neonutilities submission

[cklunch]

Submitting Author: Claire Lunch (@cklunch)
All current maintainers: (@cklunch, @bhass-neon, @znickerson8)
Package Name: neonutilities
One-Line Description of Package: neonutilities is a package for accessing and wrangling data generated and published by the National Ecological Observatory Network.
Repository Link: https://github.com/NEONScience/NEON-utilities-python
Version submitted: v1.0.1
EiC: @cmarmo
Editor: @JuliMillan
Reviewer 1: @ethanwhite
Reviewer 2: @benjamindonnachie
Archive: TBD
JOSS DOI: TBD
Version accepted: v1.1.0
Date accepted (month/day/year): 05/ 10/2025

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Description

The neonutilities Python package provides utilities for discovering, downloading, and working with data files published by the National Ecological Observatory Network (NEON). NEON data files can be downloaded from the NEON Data Portal or API. The neonutilities package includes wrapper functions for the API and functions to reformat and stack NEON tabular data for analysis. This is a Python-native adaptation of the heavily used neonUtilities R package.

Scope

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  • Data retrieval
  • Data extraction
  • Data processing/munging
  • Data deposition
  • Data validation and testing
  • Data visualization¹
  • Workflow automation
  • Citation management and bibliometrics
  • Scientific software wrappers
  • Database interoperability

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• Geospatial
• Education

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  • Who is the target audience and what are scientific applications of this package?

The target audience is scientists doing research using NEON data. The package enables programmatic workflows for data downloading, and provides a standardized way to merge the product-site-month data files NEON publishes, making them analysis-ready.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

There is an incomplete package on PyPi here that was started in 2020 by a student at a coding camp. It doesn't appear to have been finished, and is not maintained. Some NEON users have developed their own code to do some of the functionality covered by neonutilities, but as far as I know none of them have shared it broadly.

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• includes documentation with examples for all functions.
• contains a tutorial with examples of its essential functions and uses.
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[cmarmo]

Editor in Chief checks

Hi @cklunch! Thank you for submitting your package for pyOpenSci review.
Below are the basic checks that your package needs to pass to begin our review.
If some of these are missing, we will ask you to work on them before the review process begins.

Please check our Python packaging guide for more information on the elements below.

• Installation The package can be installed from a community repository such as PyPI (preferred), and/or a community channel on conda (e.g. conda-forge, bioconda).
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  • User-facing documentation that overviews how to install and start using the package.
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Editor comments

Here my comments to clarify why I haven't ticked all the check-boxes.

• Documentation: I've found a lot of relevant information in the https://www.neonscience.org/ page, however there is no standalone documentation for the package, even if a docs directory is present in the repo with an empty index.md. I strongly recommend to add some documentation pages in order to structure the access to the information. There is no need to rewrite what is already on https://www.neonscience.org/, just linking and structuring, following for example the structure suggested in the pre-review checks. Also, it is not clear to me what is part of the Neon Data API and what is part of the python implementation.
• The README does not contain the documentation about how to contribute: it is true that the CONTRIBUTING file specifies that external contributions will not be considered for now. Perhaps a link to the CONTRIBUTING would be enough.
• As opening issues is the only way to contribute for now, it would be nice to have issue templates for different kind of contributions (bug reports, new feature suggestions, documentation,...)

I think the fluidity of the review process will benefit from those improvements.

Thank you so much for your understanding!

[lwasser]

hey there @cklunch @bhass-neon @znickerson8 👋🏻 it's nice to see you here on GitHub! I have a question for you about your contributing doc which says:

The neonutilities package is currently not accepting external contributions. If you have a suggestion for a fix or enhancement to the package, please create an Issue in this repository, or contact us using the NEON Contact Us page.

We do consider opening issues to report bugs and to request useful features to be contributions. They are a different type than a PR of course. What is the intent of "we are not accepting contributions" is in this case? We are having some discussions around our pyOpenSci policies, maintainer responsiveness to users and open source processes in general related to this package. Any input from you would be super helpful! thank you!!

[cklunch]

@cmarmo @lwasser Thanks for the feedback!

For documentation, the intent was for the tutorials that are linked in the readme to provide the documentation users need to understand how to use the package. The Download and Explore tutorial provides instructions in the most commonly used functions, and some context and common follow-up data wrangling, and the neonUtilities tutorial provides a function index. If this isn't what you're looking for, or if different content is needed, do you have an example of documentation that would be appropriate?

For contributing, of course bug reports and requests are always welcome! We've found with the R package that it isn't realistic for external folks to contribute code directly. The package is so specific to the NEON publication system, it's hard for people who aren't deeply familiar with that system to write generic code for it. It's almost always easier for us to incorporate requested changes ourselves than to work with external PRs. But if there's a better way to express that in the documentation, I'm very happy to.

I'll get issue templates set up in the repo, and wait to update documentation based on what we decide in this discussion. Thanks!

[lwasser]

hey there @cklunch

Have a look at our packaging guide here. Typically, python packages have a documentation "website". You might also have a look at some of the structures for other packages in our ecosystem.

tutorials are great, but it's also important to document the code base for easier future maintenance, help people get started with installing the package, etc. Please have a look at those resources and let us know if you have any questions!

[cmarmo]

For documentation, the intent was for the tutorials that are linked in the readme to provide the documentation users need to understand how to use the package. The Download and Explore tutorial provides instructions in the most commonly used functions, and some context and common follow-up data wrangling, and the neonUtilities tutorial provides a function index. If this isn't what you're looking for, or if different content is needed, do you have an example of documentation that would be appropriate?

Indeed, that's why I said that a lot of information is already there. The way it is structured though is not easy to browse for someone new to the neon ecosystem.
It would be easier also for the review, to have a reference documentation page (like your index.md), rendered by github pages or similar, with a table of contents and the essential information: Getting started, tutorials, API, and then the links to the related pages already available in the neon website.
Does that sound reasonable?

[cklunch]

@lwasser @cmarmo Thanks for the clarification. I'll see about creating a dedicated page.

[cklunch]

@lwasser @cmarmo Changes to neonutilities have been pushed, including creating issue templates, clarifying in the CONTRIBUTING file, and creating a ReadTheDocs page. Thank you for your guidance!

https://github.com/NEONScience/NEON-utilities-python

[cmarmo]

Thank you for your work @cklunch !
I have checked the related items in my initial comment.... just a nitpick ... at the end of the get started page the link to the tutorials is not linked....

I'm going to start looking for an editor.

[cklunch]

Thanks @cmarmo ! I've added a link to the Tutorials reference you pointed out.

[lwasser]

hey @cklunch my apologies for the delay! i am putting out a call for editors today on social (bluesky, fosstodon and linked in). we will need to onboard someone new. Please bare with us. The state of the world is hitting us all I think so things are moving more slowly now. I hope you and everyone at NEON are doing well.

[cklunch]

@lwasser No problem, thanks for the update!

[JuliMillan]

Hi @cklunch !
I wanted to let you know that I'll be serving as editor for NEONutilities.
We are currently looking for reviewers and will let you know as soon as that is settled.
Thank you for your patience.

[JuliMillan]

Editor response to review:

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Editor comments

👋 Hi @ethanwhite and @benjamindonnachie! Thank you for volunteering to review for pyOpenSci! It's great to have you both here.

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Reviewers: @ethanwhite, @benjamindonnachie
Due date: April 4 2025

[ethanwhite]

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

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• Examples for all user-facing functions.
• Community guidelines including contribution guidelines in the README or CONTRIBUTING.
• Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

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The package meets the readme requirements below:

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Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 5

---

Review Comments

The package is valuable, well-documented, and easy to use and I commend the maintainers for further improvements to this package since I gave them a friendly review of it a while back.
Having this functionality available in Python is a major contribution to the field.

There are a few checkboxes that still need to be addressed (plus a couple of things for the maintainers to optionally consider):

• None of the recommended badges are present in the README.md file.
• README lacks citation information
• The CONTRIBUTING.md file indicates that the package isn't taking external PRs and to open an issue if you want something. I can see why NEON might need to manage expectations/contributions, but I wonder if a more welcoming version might be something like "If you are interested in contributing changes to the codebase, please open an issue for discussion prior to submitting a pull request." This would let the maintainers moderate contributions without closing the door as firmly.
• There is currently no docs url in the pyproject.toml file. I've opened a PR that addresses this along with some other minor docs issues.
• In the portion of the 'Download and Explore NEON Data' tutorial that involves manually downloading data, I would personally find it more straightforward if the code assumed the zip file had been downloaded to the working directory, but this is likely a matter of personal preference and so just something for the maintainers to consider.
• In the 'Explore isotope data by species' section of the 'Download and Explore NEON Data' tutorial, the plt.show() command is missing to display the plot.
• The flake8 checks included in the CI show lots of minor cleanup most of which could be automatically cleaned up with flake8

I have submitted a PR that makes a handful of small fixes to documentation and metadata aspects of the package:
NEONScience/NEON-utilities-python#16

[benjamindonnachie]

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README.
• Installation instructions: for the development version of the package and any non-standard dependencies in README.
• Vignette(s) demonstrating major functionality that runs successfully locally.
• Function Documentation: for all user-facing functions.
• Examples for all user-facing functions.
• Community guidelines including contribution guidelines in the README or CONTRIBUTING.
• Metadata including author(s), author e-mail(s), a url, and any other relevant metadata e.g., in a pyproject.toml file or elsewhere.

Readme file requirements
The package meets the readme requirements below:

• Package has a README.md file in the root directory.

The README should include, from top to bottom:

• The package name
• Badges for:
  • Continuous integration and test coverage,
  • Docs building (if you have a documentation website),
  • A repostatus.org badge,
  • Python versions supported,
  • Current package version (on PyPI / Conda).

NOTE: If the README has many more badges, you might want to consider using a table for badges: see this example. Such a table should be more wide than high. (Note that the a badge for pyOpenSci peer-review will be provided upon acceptance.)

• Short description of package goals.
• Package installation instructions
• Any additional setup required to use the package (authentication tokens, etc.)
• Descriptive links to all vignettes. If the package is small, there may only be a need for one vignette which could be placed in the README.md file.
  • Brief demonstration of package usage (as it makes sense - links to vignettes could also suffice here if package description is clear)
• Link to your documentation website.
• If applicable, how the package compares to other similar packages and/or how it relates to other packages in the scientific ecosystem.
• Citation information

Usability

Reviewers are encouraged to submit suggestions (or pull requests) that will improve the usability of the package as a whole.
Package structure should follow general community best-practices. In general please consider whether:

• Package documentation is clear and easy to find and use.
• The need for the package is clear
• All functions have documentation and associated examples for use
• The package is easy to install

Functionality

• Installation: Installation succeeds as documented.
• Functionality: Any functional claims of the software been confirmed.
• Performance: Any performance claims of the software been confirmed.
• Automated tests:
  • All tests pass on the reviewer's local machine for the package version submitted by the author. Ideally this should be a tagged version making it easy for reviewers to install.
  • Tests cover essential functions of the package and a reasonable range of inputs and conditions.
• Continuous Integration: Has continuous integration setup (We suggest using Github actions but any CI platform is acceptable for review)
• Packaging guidelines: The package conforms to the pyOpenSci packaging guidelines.
  A few notable highlights to look at:
  • Package supports modern versions of Python and not End of life versions.
  • Code format is standard throughout package and follows PEP 8 guidelines (CI tests for linting pass)

Final approval (post-review)

• The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: Seven.

---

Review Comments

I concur with @ethanwhite's comments above. Overall, I'm impressed by the level of comments in the code and found it easy to follow.

• There's lots of great input validation before sending to the API. However, if the API ever changes, I wonder if this might be difficult to maintain. I appreciate you may wish to minimise calls to the service, but it might be less of a maintenance overhead to return errors from the API instead.

• Console output has the potential to be confusing if included as part of a bigger program - for example, rather than "Finding available files", "Stacking data files", "Downloading files" etc., whether a message slightly more descriptive, such as "Finding available NEON files" (or similar) might be more informative for users?

• I submitted a PR for a minor typo in the example file together with a suggestion for a potentially more maintainable version of convert_byte_size: Typo in nu_example.py NEONScience/NEON-utilities-python#13 and Potential revision to optimise convert_byte_size NEONScience/NEON-utilities-python#14

• requirements.txt does not list any version numbers - could be an opportunity to specify minimum versions of major libraries - requirements.txt does not include version numbers NEONScience/NEON-utilities-python#15

• Contributing.md states not accepting external pull requests and instead create an issue. As a result, not entirely clear on what basis contributions are accepted.

• I'd be interested to learn more about the CSV files under resources - is the content static? If not, is there an opportunity to retrieve the latest version using the API instead?

• test_aop_download.py under tests references https://github.com/NEONScience/nu-python-testing, but this returns a 404 error.

• validate_year in aop_download.py uses a regex to ensure that it is within the range 2010 - 2099. However, I think that data is only available from January 2012 onwards? It may be better to revise this function or, alternatively, allow the API to complete the validation.

The above are minor recommendations. The documentation is comprehensive and it's been a joy to review your code.

[cklunch]

@ethanwhite @benjamindonnachie Thank you both so much for your reviews! We will work on incorporating your suggestions.

[JuliMillan]

Hi @cklunch !
Just checking in to see how the revisions are going and if you any timeline in mind.

[cklunch]

@JuliMillan Yes, we are almost done with revisions! We've had some unexpected demands on our time that took us away from this project, but we should be able to respond in the next week or so. Thanks for your patience!

[cklunch]

@benjamindonnachie @ethanwhite Thank you for your very helpful reviews, and thanks for your patience for our response. We've merged in the PRs you submitted, and made a number of updates to the package and documentation:

Comments from @ethanwhite

None of the recommended badges are present in the README.md file.

Badges added.

README lacks citation information

We added a CITATION.cff file, and linked to it and to the general NEON citation guidance page from the readme.

The CONTRIBUTING.md file indicates that the package isn't taking external PRs and to open an issue if you want something. I can see why NEON might need to manage expectations/contributions, but I wonder if a more welcoming version might be something like "If you are interested in contributing changes to the codebase, please open an issue for discussion prior to submitting a pull request." This would let the maintainers moderate contributions without closing the door as firmly.

Thanks, we've updated the CONTRIBUTING file using your suggested language.

In the portion of the 'Download and Explore NEON Data' tutorial that involves manually downloading data, I would personally find it more straightforward if the code assumed the zip file had been downloaded to the working directory, but this is likely a matter of personal preference and so just something for the maintainers to consider.

This is a good point, NEON tutorials are currently a bit inconsistent about downloading to the working directory vs elsewhere, and I agree the working directory is simpler. I'm anticipating a broad update to tutorials in the fall, I'll see if we can standardize this at that point.

In the 'Explore isotope data by species' section of the 'Download and Explore NEON Data' tutorial, the plt.show() command is missing to display the plot.

Fixed!

The flake8 checks included in the CI show lots of minor cleanup most of which could be automatically cleaned up with flake8

Done, minor issues resolved.

Comments from @benjamindonnachie

There's lots of great input validation before sending to the API. However, if the API ever changes, I wonder if this might be difficult to maintain. I appreciate you may wish to minimise calls to the service, but it might be less of a maintenance overhead to return errors from the API instead.

Interesting point. The NEON API has been very stable, so this hasn't been an issue with the R version of this package, but definitely something we'll keep in mind as we make updates.

Console output has the potential to be confusing if included as part of a bigger program - for example, rather than "Finding available files", "Stacking data files", "Downloading files" etc., whether a message slightly more descriptive, such as "Finding available NEON files" (or similar) might be more informative for users?

We've added to these messages, specifying "NEON" in many places and the specific data product ID where relevant.

requirements.txt does not list any version numbers - could be an opportunity to specify minimum versions of major libraries - NEONScience/NEON-utilities-python#15

Added version numbers to requirements.txt

Contributing.md states not accepting external pull requests and instead create an issue. As a result, not entirely clear on what basis contributions are accepted.

Text is updated using the language Ethan recommended.

I'd be interested to learn more about the CSV files under resources - is the content static? If not, is there an opportunity to retrieve the latest version using the API instead?

We removed one file that wasn't used. The others are unfortunately not available via the API - we would prefer to get them there if we could! But, they are very rarely updated.

test_aop_download.py under tests references https://github.com/NEONScience/nu-python-testing, but this returns a 404 error.

Fixed, removed pointer to internal repo.

validate_year in aop_download.py uses a regex to ensure that it is within the range 2010 - 2099. However, I think that data is only available from January 2012 onwards? It may be better to revise this function or, alternatively, allow the API to complete the validation.

Regex updated.

[ethanwhite]

Thanks @cklunch! The changes all look great! I have now completed my checklist and recommend approving this incredibly valuable!) package!

[benjamindonnachie]

I concur, amendments look good! Since the API has remained stable, validation in the application shouldn't be an issue for now, but certainly if there are changes, it is worth considering moving validation to the api - although I accept there may be a desire to trade off maintainability with reduced traffic.

Approved - I will update my checklist now. Thanks again for submitting this package for review!

[JuliMillan]

---

🎉 Neonutilities has been approved by pyOpenSci! Thank you @cklunch for submitting neonutilities and many thanks to @ethanwhite and @benjamindonnachie for reviewing this package! 😸

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• Change the status tag of the issue to 6/pyOS-approved6 🚀🚀🚀.
• Invite the package maintainer(s) and both reviewers to slack if they wish to join.
• If the author submits to JOSS, please continue to update the labels for JOSS on this issue until the author is accepted (do not remove the 6/pyOS-approved label). Once accepted add the label 9/joss-approved to the issue. Skip this check if the package is not submitted to JOSS.
• If the package is JOSS-accepted please add the JOSS doi to the YAML at the top of the issue.

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If you have any feedback for us about the review process please feel free to share it here. We are always looking to improve our process and documentation in the peer-review-guide.

[cklunch]

@ethanwhite @benjamindonnachie Thank you so much!

@JuliMillan I can't check the boxes in your comment, but I've activated the Zenodo watching and DOI, and added the DOI and pyOpenSci badges to the repo. I filled out the survey. Let me know if there are any other actions needed!

[JuliMillan]

@cklunch Fantastic! Thank you so much, I'll close the issue and get in contact later about the rest.