integrate_module 0.99.3

Localized probabilistic data integration

INTEGRATE Python Module

This repository contains the INTEGRATE Python module for localized probabilistic data integration in geophysics.

Installation

Assuming you already have Python 3.10+ installed:

pip install integrate_module

On Windows, this will also install the Python wrapper for GA-AEM (1D EM forward modeling - GPL v2 code): ga-aem-forward-win

On Linux/macOS, you will need to install GA-AEM manually.

Using uv (recommended, from PyPI)

uv is a fast Python package manager. Install it first if needed:

# Install uv (Linux/macOS)
curl -LsSf https://astral.sh/uv/install.sh | sh
# or: pip install uv

# Create virtual environment in .venv/ inside the module root
cd path/to/integrate_module
uv venv .venv --python 3.11

# Activate
source .venv/bin/activate      # Linux/macOS
.venv\Scripts\activate         # Windows

# Install integrate module
uv pip install integrate_module

Using uv (from source)

# Install uv (Linux/macOS)
curl -LsSf https://astral.sh/uv/install.sh | sh
# or: pip install uv

# Create .venv and install all dependencies in one step (recommended for development)
cd path/to/integrate_module
uv sync

# Activate
source .venv/bin/activate      # Linux/macOS
.venv\Scripts\activate         # Windows

Using pip + venv (from PyPI, on Ubuntu)

# Install python3-venv
sudo apt install python3-venv

# Create virtual environment in .venv/ inside the module root
cd path/to/integrate_module
python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip

# Install integrate module
pip install integrate_module

Using pip + venv (from source, on Ubuntu)

# Install python3-venv
sudo apt install python3-venv

# Create virtual environment in .venv/ inside the module root
cd path/to/integrate_module
python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip

# Install integrate module from source
pip install -e .

Installing documentation dependencies

To also install the packages needed to build the Sphinx documentation, use the docs extra:

# With uv (from source)
uv sync --extra docs

# With uv pip (from source)
uv pip install -e ".[docs]"

# With pip (from source)
pip install -e ".[docs]"

Using Conda + pip (from PyPI)

Create a Conda environment (called integrate) and install the required modules:

conda create --name integrate python=3.10 numpy pandas matplotlib scipy tqdm requests h5py psutil
conda activate integrate
pip install integrate_module

Using Conda + pip (from source)

Create a Conda environment (called integrate) and install the required modules:

conda create --name integrate python=3.10 numpy pandas matplotlib scipy tqdm requests h5py psutil
conda activate integrate
pip install -e .

GA-AEM

In order to use GA-AEM for forward EM modeling, the 'gatdaem1d' Python module must be installed. Follow instructions at https://github.com/GeoscienceAustralia/ga-aem or use the information below.

PyPI package for Windows

On Windows, the ga-aem-forward-win package will be automatically installed, providing access to the GA-AEM forward code. It can be installed manually using:

pip install ga-aem-forward-win

Pre-compiled Python module for Windows

1. Download the pre-compiled version of GA-AEM for Windows from the latest release: https://github.com/GeoscienceAustralia/ga-aem/releases (GA-AEM.zip)

2. Download precompiled FFTW3 Windows DLLs from https://www.fftw.org/install/windows.html (fftw-3.3.5-dll64.zip)

3. Extract both archives:

   • unzip GA-AEM.zip to get GA-AEM
   • unzip fftw-3.3.5-dll64.zip to get fftw-3.3.5-dll64

4. Copy FFTW3 DLLs to GA-AEM Python directory:

   cp fftw-3.3.5-dll64/*.dll GA-AEM/python/gatdaem1d/

5. Install the Python gatdaem1d module:

cd GA-AEM/python/
pip install -e .

# Test the installation
cd examples
python integrate_skytem.py

Compile GA-AEM Python module on Debian/Ubuntu/Linux

A script that downloads and installs GA-AEM is located in scripts/cmake_build_script_DebianUbuntu_gatdaem1d.sh. This script has been tested and confirmed to work on both Debian and Ubuntu distributions. Be sure to use the appropriate Python environment and then run:

sh scripts/cmake_build_script_DebianUbuntu_gatdaem1d.sh
cd ga-aem/install-ubuntu/python
pip install .

Compile GA-AEM Python module on macOS/Homebrew

First install Homebrew, then run:

sh ./scripts/cmake_build_script_homebrew_gatdaem1d.sh
cd ga-aem/install-homebrew/python
pip install .

Development

The main branch is the most stable, with less frequent updates but larger changes.

The develop branch contains the current development code and may be updated frequently. Some functions and examples may be broken.

An extra set of tests and examples are located in the experimental sub-branch https://github.com/cultpenguin/integrate_module_experimental/ <https://github.com/cultpenguin/integrate_module_experimental/>_. Please ask the developers for access to this branch if needed. To clone the main repository with the experimental branch, use:

git clone --recurse-submodules [e-mail]:AUProbGeo/integrate_module.git

You may need to run the following command to update the submodules:

cd experimental
git submodule update --init --recursive