Install¶

Local installation¶

Make sure to run flyvis in your active python environment.

Option 1: Install from PyPI¶

pip install flyvis

flyvis is tested on Linux for python 3.9, 3.10, 3.11, 3.12.

Option 2: Install from source¶

Clone the repository: git clone https://github.com/TuragaLab/flyvis.git
Navigate to the repo: cd flyvis
Install in developer mode: pip install -e .

For development, documentation, or to run examples, you can install additional dependencies: - pip install -e ".[dev,examples,docs]"

Download pretrained models¶

After installation, download the pretrained models by running:

flyvis download-pretrained

Set environment variables¶

flyvis uses environment variables for configuration. These can be set using a .env file or manually.

Option 1: Using .env file¶

Create a .env file in one of these locations (in order of precedence):

Your current working directory (where you run your scripts)
The root directory of your project
Any parent directory of your working directory

Example .env file contents:

# Set your preferred data directory (default: './data' relative to package directory)
FLYVIS_ROOT_DIR='path/to/your/data'

Option 2: Setting environment variables manually¶

You can also set the environment variables directly in your shell:

export FLYVIS_ROOT_DIR='path/to/your/data'

Note: The data directory is where flyvis will store downloaded models, cached data, and other files. If FLYVIS_ROOT_DIR is not set, it defaults to a data folder in the package directory.

Training new models¶

For training new models with custom settings, the following command will create a default config in your current working directory to be able to create overrides.

flyvis init-config

See the config hydra config docs for more details.