Installation#
Python Environment Management#
Before installing ArcFISH, it’s highly recommended to create an isolated Python environment. This prevents conflicts between different packages and ensures reproducible installations. You can use either conda or venv for this purpose:
Conda#
Conda is a popular package and environment manager that comes with Anaconda or Miniconda. It can manage packages from multiple languages (not just Python) and handles complex dependencies efficiently.
Installation:
Python venv#
venv is Python’s built-in virtual environment tool. It’s lightweight and comes standard with Python 3.3+, requiring no additional installation.
Features:
Creates isolated Python environments using only pip for package management
Smaller footprint and faster environment creation
Uses the same Python version as your system installation
Create an environment and install ArcFISH#
Choose one of the following methods to create a new Python environment and install ArcFISH:
conda create --name arcfish_env python==3.12.2
conda activate arcfish_env
python -m pip install arcfish
python -m venv arcfish_env
source .arcfish_env/bin/activate
python -m pip install arcfish
Local installation for development#
To install the latest version on github and the dependencies to build the sphinx documentation:
conda create --name arcfish_env python==3.12.2
conda activate arcfish_env
git clone https://github.com/hyuyu104/arcfish
cd arcfish
python -m pip install -e ".[docs]"
python -m venv arcfish_env
source .arcfish_env/bin/activate
git clone https://github.com/hyuyu104/arcfish
cd arcfish
python -m pip install -e ".[docs]"
This will create an editable install, meaning that all modifications made on the source code will be reflected immediately without requiring re-installing the package. To compile the sphinx documentation, cd docs and then run make clean && make html.