integrate-module 0.99.0__tar.gz → 0.99.2__tar.gz

{integrate_module-0.99.0/integrate_module.egg-info → integrate_module-0.99.2}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: integrate_module
-Version: 0.99.0
+Version: 0.99.2
 Summary: Localized probabilistic data integration
 Author-email: Thomas Mejer Hansen <tmeha@geo.au.dk>
 License: MIT
-Project-URL: Homepage, https://github.com/cultpenguin/integrate_module
-Project-URL: Documentation, https://cultpenguin.github.io/integrate_module/
-Project-URL: Repository, https://github.com/cultpenguin/integrate_module
-Project-URL: Issues, https://github.com/cultpenguin/integrate_module/issues
+Project-URL: Homepage, https://github.com/AUProbGeo/integrate_module
+Project-URL: Documentation, https://auprobgeo.github.io/integrate_module/
+Project-URL: Repository, https://github.com/AUProbGeo/integrate_module
+Project-URL: Issues, https://github.com/AUProbGeo/integrate_module/issues
 Keywords: inversion,electromagnetic,geophysics,geology,prior,tarantola
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
@@ -24,20 +24,32 @@ Requires-Dist: geoprior1d>=0.9
 Requires-Dist: ga-aem-forward-win; platform_system == "Windows"
 Requires-Dist: jupyter>=1.0.0
 Requires-Dist: jupytext
+Requires-Dist: ipykernel
 Requires-Dist: pandas
 Requires-Dist: pyvista
 Requires-Dist: litellm
 Requires-Dist: streamlit
+Requires-Dist: libaarhusxyz
+Requires-Dist: jax
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: black; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Requires-Dist: sphinx-gallery; extra == "docs"
+Requires-Dist: pandoc; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: tomli; python_version < "3.11" and extra == "docs"
 Dynamic: license-file
 
 # INTEGRATE Python Module
 
-[![Build Status](https://github.com/cultpenguin/integrate_module/actions/workflows/docs.yml/badge.svg?branch=main)](https://github.com/cultpenguin/integrate_module/actions/workflows/docs.yml)
+[![Build Status](https://github.com/AUProbGeo/integrate_module/actions/workflows/docs.yml/badge.svg?branch=main)](https://github.com/AUProbGeo/integrate_module/actions/workflows/docs.yml)
 [![PyPI](https://badge.fury.io/py/integrate-module.svg)](https://badge.fury.io/py/integrate-module)
-[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://cultpenguin.github.io/integrate_module/)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://auprobgeo.github.io/integrate_module/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 
@@ -48,42 +60,86 @@ This repository contains the INTEGRATE Python module for localized probabilistic
 
 Assuming you already have Python 3.10+ installed:
 
-`libaarhusxyz` must be installed manually before installing `integrate_module`, because the version that supports Python >= 3.12 is only available on GitHub (not PyPI):
-
-    pip install git+https://github.com/cultpenguin/libaarhusxyz
     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](https://pypi.org/project/ga-aem-forward-win/)
 
 On Linux/macOS, you will need to install GA-AEM manually.
 
-### Using pip (from PyPI, on Ubuntu)
+### Using uv (recommended, from PyPI)
+
+[uv](https://github.com/astral-sh/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
 
-    # Install python3 venv
+### 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
-    python3 -m venv ~/integrate
-    source ~/integrate/bin/activate
+
+    # 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 (from source, on Ubuntu)
 
-    # Install python3 venv
+### Using pip + venv (from source, on Ubuntu)
+
+    # Install python3-venv
     sudo apt install python3-venv
 
-    # Create virtual environment
-    python3 -m venv ~/integrate
-    source ~/integrate/bin/activate
+    # 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
-    cd path/to/integrate_module
+    # 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: 
@@ -165,7 +221,7 @@ The `develop` branch contains the current development code and may be updated fr
 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 git@github.com:cultpenguin/integrate_module.git
+    git clone --recurse-submodules git@github.com:AUProbGeo/integrate_module.git
 
 You may need to run the following command to update the submodules:
 

{integrate_module-0.99.0 → integrate_module-0.99.2}/README.md

@@ -1,8 +1,8 @@
 # INTEGRATE Python Module
 
-[![Build Status](https://github.com/cultpenguin/integrate_module/actions/workflows/docs.yml/badge.svg?branch=main)](https://github.com/cultpenguin/integrate_module/actions/workflows/docs.yml)
+[![Build Status](https://github.com/AUProbGeo/integrate_module/actions/workflows/docs.yml/badge.svg?branch=main)](https://github.com/AUProbGeo/integrate_module/actions/workflows/docs.yml)
 [![PyPI](https://badge.fury.io/py/integrate-module.svg)](https://badge.fury.io/py/integrate-module)
-[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://cultpenguin.github.io/integrate_module/)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://auprobgeo.github.io/integrate_module/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 
@@ -13,42 +13,86 @@ This repository contains the INTEGRATE Python module for localized probabilistic
 
 Assuming you already have Python 3.10+ installed:
 
-`libaarhusxyz` must be installed manually before installing `integrate_module`, because the version that supports Python >= 3.12 is only available on GitHub (not PyPI):
-
-    pip install git+https://github.com/cultpenguin/libaarhusxyz
     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](https://pypi.org/project/ga-aem-forward-win/)
 
 On Linux/macOS, you will need to install GA-AEM manually.
 
-### Using pip (from PyPI, on Ubuntu)
+### Using uv (recommended, from PyPI)
+
+[uv](https://github.com/astral-sh/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
 
-    # Install python3 venv
+### 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
-    python3 -m venv ~/integrate
-    source ~/integrate/bin/activate
+
+    # 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 (from source, on Ubuntu)
 
-    # Install python3 venv
+### Using pip + venv (from source, on Ubuntu)
+
+    # Install python3-venv
     sudo apt install python3-venv
 
-    # Create virtual environment
-    python3 -m venv ~/integrate
-    source ~/integrate/bin/activate
+    # 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
-    cd path/to/integrate_module
+    # 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: 
@@ -130,7 +174,7 @@ The `develop` branch contains the current development code and may be updated fr
 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 git@github.com:cultpenguin/integrate_module.git
+    git clone --recurse-submodules git@github.com:AUProbGeo/integrate_module.git
 
 You may need to run the following command to update the submodules:
 

{integrate_module-0.99.0 → integrate_module-0.99.2}/integrate/__init__.py

@@ -18,8 +18,9 @@ from integrate.integrate_rejection import create_shared_memory
 from integrate.integrate_rejection import compute_hypothesis_probability
 
 # Import other functions from main module
-from integrate.integrate import integrate_update_prior_attributes   
+from integrate.integrate import integrate_update_prior_attributes
 from integrate.integrate import integrate_posterior_stats
+from integrate.integrate import prior_set
 from integrate.integrate import logl_T_est
 from integrate.integrate import lu_post_sample_logl
 from integrate.integrate import prior_data