Joss-reviews: [REVIEW]: wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets

[whedon]

Submitting author: @zkuralt (Žan Kuralt)
Repository: https://github.com/romunov/wolfexplorer
Version: v0.9
Editor: @trallard
Reviewer: @amoeba
Archive: 10.5281/zenodo.1890358

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/1250a1c97f53a38efece1c973b499104"><img src="http://joss.theoj.org/papers/1250a1c97f53a38efece1c973b499104/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/1250a1c97f53a38efece1c973b499104/status.svg)](http://joss.theoj.org/papers/1250a1c97f53a38efece1c973b499104)

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

@amoeba, 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 @trallard know.

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

Review checklist for @amoeba

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 (v0.9)?
• [x] Authorship: Has the submitting author (@zkuralt) 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. @amoeba 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:

[amoeba]

Hi @trallard I've made my review (Sorry its one day late). I accept with minor revisions. I left some notes for the authors on https://github.com/romunov/wolfexplorer/issues/42 but checked most everything off. One thing I didn't know about was whether the paper should go in a joss subfolder or the usual paper subfolder at the root of the repo. Do you know?

For now, I'll wait to hear back from the authors on my review and you on the above paper.md location question. Thanks!

[trallard]

hey @amoeba thanks for the speedy review

I have looked at . a number of accepted submissions and it seems that there is a mixture of approaches as where to place the paper, some packages have it under a paper directory and other under joss I think that since the final paper is archived within JOSS itself this _is not a blocker_

---

@zkuralt I am going to recompile the paper here as the pre-review issue is closed now

[trallard]

@whedon generate pdf from branch joss_review

[whedon]

Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1064 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 15 0 15 0 0 324 0 --:--:-- --:--:-- --:--:-- 326
Error reading bibliography ./paper.bib (line 121, column 5):
unexpected "y"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[arfon]

@zkuralt - looks like you're missing a comma on this line: https://github.com/romunov/wolfexplorer/blob/joss_review/joss/paper.bib#L120

[zkuralt]

@arfon Thanks, I missed it when adding DOI to the bibliography item.

[trallard]

hi @zkuralt I can see there are still a couple of unticked items on the review checklist so I just wanted to check how you were getting on with this

[amoeba]

Hi @trallard, all review checklist items have been satisfactorily met by the authors and I now change my review to Accept.

[trallard]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[trallard]

@zkuralt since @amoeba has now recommended the acceptance of the package we need you to complete the following actions:

• [x] confirm that the version of the paper in the master branch is the final version
• [x] make a new release of the package, upload the revised software to your DOI-granting data/software repository, and post the DOI here

[romunov]

I have confirmed that the latest release corresponds to what has been put up for review and includes subsequent changes suggested by the reviewer.

Source code of v0.9 release has been deposited in Zenodo under DOI 10.5281/zenodo.1890359.

[trallard]

@romunov @zkuralt this looks good to me so will proceed to recommend for acceptance

[trallard]

@whedon set 10.5281/zenodo.1890358 as archive

[whedon]

OK. 10.5281/zenodo.1890358 is the archive.

[trallard]

@arfon: this submission is accepted and ready to be published 🎉👾

@amoeba thank you very much for your time and valuable contribution to JOSS as a reviewer for this submission 🙌🏻

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/111

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/111, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@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/112
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01064
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...

[arfon]

@amoeba - many thanks for your review here and to @trallard for editing this submission ✨

@zkuralt - your paper is now accepted into JOSS :zap::rocket::boom:

[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.01064/status.svg)](https://doi.org/10.21105/joss.01064)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01064">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01064/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01064/status.svg
   :target: https://doi.org/10.21105/joss.01064

This is how it will look in your documentation:

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