Joss-reviews: [REVIEW]: mitolina: MITOchondrial LINeage Analysis

[whedon]

Submitting author: @mikldk (Mikkel Meyer Andersen)
Repository: https://github.com/mikldk/mitolina
Version: v0.0.1
Editor: @lpantano
Reviewer: @jdeligt
Archive: 10.5281/zenodo.2574400

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/1819fd2f15585545474c1c82bf97f213"><img src="http://joss.theoj.org/papers/1819fd2f15585545474c1c82bf97f213/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/1819fd2f15585545474c1c82bf97f213/status.svg)](http://joss.theoj.org/papers/1819fd2f15585545474c1c82bf97f213)

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) 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

@jdeligt, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @lpantano know.

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

Review checklist for @jdeligt

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: Does the release version given match the GitHub release (v0.0.1)?
• [x] Authorship: Has the submitting author (@mikldk) 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. @jdeligt it looks like you're currently assigned as the reviewer for 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 @mikldk,

We are starting the review process in this issue tracker.

To expedite the review process do you mind going through the above list of checkboxes and make sure they can be ticked (you can't tick them). Also, check the PDF output carefully.

Please, Ping us here when you are done.

Cheers

Lorena

[mikldk]

Hi @lpantano. Ping: I went though the list and I seem to have addressed all.

[jdeligt]

Hi @mikldk I just raised a minor issue on not having a release in the repo. Could you please look into this while I continue with the rest of the review.
https://github.com/mikldk/mitolina/issues/2

[jdeligt]

Now hit a bigger issue: https://github.com/mikldk/mitolina/issues/3.
I have to manually install dependencies which rely on a 'non standard library': libudunits2.so

[jdeligt]

@mikldk please let me know when you've looked at this so I can check the last steps. Apart from the software side of things I would like to hear your take on the Biparental inheritance published in November: https://doi.org/10.1073/pnas.1810946115 and how your software deals with this. I think its an important thing to note for potential users especially if you're targeting forensics where edge cases matter a lot.

[mikldk]

@jdeligt:
Thanks for all your inputs!

1) Regarding a release (mikldk/mitolina#2): I thought I should wait until after potential acceptance. But I now made one here.
2) Vignette not loading (mikldk/mitolina#3): I have now updated README.md to compile these by default (remotes::install_github("mikldk/mitolina", build_opts = c("--no-resave-data", "--no-manual"))). Thanks.
3) Dependencies: I have now adapted the vignette so that it checks whether the suggested ggraph is installed. This ought to remove the "'non standard library': libudunits2.so" warning. Thanks.
4) Regarding 10.1073/pnas.1810946115: There is still very much debate about this. See e.g. 10.1073/pnas.1820533116. Still, the general belief is that mtDNA is maternally inherited.

Please let me know if I can assist further.

[jdeligt]

@mikldk thanks fro the quick response and resolving the issues. As far as the software/paper is concerned I'm happy to accept this and move it forward. I would personally add a (small) disclaimer about the fact that this software operates under the maternal only model, just so that users are aware of it.
@lpantano please move this paper forward.

[pjotrp]

Haha, don't close just yet :)

[lpantano]

Thanks so much for the review @jdeligt!

@mikldk, do you think you could add a note as @jdeligt mentioned? I think is a good point.

I will move this forward after that.

Thanks!

[mikldk]

@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

[mikldk]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[lpantano]

Hey @mikldk,

did you add the note as @jdeligt mentioned? if you so, can you comment with the commit here, so I can follow up?

Thanks!

[mikldk]

Thanks, @jdeligt, @pjotrp and @lpantano. I have now added the note "This software operates under the maternal inheritance only model, i.e. that mtDNA is only passed on by mothers to children." in both README.md and paper.md. I have also deleted the old release and made a new: https://github.com/mikldk/mitolina/releases. I have also added Zenodo, and this new release has DOI: https://doi.org/10.5281/zenodo.2574140.

[mikldk]

@lpantano , yes indeed. I just wanted to check the proof before I wrote you :-). The note was added in mikldk/mitolina@ae28a61f9c137fe1574ba0d59f320b6ff6414069.

[lpantano]

Thanks so much! I will proceed with the acceptance in 1 hour.

[pjotrp]

One of the fastest reviews ever :+1:

[mikldk]

Indeed! Thanks for the splendid service!

[lpantano]

@whedon set https://doi.org/10.5281/zenodo.2574140 as archive

[whedon]

OK. 10.5281/zenodo.2574140 is the archive.

[lpantano]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• http://doi.org/10.1371/journal.pgen.1007028 is OK
• http://doi.org/10.1371/journal.pgen.1007774 is OK
• http://doi.org/10.1016/j.fsigen.2012.11.004 is OK
• http://doi.org/10.1016/j.jtbi.2013.03.009 is OK
• http://doi.org/10.7287/peerj.preprints.3188v1 is OK
• http://doi.org/10.1016/j.ajhg.2009.05.001 is OK
• http://doi.org/10.1093/molbev/msu222 is OK
• http://doi.org/10.1038/s41598-017-05673-7 is OK
• http://doi.org/10.21105/joss.00684 is OK
• http://doi.org/10.1016/j.fsigen.2014.09.021 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/513

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/513, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[lpantano]

Hi @pjotrp,

all is good, should you do the deposit, or I do?

I read in the docs that I should ping: @openjournals/joss-eics

Thanks!

[labarba]

(We don't remove the "review" label.)

[labarba]

👋 @mikldk — Could you edit the metadata of your Zenodo archive so it matches the title of the JOSS paper? Thanks.

[labarba]

You may also want to add case protection with {} to the bibtex entry for Butler (2009), so you get _DNA_ instead of _dna_.

[lpantano]

@labarba, is the metadata to change the one that is saying now: mikldk/mitolina: v0.0.1? (just to learn for the next time) and (sorry about the label).

[labarba]

Yes: the title of the Zenodo archive matching the title of the JOSS paper.

[labarba]

(Authors often need to be manually edited, too, as Zenodo automatically lists everyone who has a commit.)

[mikldk]

@lpantano @labarba I'll look at Zenodo metadata. And the reference. And recompile paper. I guess I should then delete Github release and make a new afterwards?

[mikldk]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[mikldk]

@lpantano @labarba : I have updated paper.bib, deleted the old release and created a new. The new DOI at Zenodo is 10.5281/zenodo.2574400. I have changed the Zenodo title at https://zenodo.org/record/2574400. I hope I have done everything right?

[labarba]

ah! No need to get a new DOI at Zenodo, but alright!

[labarba]

@whedon set 10.5281/zenodo.2574400 as archive

[whedon]

OK. 10.5281/zenodo.2574400 is the archive.

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• http://doi.org/10.1371/journal.pgen.1007028 is OK
• http://doi.org/10.1371/journal.pgen.1007774 is OK
• http://doi.org/10.1016/j.fsigen.2012.11.004 is OK
• http://doi.org/10.1016/j.jtbi.2013.03.009 is OK
• http://doi.org/10.7287/peerj.preprints.3188v1 is OK
• http://doi.org/10.1016/j.ajhg.2009.05.001 is OK
• http://doi.org/10.1093/molbev/msu222 is OK
• http://doi.org/10.1038/s41598-017-05673-7 is OK
• http://doi.org/10.21105/joss.00684 is OK
• http://doi.org/10.1016/j.fsigen.2014.09.021 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/514

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/514, 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]

🚨🚨🚨 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/515
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01266
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, @mikldk, your paper is published!

Big thanks to the handling editor, @lpantano, and the reviewer, @jdeligt 🙏

[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](http://joss.theoj.org/papers/10.21105/joss.01266/status.svg)](https://doi.org/10.21105/joss.01266)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01266">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01266/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01266/status.svg
   :target: https://doi.org/10.21105/joss.01266

This is how it will look in your documentation:

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=

[mikldk]

Thanks to everybody!