[REVIEW]: Stripy: A Python module for (constrained) triangulation in Cartesian coordinates and on a sphere

[whedon]

Submitting author: @lmoresi (Louis Moresi)
Repository: https://github.com/underworldcode/stripy
Version: 1.0.1
Editor: @VivianePons
Reviewers: @santisoler, @rrenka
Archive: 10.5281/zenodo.3243511

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/2e1e7ec491a953ca7c69f277bc877e0b"><img src="http://joss.theoj.org/papers/2e1e7ec491a953ca7c69f277bc877e0b/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/2e1e7ec491a953ca7c69f277bc877e0b/status.svg)](http://joss.theoj.org/papers/2e1e7ec491a953ca7c69f277bc877e0b)

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 & @rrenka, 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 @VivianePons know.

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

Review checklist for @santisoler

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: 1.0.1
• Authorship: Has the submitting author (@lmoresi) 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)?

Review checklist for @rrenka

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: 1.0.1
• Authorship: Has the submitting author (@lmoresi) 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, a robot that can help you with some common editorial tasks. @santisoler it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

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:

2. 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]

PDF failed to compile for issue #1410 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1410 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[santisoler]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

PDF failed to compile for issue #1410 with the following error:

sh: 1: cd: can't cd to tmp/1410
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1410 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/lib/whedon/processor.rb:57:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-a1723d160bb6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[santisoler]

@VivianePons seems like whedon is having some problems generating the PDF.
Is this related to the fact that the repository ulr is pointing to the paper branch instead of pointing to the repo itself (https://github.com/underworldcode/stripy/)?

[santisoler]

Hi @lmoresi and @brmather. I was assigned as reviewer for your submitted paper.
Let me read through your PDF, explore your stripy repo and experiment with your software.
I'll try to meet the two weeks deadline, but in case I get delayed I'll let you know so you don't get worried about the status of the review.

I'm still thinking my review strategy, but I'll probably will open issues on your repo regarding each section of the checklist (e.g. General Checks, Functionality, Documentation, Software Paper).
Besides that, I'm open to help you solve the issues that may appear. My goal is to contribute to get this published! So don't hesitate asking for help or guidance, I'm willing to help with everything that's on my reach.

I'm sure this will be a nice experience for all of us. Be patient, I'll contact you when I have some news.

[lmoresi]

Thanks - we’ll work with the way you prefer to review. issues sounds like the obvious strategy. We have a “paper” branch of the code to make sure that any developments we make during the review process do not cause problems for you. Any suggestions you make st this stage will be merged back when the process is done. Prof Louis Moresi louis.moresi@unimelb.edu.au<mailto:louis.moresi@unimelb.edu.au> (w) +61 3 8344 1217 (m) +61 4 0333 1413 (us) +1 505 349 4425 www.moresi.info<http://www.moresi.info/> www.facebook.com/underworldcode<http://www.facebook.com/underworldcode> @LouisMoresi<https://twitter.com/LouisMoresi> On 24 Apr 2019, 07:20 -0700, Santiago Soler <notifications@github.com>, wrote: Hi @lmoresi<https://github.com/lmoresi> and @brmather<https://github.com/brmather>. I was assigned as reviewer for your submitted paper. Let me read through your PDF, explore your stripy repo and experiment with your software. I'll try to meet the two weeks deadline, but in case I get delayed I'll let you know so you don't get worried about the status of the review. I'm still thinking my review strategy, but I'll probably will open issues on your repo regarding each section of the checklist (e.g. General Checks, Functionality, Documentation, Software Paper). Besides that, I'm open to help you solve the issues that may appear. My goal is to contribute to get this published! So don't hesitate asking for help or guidance, I'm willing to help with everything that's on my reach. I'm sure this will be a nice experience for all of us. Be patient, I'll contact you when I have some news. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#1410 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ADABPI5V7F7RR6NJBZEVFJLPSBUAVANCNFSM4HID64OA>.

[VivianePons]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

👉 Check article proof 📄 👈

[santisoler]

@lmoresi @brmather

We have a “paper” branch of the code to make sure that any developments we make during the review process do not cause problems for you. Any suggestions you make st this stage will be merged back when the process is done.

Thanks for pointing this out. I've started reviewing some of the more basic aspects of the publication.
I'll open some issues on your repo so we can start talking about them.
I'll try to get into the other subjects next week, so I can continue opening issues if they are needed.
So far the paper is looking great and most of the issues I found are really minor and very easy to tackle down.

[santisoler]

Hi @VivianePons. I have a small question regarding how versioning works on the review process.
The authors have submitted the 0.7.0 version of stripy, although on the review process they'll surely make some changes.
Is it possible that after acceptance the authors create a new release, 0.7.1 for instance, and make that the final version?
Thanks in advance!

[VivianePons]

Yes, don't worry about the version. When the paper is approved, we update the version before the final publication

[VivianePons]

I have a question for @arfon : I have contacted Robert Renka to be a second reviewer on this paper (as suggested by the author). He would be willing to do it but he is also the author of the original Fortran code on which the software is based. He is wondering if this is a case of conflict of interest.

I believe it's ok. I actually think that his opinion on the paper would be very valuable. Besides, we have a second independent reviewer so the publication is not based on his opinion alone. What do you think?

[arfon]

I believe it's ok. I actually think that his opinion on the paper would be very valuable. Besides, we have a second independent reviewer so the publication is not based on his opinion alone. What do you think?

👍 this sounds OK to me. Thanks for checking.

[santisoler]

Yes, don't worry about the version. When the paper is approved, we update the version before the final publication

Thanks for answering this @VivianePons!

[VivianePons]

@whedon add @rrenka as reviewer

[whedon]

OK, @rrenka is now a reviewer

[lmoresi]

@whedon generate pdf from branch master

[whedon]

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

[whedon]

👉 Check article proof 📄 👈

[whedon]

OK DOIs

- 10.1016/j.tecto.2016.12.004 is OK
- 10.1029/2007GC001743 is OK
- 10.1145/275323.275329 is OK
- 10.1145/275323.275330 is OK
- 10.1145/225545.225546 is OK
- 10.1145/225545.225547 is OK
- 10.1002/2013JB010626 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#755

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#755, 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 generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1016/j.tecto.2016.12.004 is OK
- 10.1029/2007GC001743 is OK
- 10.1145/275323.275329 is OK
- 10.1145/275323.275330 is OK
- 10.1145/225545.225546 is OK
- 10.1145/225545.225547 is OK
- 10.1002/2013JB010626 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#756

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#756, 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]

🐦🐦🐦 👉 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 👉 Creating pull request for 10.21105.joss.01410 joss-papers#757
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01410
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...

[arfon]

@santisoler, @rrenka - many thanks for your reviews and to @VivianePons for editing this submission ✨

@lmoresi - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.01410/status.svg)](https://doi.org/10.21105/joss.01410)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01410">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01410/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01410/status.svg
   :target: https://doi.org/10.21105/joss.01410

This is how it will look in your documentation:

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[QuLogic]

The Software repository link on the final article is 404. It should probably point to the repo, not a subdirectory.

[lmoresi]

I have added a ‘paper’ tag to the repo that snapshots the current / published state so that the link no longer fails. However, this is a snapshot of the published release and I am not sure that this is what is intended by that link. Prof Louis Moresi louis.moresi@unimelb.edu.au<mailto:louis.moresi@unimelb.edu.au> (w) +61 3 8344 1217 (m) +61 4 0333 1413 (us) +1 505 349 4425 www.moresi.info<http://www.moresi.info/> www.facebook.com/underworldcode<http://www.facebook.com/underworldcode> @LouisMoresi<https://twitter.com/LouisMoresi> On 14 Jun 2019, 5:27 AM +0100, Elliott Sales de Andrade <notifications@github.com>, wrote: The Software repository link on the final article is 404. It should probably point to the repo, not a subdirectory. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#1410?email_source=notifications&email_token=ADABPI7KPCXRBCY5WU3IKXTP2MM27A5CNFSM4HID64OKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXVVS2I#issuecomment-501963113>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ADABPI2JNT4NTI6PLGAIFPDP2MM27ANCNFSM4HID64OA>.

[arfon]

This is fixed now. Thanks for catching this.