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korikuzma committed Nov 5, 2024
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# VRS Python Getting Started Notebook Series

This series of notebooks is intended to be the fastest way to becoming productive with the
[vrs-python](https://github.com/ga4gh/vrs-python) package. The
intent of each notebook in this series is to be an interactive introduction to functionally contained in the vrs-python package.
This series of notebooks is intended to be the fastest way to becoming productive with
the [vrs-python](https://github.com/ga4gh/vrs-python) package. The intent of each
notebook in this series is to be an interactive introduction to functionally contained
in the vrs-python package.

A beginning developer level of familiarity with python, jupyter notebooks is assumed in order to run this notebook series.
You should be familiar with installing packages and running commands in your execution environment.
A beginning developer level of familiarity with python, jupyter notebooks is assumed in
order to run this notebook series. You should be familiar with installing packages and
running commands in your execution environment.

## Prerequisites
## Development Environment Setup

We provide you two options for setting up your development environment: using a Python
[virtual environment](#virtual-environment) or leveraging
[VS Code Dev Containers](#dev-containers) (useful for non-macOS users).

### Fork the Repo

Fork the repo at <https://github.com/ga4gh/vrs-python/> and initialize a development
environment.

```shell
git clone --recurse-submodules git@github.com:YOUR_GITHUB_ID/vrs-python.git
cd vrs-python
```

### Virtual Environment

You must first install python@3.12, if not already installed.

Next, run the following:

```shell
make nbready
source venv/3.12/bin/activate
```

#### Virtual Environment: Selecting the Kernel

When opening a notebook with this option, click `Select Kernel`,
`Python Environments...`, and select the first option:
`3.12 (Python 3.12.z) venv/3.12/bin/python`

_Note: Patch version may vary._

### Dev Containers

#### Prerequisites

For your convenience, this section is copied from the
[VS Code Dev Containers Tutorial](https://code.visualstudio.com/docs/devcontainers/tutorial#_prerequisites).
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[Marketplace Link](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) (if viewing from browser)

## Creating the Dev Container
#### Creating the Dev Container

Open the VS Code Command Palette: Shift + Command + P (Mac) / Ctrl + Shift + P (Windows/Linux)

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You should see `Dev Container: VRS-Python Notebooks @ desktop-linux` on the bottom left hand corner of VS Code.

## Notebooks
#### Dev Containers: Selecting the Kernel

### Selecting the kernel
When opening a notebook with this option, click `Select Kernel`,
`Python Environments...`, and select the first option:
`Python 3.12.z /usr/local/bin/python`

When opening a notebook, click `Select Kernel` and select the first option:
`Python 3.12.7 /usr/local/bin/python`
_Note: Patch version may vary._

## Notebooks

### 1 Quick Start

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