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datreant: persistent, pythonic trees for heterogeneous data

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In many fields of science, especially those analyzing experimental or simulation data, there is often an existing ecosystem of specialized tools and file formats which new tools must work around, for better or worse. Furthermore, centralized database solutions may be suboptimal for data storage for a number of reasons, including insufficient hardware infrastructure, variety and heterogeneity of raw data, the need for data portability, etc. This is particularly the case for fields centered around simulation: simulation systems can vary widely in size, composition, rules, paramaters, and starting conditions. And with increases in computational power, it is often necessary to store intermediate results obtained from large amounts of simulation data so it can be accessed and explored interactively.

These problems make data management difficult, and serve as a barrier to answering scientific questions. To make things easier, datreant is a Python package that addresses the tedious and time-consuming logistics of intermediate data storage and retrieval. It solves a boring problem, so we can focus on interesting ones.

For more information on what datreant is and what it does, check out the official documentation.

Getting datreant

See the installation instructions for installation details. The package itself is pure Python.

If you want to work on the code, either for yourself or to contribute back to the project, clone the repository to your local machine with:

git clone https://github.com/datreant/datreant.git

Contributing

This project is still under heavy development, and there are certainly rough edges and bugs. Issues and pull requests welcome!

Check out our contributor's guide to learn how to get started with contributing back.

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scipy_proceedings's Issues

"Introspecting a Treant's Tree" example could use more character

At the moment I've included a brief example of how the filesystem manipulation machinery built into Treants can be used with other packages, such as storing a pandas DataFrame and examining the file. This uses a randomly-generated DataFrame at the moment, but we could do better with a small DataFrame that has, e.g. tree nut data or bark varieties data. Currently the randomly-generated values are too long for the page column, too.

Anyone want to hammer on this? It's pretty isolated, but can be fun.

Adding citations

We need to add citations where necessary for other Python packages. This is something I'd be happy for someone else to take on while I focus on building out content.

acknowledgements

@datreant/coredevs โ€“ please add acknowledgements to the draft (e.g. any grants that you get paid on). Double-check with your PI if necessary. It is often very important that all grant numbers are listed because this is one way in which successes of grants are measured.

(We can fix this in review but it's good to be complete from the start.)

Topics for datreant proceedings paper

Over the course of today and the rest of the weekend I'll be pulling together the proceedings paper for datreant. I have a basic skeleton together already on which I'll be nucleating the content, but is there anything in particular you think should be showcased?

Similar to MDAnalysis#2:

Note that this paper should not be an in-depth view of datreant but rather a big picture "advertisement". Primarily, it should introduce the library to a wider audience and quickly allow a reader to answer the questions

  • Is datreant applicable to my problems?
  • Should I (or one of my students) give it a try?
  • What are advantages of using datreant? What might I be able to do with it that would be difficult or impossible otherwise?

Progress on main text

I am hammering on the main text now, and this issue is meant to serve as a discussion point for it as we move forward. The manuscript is coming along, but seeing as how time is short I'm drafting it quickly.

If you have a moment, have a look at what's there, and make it know here what you do/don't like about it so that we can quickly iterate it out. Thanks!

PRs are also welcome if the spirit moves you. I am happy to be the one to handle merge conflicts, so don't worry about falling behind.

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