problem is here?