troycomi / aspyre

Full Python ASPIRE package in developing to include all submodules from Matlab and other related versions.

ASPyRE

Algorithms for Single Particle Reconstruction

Installation Instructions

Linux/Mac OS X/Windows

The simplest option is to use Anaconda 64-bit for your platform, and use the provided environment.yml file to build a Conda environment to run ASPyRE.

cd /path/to/git/clone/folder
conda env create -f environment.yml
conda activate aspyre

Make sure everything works

Once ASPyRE is installed, make sure the unit tests run correctly on your platform by doing:

cd /path/to/git/clone/folder
python setup.py test

Tests currently take around 5 minutes to run. If some tests fail, you may realize that python setup.py test produces too much information. You may want to re-run tests using:

cd /path/to/git/clone/folder
PYTHONPATH=./src pytest tests

This provides a cleaner output to analyze.

Install

If the tests pass, install the ASPyRE package for the currently active Conda environment:

cd /path/to/git/clone/folder
python setup.py install

Development Guidelines

ASPyRE follows Gitflow Workflow. Please submit any PRs against the develop branch.