Environment Setup

This guide provides step-by-step instructions for creating a consistent and reproducible development environment for the glmpynet project. The environment is managed using Conda.

Prerequisites

Before you begin, ensure you have a Conda installation available on your system. We recommend installing either the full Anaconda Distribution (if you want a comprehensive scientific Python environment) or the lightweight Miniconda (if you prefer a minimal installation).

You can find installers and instructions on the official Conda website.

Step 1: Create the Conda Environment

The project includes an environment.yml file that specifies all the necessary dependencies, including the C++ toolchain, Bazel, and Python packages.

Navigate to the root directory of the glmpynet project in your terminal.
Run the following command to create the environment from the file. This will download and install all required packages into an isolated environment named glmnetpp.
```
conda env create -f environment.yml
```
This step may take several minutes, as Conda needs to resolve and download a number of large packages.

Note

What about Mamba?

You may see mamba used in some project documentation. Mamba is a fast, parallel re-implementation of the Conda package manager. It uses the same commands and environment files but can be significantly faster at resolving dependencies.

If you have Mamba installed, you can use it as a drop-in replacement for the command above for a much faster setup:

mamba env create -f environment.yml

However, Mamba is not required. Standard conda will always work.

Step 2: Activate the Environment

Once the environment is created, you must activate it before you can begin development.

conda activate glmnetpp

Your terminal prompt should now be prefixed with (glmnetpp), indicating that you are inside the correct environment.

Step 3: Verify the Installation

To ensure all core tools were installed correctly, you can run the following commands and check their output.

# Check the Bazel version
bazel --version

# Check the C++ compiler version (on Linux)
gcc --version
clang --version

With the environment activated, you are now ready to proceed with the project’s development plan.