From b472529bf99c258c82bf5044c035653b4608245c Mon Sep 17 00:00:00 2001 From: Alec Heckert Date: Wed, 17 Jan 2024 11:02:57 -0500 Subject: [PATCH] move install instructions to top of README --- README.md | 29 +++++++++++++++-------------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 1c232dd..1b18899 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,26 @@ Maximum likelihood and variational Bayes estimation for mixtures of regular Brownian motions +## Install from source + +Clone the repo, then +``` +cd emdiff +pip install -e . +``` + +Then make sure you can run the example: +``` +cd samples +python sample_script.py +``` + ## What does it do? `emdiff` is a Python analysis tool for trajectories generated by stroboscopic single particle tracking (SPT) experiments. -It takes a set of trajectories in CSV format, then returns the +It takes a set of trajectories as a `pandas.DataFrame`, then returns the estimated fraction of molecules in distinct states and the diffusion coefficient corresponding to each state. @@ -86,19 +100,6 @@ part of the standard [Anaconda](https://www.anaconda.com/products/individual) di [`matplotlib_scalebar`](https://pypi.org/project/matplotlib-scalebar/), the plots will have scalebars. So that's recommended too. -## Install - -1. Clone the repository: `git clone https://github.com/alecheckert/emdiff.git`. - -2. Navigate to the top-level `emdiff` directory. - -3. From a `conda` environment with the dependencies above, run `python setup.py develop`. - -`emdiff` is in active development. The `develop` option -will track changes in the source files as new versions become available. -To pull new versions, navigate to the `emdiff` repository and use -`git pull`. - ## Expected input Both `emdiff` and `vbdiff` take trajectories as a `pandas.DataFrame`. Each row of