Joss-reviews: [REVIEW]: Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification

[whedon]

Submitting author: @maxibor (Maxime Borry)
Repository: https://github.com/maxibor/sourcepredict
Version: v0.34
Editor: @lpantano
Reviewers: @gavinmdouglas, @giraola, @will-rowe
Archive: 10.5281/zenodo.3379604

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/f33385c6b7f2c176ae076bb1c4ad50ba/status.svg)](http://joss.theoj.org/papers/f33385c6b7f2c176ae076bb1c4ad50ba)

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

@gavinmdouglas & @giraola, 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 @lpantano know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @gavinmdouglas

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.34
• [x] Authorship: Has the submitting author (@maxibor) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @will-rowe

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.34
• [x] Authorship: Has the submitting author (@maxibor) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

:star: Important :star:

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:

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

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[lpantano]

Hi @gavinmdouglas and @giraola, just to check on how the reviewing is going and if you need anything from me. Thanks!

[gavinmdouglas]

Thanks @lpantano - I made comments (see: https://github.com/maxibor/sourcepredict/issues/3), which I believe are still being addressed by the author. I'll post here when that issue is resolved.

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[maxibor]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gavinmdouglas]

Hey @lpantano - There a small number of minor changes to the documentation that I think should be made, but all of my major comments have been addressed. Note that DOIs are not available for two of the references apparently.

[lpantano]

Thank you, @gavinmdouglas, for all the work. @maxibor, are you willing to make the changes to the documentation as the reviewer suggest?

[lpantano]

@whedon remove @giraola as reviewer

[whedon]

OK, @giraola is no longer a reviewer

[lpantano]

@whedon add @giraola as reviewer

[whedon]

OK, @giraola is now a reviewer

[maxibor]

Changes were and are being made @lpantano

[maxibor]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gavinmdouglas]

Hey @lpantano - quick note that all of my remaining minor comments have been addressed.

[lpantano]

Thanks a lot!, I’ll wait for the other reviewer.

[lpantano]

👋 @giraola, any update in the review? Thanks!

[lpantano]

Hi @maxibor, I am trying to find another reviewer since it seems @giraola is super busy right now. Sorry about the dealy. If you know other possible reviewer let me know.

[maxibor]

Hi @lpantano, @will-rowe could also be a good match for this

[will-rowe]

Happy to review if needed.

[lpantano]

@whedon add @will-rowe as reviewer

[whedon]

OK, @will-rowe is now a reviewer

[lpantano]

@whedon remove @giraola as reviewer

[whedon]

OK, @giraola is no longer a reviewer

[will-rowe]

Hi all. I've made a few minor comments over at the sourcepredict issue tracker. Nothing major - it's a nice contribution!

[maxibor]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[will-rowe]

@lpantano - My comments have been addressed and I'm happy. Thanks @maxibor

[lpantano]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1186/gb-2014-15-3-r46 is OK
• 10.7717/peerj.4600 is OK
• 10.1038/455481a is OK
• 10.1093/molbev/msw046 is OK
• 10.1128/AEM.01996-06 is OK
• 10.1038/nmeth.1650 is OK
• 10.2307/1942268 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[lpantano]

thank you, @will-rowe, for the quick review.

@maxibor, if you could make a Zenodo archive pointing to the current version, that I assumed it hasn't changed (0.33), and make sure that the title and the authors match the paper information, I can move this to the last stage, finally.

[maxibor]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[maxibor]

@lpantano I created the Zenodo archive and added the DOI badge in the README.
The version is now 0.34 (following all the modifications after this review).
The rest should be fine 😃

[lpantano]

@whedon set v0.34 as version

[whedon]

OK. v0.34 is the version.

[lpantano]

Thank you,@maxibor, can you update the title you see in the Zenodo link to match the paper title?

[maxibor]

Done

[lpantano]

@whedon set 10.5281/zenodo.3379604 as archive

[whedon]

OK. 10.5281/zenodo.3379604 is the archive.

[lpantano]

@openjournals/joss-eics, I think this is ready.

[labarba]

Some editorial fixes/requests:

• Remove the URL to the GitHub repository from the first line. The JOSS article template includes the repo as part of the margin decorators on the front page.
• Add comma after "i.e." and don't italicize
• [p.1] "Second it predicts" --> add comma
• [p.2] heading "Prediction of unknown sources proportion" --> Prediction of the proportion of unknown sources
• "Let S_i ... be a sample ... be an organism" --> pls fix verb repeat
• "of each of the ... organism" --> organisms (plural), or remove "of the"
• "is added to each U_k^S samples --> here, it's "sample" in singular: each sample
• independantly --> independently
• "Prediction of known source proportion" --> Prediction of the proportion of known sources
• [p.3] "Combining unknown and source proportion" --> proportions (plural)
• "Then for each" --> delete "Then" (you've started a new section); appears twice
• Acknowledgements --> add a \ after "Dr." to suppress the double white space (default in LaTeX for end of sentence)
• Bibliography: add case protection in titles with {} to keep the capitalization, where appropriate; for example, in "Southern Wisconsin"
• Use camel case for journal titles
• DOI for Maaten & Hinton 2008 (and caps protection)
• DOI for Patt et al. 1999?

You seem to have written the sections on p,2 as a sequence of orphan sentences. Can you group into paragraphs?

You mention scikit-bio: is there a reference you can cite for this library? What about scikit-learn?

[maxibor]

Thanks for the editorial check and comments !

Remove the URL to the GitHub repository from the first line. The JOSS article template includes the repo as part of the margin decorators on the front page.

Done

Add comma after "i.e." and don't italicize

Done

[p.1] "Second it predicts" --> add comma

Done

[p.2] heading "Prediction of unknown sources proportion" --> Prediction of the proportion of unknown sources

Done

"Let S_i ... be a sample ... be an organism" --> pls fix verb repeat

Done

"of each of the ... organism" --> organisms (plural), or remove "of the"

Done

"is added to each U_k^S samples --> here, it's "sample" in singular: each sample

Done

independantly --> independently

Done

"Prediction of known source proportion" --> Prediction of the proportion of known sources

Done

[p.3] "Combining unknown and source proportion" --> proportions (plural)

Done

"Then for each" --> delete "Then" (you've started a new section); appears twice

Done

Acknowledgements --> add a \ after "Dr." to suppress the double white space (default in LaTeX for end of sentence)

Done

Bibliography: add case protection in titles with {}to keep the capitalization, where appropriate; for example, in "Southern Wisconsin"

Done

Use camel case for journal titles

Done

DOI for Maaten & Hinton 2008 (and caps protection)

DOI for Patt et al. 1999?

As far as I could search, there is no DOI available for these articles (I couldn't find any DOI for the Journal of Machine Learning research)

You seem to have written the sections on p,2 as a sequence of orphan sentences. Can you group into paragraphs?

Done

You mention scikit-bio: is there a reference you can cite for this library?

Added a reference

What about scikit-learn?

Added a reference

[maxibor]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[maxibor]

Do you need any more input from my side @lpantano and @labarba ?

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/944

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/944, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[labarba]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/945
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01540
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...

[labarba]

Congratulations, @maxibor, your JOSS paper is published! 🚀

Big thanks to our editor: @lpantano, and reviewers: @gavinmdouglas, @will-rowe — we appreciate your contributions to JOSS! 🙏

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.01540/status.svg)](https://doi.org/10.21105/joss.01540)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01540">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01540/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01540/status.svg
   :target: https://doi.org/10.21105/joss.01540

This is how it will look in your documentation:

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[labarba]

@arfon —could you keep an eye on this paper? The DOI is not resolving yet.

[arfon]

Looks like the DOI is resolving now.

[maxibor]

Thanks @lpantano and @labarba for the editing !
Thanks a lot @gavinmdouglas and @will-rowe for the review and really helpful comments and suggestions !
First paper of my PhD, and great publishing experience with JOSS !

[arfon]

First paper of my PhD, and great publishing experience with JOSS !

🎉 congrats!