https://github.com/hdfgroup/hdf5-tutorial
A tutorial for new and intermediate HDF5 users (of all ages)
https://github.com/hdfgroup/hdf5-tutorial
Last synced: 10 months ago
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A tutorial for new and intermediate HDF5 users (of all ages)
- Host: GitHub
- URL: https://github.com/hdfgroup/hdf5-tutorial
- Owner: HDFGroup
- Created: 2023-07-07T18:09:41.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-07-30T23:43:59.000Z (almost 2 years ago)
- Last Synced: 2024-07-31T03:02:48.309Z (almost 2 years ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 3.53 MB
- Stars: 12
- Watchers: 6
- Forks: 6
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
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README
# Welcome to the HDF5 Tutorial
[](https://codespaces.new/HDFGroup/hdf5-tutorial)
👉 Check out this __[intro on YouTube](https://www.youtube.com/watch?v=3ndbhId2vuY&t=37s)__.
*HDF5 is a framework for sharing data.* Its purpose is to frame data so that it can be shared and understood on its own because it speaks for itself; it is *self-describing*. Sharing comes in different forms, for example, via files formatted in a standard way, or by providing access to data through a service endpoints. It is important that these "appearances" cohere and are uniform. For that, the framework includes a data model that is common to all implementations, including the __[HDF5 library and file format](https://github.com/HDFGroup/hdf5)__ or the __[Highly Scalable Data Service (HSDS)](https://github.com/HDFGroup/hsds)__. What makes it all work are fantastic community contributions, such as __[`h5py`](https://www.h5py.org/)__, __[HDFql](https://www.hdfql.com/)__, __[`rhdf5`](https://bioconductor.org/packages/release/bioc/html/rhdf5.html)__, or __[H5Web](https://h5web.panosc.eu/)__.
This is a tutorial for new and intermediate HDF5 users. The tutorial is
organized as a set of Jupyter notebooks that are available for download
in this __[GitHub repository](https://github.com/HDFGroup/hdf5-tutorial/)__. The notebooks are intended to be reviewed in the numbered order, but they are self-contained, and can be visited in any order.
The notebooks in this tutorial are:
1. __[C/C++ 101](./00-CPP-101.ipynb)__ - In case you've never written a C/C++ program
2. __[Theme](./01-Theme.ipynb)__ - A model problem that we will use throughout the tutorial
3. __[Variation 1](./02-Variation1.ipynb)__ - A slightly more complex variant of the problem
4. __[Variation 2](./03-Variation2.ipynb)__ - MPI-parallel HDF5
5. __[Python Bliss](./04-Python-Bliss.ipynb)__ - Where most HDF5 users will spend their time
6. __[HSDS](./05-HSDS.ipynb)__ - How to tackle the model problem with HDF5-as-a-Service
7. __[REST VOL](./06-LibHDF5-to-HSDS.ipynb)__ - Talking to HSDS from the HDF5 library
8. __[S3 & Cloud](./07-S3-and-the-Cloud.ipynb)__ - Reading data directly from the Cloud
9. __[PureHDF](./10-PureHDF.ipynb)__ - How to tackle the model problem in C#
10. __[HDFql](./11-HDFql.ipynb)__ - The easy way to manage HDF5 data
This tutorial is intended to be executed in a Web browser without installing any software. To this end, this repository comes with a prebuild __[GitHub Codespaces](https://github.com/features/codespaces)__ configuration. Launch a Codespaces environment by clicking the banner __["Open in GitHub Codespaces"](https://codespaces.new/HDFGroup/hdf5-tutorial)__ and start evaluating the Jupyter notebooks (by placing the cursor into a code cell and pressing `Ctrl+Enter` or `Shift+Enter`). When prompted for a Python kernel, select
```
hdf5-tutorial (Python 3.12.1) /opt/conda/envs/hdf5-tutorial/python
```
You are welcome to clone this repository and set up your local environment. *Notice that a few settings are specific to the Codespaces configuration and will need adjusting in a custom environment.* We recommend you review [`environment.yml`](./environment.yml) for Python package dependencies, and the files in [`.devcontainer`](./.devcontainer) for additional dependencies.
Enjoy and let us know what you think about the tutorial in the __[discussion](https://forum.hdfgroup.org/)__! Please help us improve it by reporting __[issues](https://github.com/HDFGroup/hdf5-tutorial/issues)__ or submitting __[pull requests](https://github.com/HDFGroup/hdf5-tutorial/pulls)__!