Joss-reviews: [REVIEW]: PyCurious: A Python module for computing the Curie depth from the magnetic anomaly.

[whedon]

Submitting author: @brmather (Ben Mather)
Repository: https://github.com/brmather/pycurious
Version: 1.0.2
Editor: @lheagy
Reviewers: @santisoler, @jessepisel
Archive: 10.5281/zenodo.3349511

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/7d3a0f7af69f8624092a0958860f2e38"><img src="http://joss.theoj.org/papers/7d3a0f7af69f8624092a0958860f2e38/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/7d3a0f7af69f8624092a0958860f2e38/status.svg)](http://joss.theoj.org/papers/7d3a0f7af69f8624092a0958860f2e38)

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

@santisoler, 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 @lheagy know.

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

Review checklist for @santisoler

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: 1.0.2
• [x] Authorship: Has the submitting author (@brmather) 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 @jessepisel

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: 1.0.2
• [x] Authorship: Has the submitting author (@brmather) 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. @santisoler 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:

[lheagy]

@whedon add @jessepisel as reviewer

[whedon]

OK, @jessepisel is now a reviewer

[lheagy]

Thanks for your review @jessepisel! I see pr brmather/pycurious#12 is active and am linking it here so we can keep track of the progress

[jessepisel]

@lheagy perfect, thank you for linking it!

[brmather]

Thanks for your review @jessepisel - I have merged your pull request into the master branch and addressed your comments in brmather/pycurious#12. If you notice anything else that requires attention, please feel free to open an issue ticket.

[santisoler]

Hi @brmather! Sorry for the delay. I'll start opening some issues on pycurious' repository. We can discuss them over there.

[santisoler]

@brmather I think pycurious it's a great asset for geoscientists. Curie Point Depth is a widely used tool, but there aren't well maintained and documented open source libraries to calculate it. I'm glad to review it.

I've opened some issues, although I haven't found big problems with pycurious. I need to finish reviewing it, but feel free to answer them and even open PRs while I'm still doing it. Sorry for my brevity, I wanted to compensate my delay, so I opened the issues very quickly.

[santisoler]

@lheagy I have checked off all my boxes, so I consider pycurious to be ready for publication.

Thanks for letting me review it, and thanks to the authors @brmather and @rdelhaye for the quick response to every issue I opened. I enjoy the open review system because it offers a great opportunity to learn from each other and help improving ourselves.

[lheagy]

Excellent, many thanks @santisoler and @jessepisel for taking time to review!! 🎉

@brmather, I have started a pull request with a few small corrections to the paper. I would also request that in the first paragraph, you give make a few more connections as to why the Curie depth is of interest when interpreting magnetic data. For example in or after the second sentence: would you mind adding some description as to why the Curie depth is used in the interpretation of magnetic data (e.g. it provides information on subsurface temperature, etc). I know you mention this, but it could be a bit more explicit for a non-domain expert. I left a few other comments in the pull request. Please let me know once you have had a chance to take a look.

[brmather]

Many thanks to @santisoler and @jessepisel for their extremely helpful reviews of pycurious. I have found JOSS' interactive review process very useful in improving software so that it is useful to as many people as possible. I have learnt a lot and will apply these practises to the other projects I'm actively working on. I thank the reviewers for the time they have spent on providing advice and submitting pull requests - it is very much appreciated!

Here is a summary of improvements to pycurious from the JOSS review:

• Updated contributions guide to encourage development on priority areas
• Anaconda installation support (and fixes for Cython build issues)
• Checking if windows that exceed the extent of the domain
• Correct propagation of errors with Tanaka et al. 1999 approach
• Refactor code to compute the radial power spectrum
• Updated Docstrings and Jupyter notebooks
• Updated test suite (using pytest) to test for expected functionality of core routines
• PEP8 compliant code

@lheagy thank you for coordinating the review process. I have responded to your pull request with number of additions I think broaden the appeal of the software package.

[brmather]

@whedon generate pdf from branch lheagy-patch-1

[whedon]

Attempting PDF compilation from custom branch lheagy-patch-1. Reticulating splines etc...

[whedon]

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

[brmather]

@whedon generate pdf from branch lheagy-patch-1

[whedon]

Attempting PDF compilation from custom branch lheagy-patch-1. Reticulating splines etc...

[whedon]

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

[brmather]

@whedon generate pdf from branch lheagy-patch-1

[whedon]

Attempting PDF compilation from custom branch lheagy-patch-1. Reticulating splines etc...

[whedon]

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

[lheagy]

:wave: @brmather, if you are happy with the edits to the paper, please merge in the changes and generate a new release of the software. From there, please create an archive on zenodo or similar with the title and author list being the same as the paper and then post the version number and doi here. Thanks!

[brmather]

Thanks @lheagy

I have released version 1.0.2. Some unknown error foiled the 1.0 release on Zenodo, so I had to bump the version to 1.0.2. The Docker image is on Docker Hub, the release is on PyPI, and the Zenodo doi is 10.5281/zenodo.3349511.

[lheagy]

@whedon set 1.0.2 as version

[whedon]

OK. 1.0.2 is the version.

[lheagy]

@whedon set 10.5281/zenodo.3349511 as archive

[whedon]

OK. 10.5281/zenodo.3349511 is the archive.

[lheagy]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[lheagy]

Thanks @brmather! Would you mind updating the title on the zenodo record to match the paper? e.g. "PyCurious: A Python module for computing the Curie depth from the magnetic anomaly" . Please also take a look at the proof above and give a :+1: if you are happy with it. From there, we can proceed with publishing 🎉

[brmather]

I keep getting an internal server error on Zenodo preventing me from updating the title and author fields. Aside from that, the proof looks good.

[lheagy]

Hmm... Is it possible you have it open in multiple tabs? (I am seeing the banner at the top that says "There us a new version of the upload being edited here")

[brmather]

Ha - that fixed it! Thanks @lheagy it's properly updated now.

[lheagy]

@openjournals/joss-eics, this submission is ready to be published! Congrats @brmather 🎉

[kyleniemeyer]

Hi @brmather, please merge the small PR I just submitted with some fixes in the paper: https://github.com/brmather/pycurious/pull/33

[brmather]

No problem. Merged to master branch.

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/867

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/867, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kyleniemeyer]

@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/868
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01544
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...

[kyleniemeyer]

@brmather congrats on your article's publication in JOSS!

Thanks to @santisoler and @jessepisel for reviewing, and to @lheagy for editing!

[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.01544/status.svg)](https://doi.org/10.21105/joss.01544)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01544">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01544/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01544/status.svg
   :target: https://doi.org/10.21105/joss.01544

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://numfocus.salsalabs.org/donate-to-joss