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[REVIEW]: lightr: import spectral data and metadata in R #1857

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whedon opened this issue Nov 1, 2019 · 32 comments
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@whedon whedon commented Nov 1, 2019

Submitting author: @Bisaloo (Hugo Gruson)
Repository: https://www.github.com/ropensci/lightr
Version: v0.1
Editor: @danielskatz
Reviewer: @danielskatz
Archive: 10.5281/zenodo.3525016

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7f76d78642d3dc72ea9d8c2597ef0e27"><img src="https://joss.theoj.org/papers/7f76d78642d3dc72ea9d8c2597ef0e27/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7f76d78642d3dc72ea9d8c2597ef0e27/status.svg)](https://joss.theoj.org/papers/7f76d78642d3dc72ea9d8c2597ef0e27)

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

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

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @danielskatz know.

Please try and complete your review in the next two weeks

Review checklist for @danielskatz

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@Bisaloo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?
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@whedon whedon commented Nov 1, 2019

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

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf
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@whedon whedon commented Nov 1, 2019

Attempting PDF compilation. Reticulating splines etc...
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@danielskatz danielskatz commented Nov 1, 2019

Note: This package has been peer-reviewed by rOpenSci (v. 0.1): ropensci/software-review#267

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@whedon whedon commented Nov 1, 2019

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@danielskatz danielskatz commented Nov 1, 2019

@Bisaloo - Can you please merge ropensci/lightr#8

Also, the text in the paper that says

It is for example planned to become a dependency to the vision model package pavo.

was not possible for me to fully parse so that I could suggest a change. What is the subject of this sentence? Can you suggest a rephrasing of this sentence?

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@Bisaloo Bisaloo commented Nov 1, 2019

lightr can serve as a basis for colour analysis R packages to deal with the
file import step (future versions of pavo for example will include lightr as a dependency). Most packages can indeed currently only read a limited variety of file formats.
Here is an example of a workflow where lightr is used to import the spectral data, which is then analysed with pavo:

library(lightr)
specs <- lr_get_spec(where = "yourfolder", ext = "ProcSpec")

library(pavo)
plot(specs, col = spec2rgb(specs))

Does that make more sense?

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@danielskatz danielskatz commented Nov 1, 2019

yes.

Can you change

It is for example planned to become a dependency to the vision model package pavo.

to

Future versions of pavo, for example, will include lightr as a dependency.

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@Bisaloo Bisaloo commented Nov 1, 2019

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

No archive DOI set. Exiting...

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@danielskatz danielskatz commented Nov 1, 2019

@Bisaloo - can you please archive the software in a repository, e.g., Zenodo, figshare, and let me know the DOI of the deposit?

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@Bisaloo Bisaloo commented Nov 1, 2019

Sorry for the delay. For some reason, I couldn't use GitHub integration feature on the rOpenSci repo so I mirrored it on my own account.

The DOI is 10.5281/zenodo.3525016. Record is here: https://zenodo.org/record/3525016

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@danielskatz danielskatz commented Nov 1, 2019

@whedon set 10.5281/zenodo.3525016 as archive

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@whedon whedon commented Nov 1, 2019

OK. 10.5281/zenodo.3525016 is the archive.

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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept

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@whedon whedon commented Nov 1, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Nov 1, 2019


OK DOIs

- 10.1016/j.visres.2008.06.018 is OK
- 10.1086/303160 is OK
- 10.1086/285711 is OK
- 10.1111/2041-210X.12069 is OK
- 10.1111/evo.12551 is OK
- 10.1073/pnas.0501891102 is OK
- 10.1111/2041-210X.13174 is OK
- 10.1093/biostatistics/kxp014 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Nov 1, 2019

Check final proof 👉 openjournals/joss-papers#1071

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1071, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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@danielskatz danielskatz commented Nov 1, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Nov 1, 2019
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@whedon whedon commented Nov 1, 2019

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Nov 1, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Nov 1, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1072
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01857
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@danielskatz danielskatz commented Nov 1, 2019

Thanks @Bisaloo for submitting this to JOSS as well - it's all done now!

@danielskatz danielskatz closed this Nov 1, 2019
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@whedon whedon commented Nov 1, 2019

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01857/status.svg)](https://doi.org/10.21105/joss.01857)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01857">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01857/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01857/status.svg
   :target: https://doi.org/10.21105/joss.01857

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@Bisaloo Bisaloo commented Nov 1, 2019

@danielskatz, sorry, I just realized (a couple of seconds too late) that the ORCID for Thomas White is wrong. Is there a way to update it?

The correct ORCID is 0000-0002-3976-1734

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@danielskatz danielskatz commented Nov 1, 2019

@Bisaloo - please change the .md file to fix this, then let us know it is done
@arfon - can you then regenerate the PDF and metadata

@danielskatz danielskatz reopened this Nov 1, 2019
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@Bisaloo Bisaloo commented Nov 1, 2019

I already did it in ropensci/lightr@e0e25a6.

Thanks!

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@danielskatz danielskatz commented Nov 1, 2019

@arfon, can you regenerate the PDF and metadata and replace the old versions in the various places?

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@arfon arfon commented Nov 1, 2019

@arfon, can you regenerate the PDF and metadata and replace the old versions in the various places?

That sounds be updated now.

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@danielskatz danielskatz commented Nov 1, 2019

thanks!

@danielskatz danielskatz closed this Nov 1, 2019
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@whedon whedon commented Nov 1, 2019

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01857/status.svg)](https://doi.org/10.21105/joss.01857)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01857">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01857/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01857/status.svg
   :target: https://doi.org/10.21105/joss.01857

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@Bisaloo Bisaloo commented Nov 1, 2019

Thanks a bunch for reviewing @danielskatz and to you both for fixing my mistakes!

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