[REVIEW]: PyMap3D: 3-D coordinate conversions for terrestrial and geospace environments

[whedon]

Submitting author: @scivision (Michael Hirsch)
Repository: https://github.com/scivision/pymap3d
Version: v1.6.0
Editor: @lheagy
Reviewer: @hugoledoux
Archive: 10.5281/zenodo.213676

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Reviewer instructions & questions: @hugoledoux

@hugoledoux, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.6.0)?
• Authorship: Has the submitting author (@scivision) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Reviewer instructions & questions: @leouieda

@hugoledoux, 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.

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.5.0)?
• Authorship: Has the submitting author (@scivision) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @hugoledoux it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof 📄 <--

[lheagy]

👋 Hi @hugoledoux and @leouieda, here is the issue for the review. I have put 2 checklists in the top of the issue, one for each of you. Please let me know if you have any questions!

[lheagy]

Hi @leouieda: would you be willing to do a first go on looking through the software? @hugoledoux had a lot on his plate at the moment and mentioned that he would be able to jump in near the end of the month. Please let me know if you have any questions!

[leouieda]

Hi @lheagy, I can get started on this tomorrow. I had a look at the guidelines and review questions.

It seems that there has been a new release (1.6.0) since the paper was submitted. Should @scivision update the paper/issue content to match?

[lheagy]

Thanks @leouieda, yes, that is a good catch. @arfon: how do we update the version on this issue? manually? or should this be done with whedon?

[arfon]

@arfon: how do we update the version on this issue? manually? or should this be done with whedon?

You can simply edit the comment by @whedon at the top of the issue.

[scivision]

Thanks, I updated paper.md to mention the Fortran code. The Matlab and Fortran code are completely independent standalone codes for those langauges.

[hugoledoux]

@scivision

I am a GIS person used to work with proj4 (pyproj), and the Python package works as advertised and is surely useful to people in that community. For a GIS person, proj4 is "standard" and everyone uses it.

I only tested the Python version, since I don't have the 1000$ to buy Matlab...

README

I find the README a bit confusing sometimes to be honest.

install

You state in INSTALL that there are 3 packages, but you give two installations...

prereqs

I'd write "prerequisites", but okay fair enough.

What is not clear to me: if I want to use numpy for instance, do I have to do something? It's on my system, is it used automatically? Same thing for AstroPy.

Also a link to AstroPy could help the user.

version

The version is 1.6.0, I changed the from 1.5.0. I assume this is not a problem.

pyproj

I believe there are conversions that you perform that are impossible with proj4, no? State a few... For me the argument of not pure python is not very strong, it's trivial to install proj4 on most platform.

installation

I think it could be written that everything is on PyPI and just doing pip install pymap3d works (that's how I installed it under Python 2.7)

functions

I am not familiar with the terms such as 'aer', 'ned', etc. Are these explained somewhere? That is needed in my opinion, now the docs doesn't really explain them either.

Software paper

• geospace coordinate systems --> geographic coordinate systems is a better term in my opinion

usage

Not totally clear why there are numbers there az,el,range = pm.geodetic2aer(lat, lon, alt, 42, -82, 0), I mean the 42 and -82. Perhaps just explain?

community guidelines

I don't see any file there.

[scivision]

These issues have been addressed in the latest git commits, thanks

[lheagy]

Thanks @scivision, @hugoledoux, @leouieda: could you please take a look and see if your comments have been addressed? Thanks!

[hugoledoux]

Everything related to my comments was done, except I don't see anything for this point "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"

If it's done then all good with me.

[scivision]

Thank you this has been added in
https://github.com/scivision/pymap3d/blob/master/docs/CONTRIBUTING.md

[leouieda]

@lheagy @scivision sorry for the delay. I went over all the changes, installed the package, and ran the tests on my machine. Everything works as advertised and I ticked off all the review items. I have no other issues and it seems good to go for me.

I added a few more issues to the repository with suggestions for improving some parts of the documentation. These are not requirements for acceptance, just suggestions.

[lheagy]

Thanks @hugoledoux and @leouieda for the review! @leouieda: there is still one outstanding check-box in the Documentation: the community guidelines. Did this just get missed or is it still outstanding?

[leouieda]

@lheagy sorry, it just got missed. Checked now.

[lheagy]

@scivision: Can you confirm that this is the correct DOI for the project: 10.5281/zenodo.213676 ?

[scivision]

Yes that's the correct DOI

[lheagy]

@whedon set 10.5281/zenodo.213676 as archive

[whedon]

OK. 10.5281/zenodo.213676 is the archive.

[lheagy]

@arfon: this submission is ready for publication in JOSS.

Congratulations @scivision! Thanks @hugoledoux and @leouieda for reviewing!

[arfon]

@hugoledoux and @leouieda - many thanks for your reviews here and to @lheagy for editing this submission ✨

@scivision - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00580 ⚡ 🚀 💥

[whedon]

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