[REVIEW]: The MTPy software package for magnetotelluric data analysis and visualisation

[whedon]

Submitting author: @alkirkby (Alison Kirkby) Repository: https://github.com/MTgeophysics/mtpy Version: v1.0 Editor: @lheagy Reviewer: @JKutt Archive: 10.5281/zenodo.2698634

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/ccb44c5f422e8f52c244665ae4794f76"><img src="http://joss.theoj.org/papers/ccb44c5f422e8f52c244665ae4794f76/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/ccb44c5f422e8f52c244665ae4794f76/status.svg)](http://joss.theoj.org/papers/ccb44c5f422e8f52c244665ae4794f76)

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

@JKutt, 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 @lheagy know.

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

Review checklist for @JKutt

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: v1.0
• [x] Authorship: Has the submitting author (@alkirkby) 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)?

[lheagy]

:wave: @alkirkby, excellent! Would you mind updating the title in the zenodo archive to match the title of the paper: "The MTPy software package for magnetotelluric data analysis and visualisation". After that, we are good to go!

[alkirkby]

@lheagy, ok no worries, done.

[lheagy]

Many thanks @JKutt for your speedy review! and congratulations @alkirkby and team on your submission 🎉

👋 @openjournals/joss-eics, this submission is ready to be accepted!

[danielskatz]

Thanks to @JKutt for reviewing and @lheagy for editing!

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1111/j.1365-246x.2005.02779.x is OK
- 10.1111/j.1365-246X.2004.02281.x is OK
- 10.1111/j.1365-246X.2004.02203.x is OK
- 10.1029/JB092iB01p00633 is OK
- 10.1190/1.1442813 is OK
- 10.1111/j.1365-246X.2011.05347.x is OK
- 10.1016/j.cageo.2014.01.010 is OK
- 10.1016/J.CAGEO.2014.07.013 is OK
- 10.1190/1.1438799 is OK
- 10.1111/j.1365-246X.1962.tb02992.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/709

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/709, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@alkirkby - I see a couple of reference problems that I've tried to fix via https://github.com/MTgeophysics/mtpy/pull/82

One is opening quotes that were backwards, and the other is an underscore that caused a URL to not work right. I'm sure my fix will work for the quotes, but I'm not sure it will work for the URL. Can you accept the PR, and see if paper will compile? If not, we can try to fix the underscore in the URL another way.

[danielskatz]

@whedon generate pdf

[alkirkby]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1358 with the following error:

Can't find any papers to compile :-(

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1358 with the following error:

sh: 0: getcwd() failed: No such file or directory sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.01358.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

[whedon]

OK DOIs

- 10.1111/j.1365-246x.2005.02779.x is OK
- 10.1111/j.1365-246X.2004.02281.x is OK
- 10.1111/j.1365-246X.2004.02203.x is OK
- 10.1029/JB092iB01p00633 is OK
- 10.1190/1.1442813 is OK
- 10.1111/j.1365-246X.2011.05347.x is OK
- 10.1016/j.cageo.2014.01.010 is OK
- 10.1016/J.CAGEO.2014.07.013 is OK
- 10.1190/1.1438799 is OK
- 10.1111/j.1365-246X.1962.tb02992.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/710

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/710, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@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:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/711
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01358
2. If everything looks good, then close this review issue.

3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[alkirkby]

Hi @danielskatz just wondering if the DOI issue should have resolved by now? It's still failing to load the document for me.

[alkirkby]

It's working now, sorry I was just impatient :)

[danielskatz]

Yes, that’s why the review is still open. Let’s see if it resolves a little later; that’s usually the case.

[danielskatz]

Actually, it’s now working for me, though it might be cached for you.

[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.01358/status.svg)](https://doi.org/10.21105/joss.01358)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01358">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01358/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01358/status.svg
   :target: https://doi.org/10.21105/joss.01358

This is how it will look in your documentation:

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[alkirkby]

Thanks @danielskatz, yep it's working now, I was just a bit impatient. And thanks @lheagy and @JKutt for editing and reviewing!