[REVIEW]: Pyoints: A Python package for point cloud, voxel and raster processing.

[whedon]

Submitting author: @laempy (Sebastian Lamprecht)
Repository: https://github.com/laempy/pyoints
Version: v0.2.0rc3
Editor: @lheagy
Reviewer: @kbevers, @scivision
Archive: 10.5281/zenodo.2619945

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/74503e9ec493adc91fc43e47b82a2e8e"><img src="http://joss.theoj.org/papers/74503e9ec493adc91fc43e47b82a2e8e/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/74503e9ec493adc91fc43e47b82a2e8e/status.svg)](http://joss.theoj.org/papers/74503e9ec493adc91fc43e47b82a2e8e)

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

@kbevers & @scivision, 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 @kbevers

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 (v0.2.0a2)?
• Authorship: Has the submitting author (@laempy) 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 @scivision / @lheagy

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 (v0.2.0a2)?
• Authorship: Has the submitting author (@laempy) 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. @kbevers, 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]

👉 Check article proof 📄 👈

[lheagy]

Many thanks @kbevers and @scivision for being willing to review! In the main comment thread above, there is a checklist to help guide your reviews. If possible, I would greatly appreciate if you can do your review within the next 2 weeks. Please let me know if you have any questions or if I can provide any clarification.

[lheagy]

Just checking in. Thanks @kbevers, @scivision for creating the issues. @laempy, please keep us posted on your progress addressing these

[laempy]

Thank you very much for reviewing my package. I have addressed issues 3 to 4 have. I am currently try to solve issue 2. I will push my changes altogether as soon as possible.

[scivision]

@lheagy FYI I am quite tied up on other projects till approx. Nov 15th. If this is an issue someone else can review in the meantime. Sorry about that, this is an interesting project.

[lheagy]

Hi @scivision: thanks for the heads-up! I don't think this should be a problem.
@laempy: please keep us updated on your progress and let us know when to do another pass. Thanks!

[laempy]

Hello @lheagy, I have addressed the issues and published a new version 0.2.0a3 to re-review. I have also added some comments on each issue.
Next to some minor revisions I have enabled conda installation as suggested by @kbevers. Unfortunately this took much more time than expected. Currently win-64 and linux-64 packages are provided. The installation instructions have been adapted accordingly. In addition a CONTRIBUTING.md file has been added.

[kbevers]

The changes looks good to me and I have ticked some more boxes above. I most likely won't have time to do a proper test of the code within the next week or two. It does seem to be significantly easier to get started now, good job on that!

[lheagy]

👋 Hi @scivision: would you have time to take another look through the software? Thanks!

[lheagy]

👋 Hi @scivision: Would you be willing to take a look through the software? If so, when do you think you will have time to do the review? Thank you!

[lheagy]

👋 Hi @kbevers, would you have time in the next week or so to jump back in and take a look at the unchecked functionality boxes?

[kbevers]

Holidays are coming up, but I will see if I can find the time for it. Thanks for the reminder!

[lheagy]

Many thanks @kbevers!

[kbevers]

I have now succesfully installed the software, ran the test-suite and confirmed that the package indeed does what it says on the tin. A minor issue in the test suite was found and reporting in laempy/pyoints#7. This is not a blocker for publication but would be nice see fixed in a future release.

As I am working no an unsupported platform (OS X) I did have some trouble installing the package but in the end I managed to make it work. I have not tested on a supported platform but I have no reason to believe it doesn't work there.

[laempy]

Thanks a lot @kbevers. I have fixed issue laempy/pyoints#7. Since this was just a minor issue, I will push a new version after the review of @scivision.

[lheagy]

@laempy: I have not heard anything from @scivision, so I will jump in and complete his review later this week

[lheagy]

Hi @laempy: overall, this is looking good! I just have a few comments with respect to the installation and including easy pointers to an example (preferably with a plot) in the README and / or documentation. I have outlined these in issues 8, 9, and 10. Please ping when you have addressed these and I can take another look.

[laempy]

@lheagy thank you very much for these suggestions. I will take a look at the details as soon as possible. Regarding the installation issue: In the README is a typo. conda install -c laempy pyoints should work.

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #990 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 17 0 17 0 0 168 0 --:--:-- --:--:-- --:--:-- 170
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
sh: 0: getcwd() failed: No such file or directory
pandoc: 10.21105.joss.00990.pdf: openBinaryFile: does not exist (No such file or directory)
Looks like we failed to compile the PDF

[whedon]

OK DOIs

- 10.5281/zenodo.2557574 is OK
- 10.1109/ICRA.2011.5980567 is OK
- 10.3390/rs9050505 is OK
- 10.3390/rs70809975 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #990 with the following error:

Can't find any papers to compile :-(

[danielskatz]

👋 @arfon - something's wrong here - can you help?

[whedon]

OK DOIs

- 10.5281/zenodo.2557574 is OK
- 10.1109/ICRA.2011.5980567 is OK
- 10.3390/rs9050505 is OK
- 10.3390/rs70809975 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

👋 @arfon - ping - help needed...

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.5281/zenodo.2557574 is OK
- 10.1109/ICRA.2011.5980567 is OK
- 10.3390/rs9050505 is OK
- 10.3390/rs70809975 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#601

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#601, 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]

🚨🚨🚨 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.00990 joss-papers#602
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00990
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...

[danielskatz]

@laempy sorry for the delays - Our bot @whedon was acting up, but seems to be ok again...

[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.00990/status.svg)](https://doi.org/10.21105/joss.00990)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00990">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00990/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00990/status.svg
   :target: https://doi.org/10.21105/joss.00990

This is how it will look in your documentation:

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[laempy]

Great! Thanks a lot!