paper/joss/2016-09-20-review.md

In eddelbuettel/rcppcnpy: Read-Write Support for 'NumPy' Files via 'Rcpp'

Review of RcppCNPy: Read-Write Support for NumPy Files in R

Reviewer questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

General checks

• [x] Repository: Is the source code for this software available at the repository url?

Yes, it is also available from CRAN with install.packages('rcppcnpy')

• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

Yes, except it is GNU 2, not GNU 3 or later. Also, should GNU statement be at the top of each script?

• [x] Version: Does the release version given match the GitHub release (0.2.5)?

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?

README does not list installation instructions, easy fix library(rcppcnpy) did not work for me It seems library('RcppCNPy') command is case sensitive.

• [x] Functionality: Have the functional claims of the software been confirmed?

• [x] Performance: Have any performance claims of the software been confirmed?

N/A? I did not see any performance claims in README, I found performance claims in https://cran.r-project.org/web/packages/RcppCNPy/vignettes/RcppCNPy-intro.pdf

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?

Target audience could be better stated in README and vignette

• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

I'm not sure if the authors would also like to include the list of Python dependencies since Python example code is given in the README

• [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)?

Functionality is better stated in vignette. README does not contain exhaustive list of functionality

• [ ] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?

Tests were performed, but I did not find a .md or README if that is required by this journal

• [ ] 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

Community guidelines for contributions could be better reported

Software paper

Paper PDF: 10.21105.joss.00055.pdf

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?

Author names present in paper.md but did not compile to pdf

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

• [ ] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

References do not have a DOI in pdf

Recommendations to editor

While the software works well and quickly, some additional documentation is required by JOSS for publication.

Recommendations to author

This reviewer would like to see reading and writing capability of .npz in the future. npyLoad of integer arrays produces incorrect values when not given the flag "integer." Multidimensional arrays should also be easily loadable. I was impressed that arrays of sizes (24,) , (1,24), and (24,1) all loaded correctly in R with the existing functionality.

Recommendations to JOSS

Reviewers should be left with the choice to be anonymous

eddelbuettel/rcppcnpy documentation built on Jan. 4, 2024, 6:34 p.m.