SainsburyWellcomeCentre / aeon_mecha

Project Aeon's main library for interfacing with acquired data. Contains modules for raw data file io, data querying, data processing, data qc, database ingestion, and building computational data pipelines.

aeon_mecha

Project Aeon's main repository for manipulating acquired data. Includes preprocessing, querying, plotting, and analysis modules.

Set-up Instructions

The various set-up tools mentioned below do some combination of python version, environment, package, and package dependency management. For basic information on the differences between these tools, see this blog post.

Remote set-up on SWC's HPC

Prereqs

1. Ssh into the HPC GW1 node and clone this repo to your home directory.

ssh <your_SWC_username>@ssh.swc.ucl.ac.uk
ssh hpc-gw1
mkdir ~/ProjectAeon
cd ~/ProjectAeon
git clone https://github.com/SainsburyWellcomeCentre/aeon_mecha

Set-up

Ensure you stay in the ~/ProjectAeon/aeon_mecha directory for the rest of the set-up instructions, regardless of which set-up procedure you follow below.

Option 1: miniconda (python distribution) and conda (python version manager, environment manager, package manager, and package dependency manager)

Option 2: pyenv (python version manager) and poetry (python environment manager, package manager, and package dependency manager)

Option 3: pip (python package manager) and venv (python environment manager)

Local set-up

Prereqs

1. Install git. If you are not familiar with git, just confirm the default settings during installation.

2. Clone this repository: create a 'ProjectAeon' directory in your home directory, clone this repository there, and cd into the cloned directory:

mkdir ~/ProjectAeon
cd ~/ProjectAeon
https://github.com/SainsburyWellcomeCentre/aeon_mecha
cd aeon_mecha

Set-up

Ensure you stay in the ~/ProjectAeon/aeon_mecha directory for the rest of the set-up instructions, regardless of which set-up procedure you follow below. All commands below should be run in a bash terminal (Windows users can use the 'mingw64' terminal that comes installed with git).

Option 1: miniconda (python distribution) and conda (python version manager, environment manager, package manager, and package dependency manager)

Option 2: pyenv (python version manager) and poetry (python environment manager, package manager, and package dependency manager)

Option 3: pip (python package manager) and venv (python environment manager)

Repository Contents

Todos

• add to repository contents