Installation (Checked: D)

Quick installation

It is recommended to install the package inside a dedicated Python environment (for example a Conda or a Mamba environment) rather than in the base system environment.

The minimal installation can be performed using pip:

(hofavenv) $ pip install hofa

This installs the HoFa package together with its required runtime dependencies.

Requirements:

The package requires:

• Python >= 3.12

Core runtime dependencies include:

• NumPy >= 2.0

• SciPy >= 1.13

Example using Conda:

For a minimal installation with Conda, we first create a new virtual environment:

(base) $ conda create -n hofavenv python=3.14
(base) $ conda activate hofavenv

To install the core package dependencies:

(hofavenv) $ pip install numpy scipy

To install the HoFa package:

(hofavenv) $ pip install hofa

Optional: To install notebook-related dependencies:

(hofavenv) $ pip install jupyterlab matplotlib moviepy

Optional: To install documentation dependencies:

(hofavenv) $ pip install sphinx pydata-sphinx-theme sphinx-design sphinx-autoapi myst-nb

Installation from source

Clone the repository:

$ git clone https://github.com/dglez91/hofa
$ cd hofa

Install the package in editable mode (assuming we have already acitvated a virtual environment hofavenv):

(hofavenv) $ pip install -e .

Reproducible environment

A reproducible Conda environment is provided through the full-environment.yml file.

Create the environment with:

(base) $ conda env create -f full-environment.yml -n hofavenv

Activate the environment:

(base) $ conda activate hofavenv

The environment includes:

• Runtime dependencies,

• Jupyter notebook support, and

• documentation dependencies.

Jupyter notebooks

HoFa includes example notebooks and user guides written in Jupyter format. You can find them directly in this website using the following links:

• Tutorial - A first encounter with the HoFa package (Checked: D),

• Tutorial - Denoising (Checked: D), and

• Tutorial - Higher order characters (Checked: D)

or cloning the HoFa repository from Github as explained above. In the latter case, they are located in docs/source/tutorials.

Additional notebook-related dependencies include:

• JupyterLab

• ipykernel

If the full Conda environment is installed as explained above, notebook support is already included.

Launch JupyterLab with:

(hofavenv) $ jupyter lab

Building the documentation

The documentation is built using Sphinx together with MyST-NB.

To build the HTML documentation:

(hofavenv) $ cd docs
(hofavenv) /docs$ make html

The generated HTML pages will appear in:

docs/build/html/