[REVIEW]: sandpyper: A Python package for UAV-SfM beach volumetric and behavioural analysis

[whedon]

Submitting author: @npucino (Nicolas Pucino)
Repository: https://github.com/npucino/sandpyper
Version: v1.3.3
Editor: @crvernon
Reviewer: @dbuscombe-usgs, @chrisleaman
Archive: 10.5281/zenodo.5565487

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Markdown: [![status](https://joss.theoj.org/papers/ff00f33cd9152b1834727ffb8be4122a/status.svg)](https://joss.theoj.org/papers/ff00f33cd9152b1834727ffb8be4122a)

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Review checklist for @dbuscombe-usgs

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Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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• 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?
• Contribution and authorship: Has the submitting author (@npucino) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @chrisleaman

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
• Contribution and authorship: Has the submitting author (@npucino) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dbuscombe-usgs, @chrisleaman it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1111/0031-868x.00152 is OK
- 10.1371/journal.pone.0118571 is OK
- 10.1890/10-1510.1 is OK
- 10.1038/s41598-021-83477-6 is OK
- 10.1016/j.earscirev.2017.04.011 is OK
- 10.1016/j.ecolecon.2006.10.022 is OK
- 10.1016/j.ocecoaman.2018.01.001 is OK
- 10.1016/j.isprsjprs.2015.02.009 is OK
- 10.21105/joss.01890 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Wordcount for paper.md is 1349

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.95 s (41.0 files/s, 54866.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           6           1709           1175           4856
Markdown                        17            285              0            655
Jupyter Notebook                 7              0          42186            625
TeX                              1              9              0            404
YAML                             6             25             10            191
JavaScript                       1              1              0             19
HTML                             1              2              0              9
-------------------------------------------------------------------------------
SUM:                            39           2031          43371           6759
-------------------------------------------------------------------------------


Statistical information for the repository 'a855e74a3b68ce3aa0fa37a1' was
gathered on 2021/08/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Nicolas Pucino                 187         18307          11042           94.22
npucino                         17          1078            724            5.78

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Nicolas Pucino             7760           42.4          0.4                5.66

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[crvernon]

@dbuscombe-usgs @chrisleaman @npucino 👋 the review takes place in this issue. Thanks!

[crvernon]

Also, please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://github.com/npucino/sandpyper repository. This will help everyone have a single point of reference.

[npucino]

Thank you guys for your time! Cheers

[crvernon]

📣 Mid-week rally! Just checking in to see how things are going @dbuscombe-usgs and @chrisleaman ? Don't hesitate to reach out if you have any questions.

👏 Keep up the good work!

[chrisleaman]

Thanks @crvernon, I've had a read of the paper and just summarizing my thoughts. Also planning to run the package on some of my own data to test it out 😄

[dbuscombe-usgs]

@crvernon @npucino I am having a lot of difficulty installing this package using the provided instructions. I have a detailed issue here

I have a lot of experience with conda and my perspective is that is this a suboptimal way to install a package with all of these very complicated dependencies.

[dbuscombe-usgs]

I made my own yml file installer to deal with the issues of the mixed conda/pip installation, that works a lot better and in fewer lines of code. and far fewer instructions, see here However, the __init__ script for the sandpyper pip package has broken syntax that means I get errors . So, I should now be able to run this software when @npucino gets a chance to revisit that.

Installation is typically the most difficult thing to get right with these types of python packages. I expect it will be plain sailing after that!

[npucino]

@dbuscombe-usgs thanks for the detailed issue report, I will fix this Monday. I tested the package installation and unit tested the code in github action and assumed it worked out in the real world.
Also I noticed that for some reason your pip install sandpyper downloaded a very old version 0.0.2 (with that typo in the init file), while the latest one in pip is 1.0.0 which is drastically different. I think it is becasue the pip install GDAL confilcts made pip to roll back to a previous version where the GDAL doesn't break the imports. I ll look into that!

[dbuscombe-usgs]

Great, thanks for the quick response @npucino - that sounds like a good plan. I'll check back in Monday and try to help troubleshoot. I'm pretty good at finding conda and pip issues in other people's code, so don't take it personally (I also really hate the python ecosystem for its crummy package managers!)

in the yml file I made, it does successfully create all the dependencies in conda using conda-forge. then it is looking for a version of sandpyper on pip that is compatible, That is version 0.0.2. That would explain why, I think

but it does prove that a) you can use conda entirely to set up the dependencies in a conda environment without being overly prescriptive about specific versions of packages, and that b) its all the pip-only dependencies that are breaking the install. Its not clear why, for example, why the requirements.txt in the pypi package lists the same libraries as you suggest installing into the conda environment ....

my general recommendation here is that conda environments as a rule want to install conda packages, not pip ones. It works, but only if you allow conda to take precedence for as many of the dependencies as you can, and dont cross-post dependencies between conda and pip, you'll likely have fewer install dependencies

I can also try installing on linux and report back what I find on the issues tab on the repo page

[npucino]

No no I do not take it personally @dbuscombe-usgs, please be as critic as you can I need it to grow and get better at this and improve that package! No mercy is good science. I think I will have to change the installation procedure and move it all to conda rather than pip. CHeers

[crvernon]

Thanks @dbuscombe-usgs and @npucino it looks like you are working towards a solution. Feel free to reach out if you have any questions.

[whedon]

👋 @chrisleaman, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @dbuscombe-usgs, please update us on how your review is going (this is an automated reminder).

[chrisleaman]

👋 @chrisleaman, please update us on how your review is going (this is an automated reminder).

Sorted out package installation issues, working through example notebooks at the moment.

[npucino]

@crvernon I love this Zenodo feature.

I hope I did it right but it should be fine now.

Here is the link to the Zenodo archive: https://zenodo.org/record/5565487#.YWYPHRpBwUE

DOI: 10.5281/zenodo.5565487

Thanks!

[crvernon]

@whedon set v1.3.3 as version

[whedon]

OK. v1.3.3 is the version.

[crvernon]

@whedon set 10.5281/zenodo.5565487 as archive

[whedon]

OK. 10.5281/zenodo.5565487 is the archive.

[crvernon]

🎉 @npucino thanks for putting together a really nice software product! Thanks to @dbuscombe-usgs and @chrisleaman for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1111/0031-868x.00152 is OK
- 10.1371/journal.pone.0118571 is OK
- 10.1890/10-1510.1 is OK
- 10.1038/s41598-021-83477-6 is OK
- 10.1016/j.earscirev.2017.04.011 is OK
- 10.1016/j.ecolecon.2006.10.022 is OK
- 10.1016/j.ocecoaman.2018.01.001 is OK
- 10.1016/j.isprsjprs.2015.02.009 is OK
- 10.21105/joss.01890 is OK
- 10.1038/sdata.2016.24 is OK
- 10.3390/data4020073 is OK
- 10.3390/ijgi8060267 is OK
- 10.1016/j.geomorph.2016.02.025 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2667

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2667, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[npucino]

🎉 @npucino thanks for putting together a really nice software product! Thanks to @dbuscombe-usgs and @chrisleaman for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

Thank you @crvernon for your overview and guidance and thank you @dbuscombe-usgs and @chrisleaman for helping me making this package a much better product than before!

I learned many important new things and best practices. I also set new goals to Sandpyper roadmap to make it even better in the near future.
I would recommend to go through this process to anyone involved in Open Source dev, especially at early stage coders like myself!

Thanks again everyone!
Best Regards,

Nick

[npucino]

@whedon accept deposit=true

[whedon]

I'm sorry @npucino, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[npucino]

I'm sorry @npucino, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

Ops, I thought I had to check that!
cheers

[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.03666 joss-papers#2668
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03666
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]

@dbuscombe-usgs, @chrisleaman – many thanks for your reviews here and to @crvernon for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@npucino – your paper is now accepted and published in 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:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03666/status.svg" alt="DOI badge" >
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reStructuredText:
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