Installation#
This pipeline requires Python 3.9+, and numpy <= 1.3.5 to comply with numba restrictions.
It is recommended to install using mambaforge this will drastically speed up environment creation:
Installing from source#
Linux and MacOS:
git clone https://github.com/FlynnOConnell/spk2py.git
cd path/to/spk2py
# This is for MambaForge, but you can use conda if you want
# Note if you use conda, but want to go the mamba route, you will really want to uninstall miniconda/anaconda first
wget -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge.sh -b -p "${HOME}/conda"
# !!!! FOR BASH USERS !!!!
# If you dont know what these are, then use this one
# If you use zsh, just change this to ~/.zshrc
echo ". ${HOME}/conda/etc/profile.d/conda.sh" >> ~/.bashrc
source "${HOME}/conda/etc/profile.d/conda.sh"
mamba env create -f environment.yml # this will take a while
conda activate spk2py
pip install -r requirements.txt
pip install -e .
Additionally, though not recommended, spk2py can be installed directly from pip:
Warning
pip installing has not been tested on systems other than linux.
Using mamba has been tested on each platform.
As has docker.
pip install spk2py
Mamba Installation#
We recommend that you start with the Mambaforge distribution.
Mambaforge comes with the popular conda-forge channel preconfigured, but you can modify the configuration to use any channel you like.
Note that Anaconda channels are generally incompatible with conda-forge, so you should not mix them.
Note
For both mamba and conda, the base environment is meant to hold their dependencies.
It is strongly discouraged to install anything else in the base envionment.
Doing so may break mamba and conda installation.
Existing conda install (not recommended)#
Warning
This way of installing Mamba is not recommended. We strongly recommend to use the Mambaforge method (see above).
To get mamba, just install it into the base environment from the conda-forge channel:
# NOT RECOMMENDED: This method of installation is not recommended, prefer Mambaforge instead (see above)
# conda install -n base --override-channels -c conda-forge mamba 'python_abi=*=*cp*'
Warning
Installing mamba into any other environment than base is not supported.
Docker images#
In addition to the Mambaforge standalone distribution (see above), there are also the condaforge/mambaforge docker images:
docker run -it --rm condaforge/mambaforge:latest mamba info