afscgap: Ocean health tools for NOAA AFSC GAP species presence data [presubmission]

[sampottinger]

Submitting Author: Sam Pottinger (@sampottinger)
Package Name: afscgap
One-Line Description of Package: Community contributed Python-based tools for working with public bottom trawl surveys data from the NOAA Alaska Fisheries Science Center Groundfish Assessment Program (NOAA AFSC GAP).
Repository Link (if existing): https://github.com/SchmidtDSE/afscgap

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Description

Python-based tool set for interacting with bottom trawl surveys from the Ground Fish Assessment Program (GAP). This provides information about where certain species were seen and when under what conditions, information useful for research in ocean health.

It offers:

• Pythonic access to the official NOAA AFSC GAP API service.
• Memory-efficient tools for inference of the "negative" observations not provided by the API service but required for some common types of analysis.
• Visualization tools for quickly exploring and creating comparisons within the dataset that provide an "on-ramp" to deeper analysis. The visual analytics components aim to serve both expert programmers and audiences with limited programming experience.

Note that GAP is an excellent dataset produced by the Resource Assessment and Conservation Engineering (RACE) Division of the Alaska Fisheries Science Center (AFSC) as part of the National Oceanic and Atmospheric Administration's Fisheries organization (NOAA Fisheries).

Additional information at https://pyafscgap.org/.

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Scope

• Please indicate which category or categories this package falls under:

• Please indicate which category or categories.
  Check out our package scope page to learn more about our
  scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

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

• Domain Specific & Community Partnerships

  • Geospatial
  • Education
  • Pangeo
  • Unsure/Other (explain below)

• Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:

This library supports retrieval of data from the official NOAA AFSC GAP REST API service but, as that service on its own is often not sufficient due to certain data limitations, it also offers negative inference as required for a number of common types of investigations (hence data processing). Finally, given the needs of the community and the vast breadth of the dataset, it offers a community application to explore the data which, in turn, can generate Python code to help users get started with continued analysis within their own scripts.

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

This project largely benefits scientific researchers in the ocean health space as this dataset is useful for fisheries management, biodiversity research, and marine science more generally. An example of what this analysis may look like is provided in our example notebook hosted on mybinder.org.

• Are there other Python packages that accomplish similar things? If so, how does yours differ?

We are not aware of other Python packages working with the AFSC GAP dataset.

• Any other questions or issues we should be aware of:

We've found the visualization tool to be an important part of this broader toolset, useful for lowering barrier to entry, starting investigations, and inviting a broader group of folks into discourse. That said, while related and subject to automated tests, CI / CD, and doc requirements, pyopensci may choose to consider afscgapviz as a form of documentation from the perspective of the python library.

P.S. Have feedback/comments about our review process? Leave a comment here

[NickleDave]

👋 Welcome @sampottinger!

Thank you for filling out a presubmission inquiry.

afscgap is definitely in scope. Please do go ahead and make a full submission.

You've done a great job of filling out the form here (I actually thought this was a full submission already, hence the delay while I started doing checks, sorry about that 😳 ). If there are other maintainers please be sure to include them and please have everyone fill out the pre-submission survey.

Once you do so I'll close this issue, start editor checks, and proceed with finding an editor.
Thanks! afscgap looks like a really useful tool, happy to get you a review

[sampottinger]

Amazing! Thanks very much @NickleDave! I'll go ahead and fill out the full submission (hopefully this evening). Sorry I just want to confirm that the onboarding survey is https://forms.gle/F9mou7S3jhe8DMJ16?

[NickleDave]

You've got it, thank you @sampottinger

[sampottinger]

Hey @NickleDave! We completed the survey and I have a draft of the full submission ready. However, I think I misunderstood the docs regarding JOSS submissions through pyopensci. I wanted to confirm the paper.md should be on main at time of submission? Thanks!

[sampottinger]

@NickleDave - We went ahead and put it on main. I've submitted #93!

[NickleDave]

Perfect, thank you @sampottinger -- closing this