README.md

data processing tools installation instructions with Python v3.12.4 using conda or mamba

Prerequisites

Ensure that you have either conda or mamba installed on your system. Mamba is recommended for its faster installation speed. You can download the latest version of Miniconda with Python v3.12.4 for any OS here.

Instructions

Follow these steps to set up your environment (if you already have bioconda and mamba installed, skip to step 3:

0. Make sure bioconda is set up

   Make sure you hav access to the conda-forge and bioconda channels. To set this up, run the following commands in your terminal:

   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict
   

1. Install mamba

   Install mamba in your base environment if it's not already installed. To do so, run the following command in your terminal:

   conda install mamba

   After the installation is done, initialize it in your shell with:

   mamba init

2. Restart Terminal

   After initializing mamba, close your terminal and open a new terminal session to apply the changes.

   Check if git is available in your terminal by typing git --help. If not, you can install it typing mamba install git

3. Create a new environment for the Spread.gl data processing tools

   Create a new mamba environment called spreadgl and activate it

   mamba create -n spreadgl
   mamba activate spreadgl

4. Download Spread.gl

   Clone the Spreag.gl repository with git:

   git clone https://github.com/GuyBaele/SpreadGL.git

5. Install required dependencies

   Install all required dependencies in the requirements.txt file inside the SpreadGL/pyhon3.12.4 folder.

   mamba install --file requirements.txt

6. Install the Spread.gl processing tools

   Go to the SpreadGL/scripts folder and install the tools typing:

   pip install .

   You have now installed the Spread.gl tools. You can check that you have access to them by typing spread --help on the terminal!

data processing tools installation troubleshooting w/ python3.12.4 on MacOS Sonoma 14.5

1. Download & install Python v3.12.4. Download & install the latest version of Git for command-line use, or GitHub Desktop if you prefer a graphical user interface to clone our spread.gl repository (see the next step).
2. Open a terminal on your computer and run the following commands:
   git clone https://github.com/GuyBaele/SpreadGL.git to clone this repository to your local computer; or browse to the spread.gl GitHub repository, click '<> Code ▼' and select 'Open with GitHub Desktop' if you chose to use GitHub Desktop in the previous step;
   cd SpreadGL to enter the cloned 'SpreadGL' directory;
   python3.12 -m venv .venv to create a Python v3.12 virtual environment called '.venv';
   source .venv/bin/activate to activate the created virtual environment;
   cd scripts to change the working directory to the 'scripts' folder containing the relevant scripts;
   pip install --upgrade pip to update pip itself;
   pip install setuptools or pip install --upgrade setuptools to update to the latest version;
   pip install numpy==1.26.4 to install version 1.26.4 (February 5th, 2024) of NumPy;
   pip install geopandas to install GeoPandas (https://pypi.org/project/geopandas/);
   pip install pyproj to install pyproj (https://pyproj4.github.io/pyproj/stable/index.html);
   export PROJ_DIR=/usr/local to set the path to the base directory for PROJ;
   brew update to ensure Homebrew is up to date;
   brew install ant to install Ant (https://ant.apache.org/), used to build Java applications;
   brew install gdal --HEAD to install the GDAL (https://gdal.org/) headers files first;
   brew install gdal to install GDAL;
   cp requirements.txt ../scripts/. to copy the configuration file for use with python3.12.4 to the scripts directory;
   pip install . to install our command-line data processing tools.
3. You should now be able to process your own data for visualisation in spread.gl (but see the next sections).