integrate_module 0.99.1__tar.gz

integrate_module-0.99.1/LICENSE

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+MIT License
+
+Copyright (c) 2023-2025 Thomas Mejer Hansen and INTEGRATE Working Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

integrate_module-0.99.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: integrate_module
+Version: 0.99.1
+Summary: Localized probabilistic data integration
+Author-email: Thomas Mejer Hansen <tmeha@geo.au.dk>
+License: MIT
+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
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: h5py
+Requires-Dist: scipy
+Requires-Dist: psutil
+Requires-Dist: tqdm
+Requires-Dist: requests
+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
+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/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://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/)
+
+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](https://pypi.org/project/ga-aem-forward-win/)
+
+On Linux/macOS, you will need to install GA-AEM manually.
+
+### 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
+
+### 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](https://github.com/GeoscienceAustralia/ga-aem) or use the information below.
+
+
+### PyPI package for Windows
+
+On Windows, the [ga-aem-forward-win](https://pypi.org/project/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 git@github.com:AUProbGeo/integrate_module.git
+
+You may need to run the following command to update the submodules:
+
+    cd experimental
+    git submodule update --init --recursive
+

integrate_module-0.99.1/README.md

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+# INTEGRATE Python Module
+
+[![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://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/)
+
+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](https://pypi.org/project/ga-aem-forward-win/)
+
+On Linux/macOS, you will need to install GA-AEM manually.
+
+### 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
+
+### 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](https://github.com/GeoscienceAustralia/ga-aem) or use the information below.
+
+
+### PyPI package for Windows
+
+On Windows, the [ga-aem-forward-win](https://pypi.org/project/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 git@github.com:AUProbGeo/integrate_module.git
+
+You may need to run the following command to update the submodules:
+
+    cd experimental
+    git submodule update --init --recursive
+

integrate_module-0.99.1/integrate/__init__.py

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+import multiprocessing
+multiprocessing.freeze_support()
+
+# Import rejection sampling functions from new module
+from integrate.integrate_rejection import integrate_rejection
+from integrate.integrate_rejection import integrate_rejection_range
+from integrate.integrate_rejection import integrate_posterior_chunk
+from integrate.integrate_rejection import integrate_posterior_main
+from integrate.integrate_rejection import likelihood_gaussian_diagonal
+from integrate.integrate_rejection import likelihood_gaussian_diagonal_old
+from integrate.integrate_rejection import likelihood_gaussian_full
+from integrate.integrate_rejection import likelihood_multinomial
+from integrate.integrate_rejection import likelihood_multinomial_old
+from integrate.integrate_rejection import select_subset_for_inversion
+from integrate.integrate_rejection import cleanup_shared_memory
+from integrate.integrate_rejection import reconstruct_shared_arrays
+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_posterior_stats
+from integrate.integrate import logl_T_est
+from integrate.integrate import lu_post_sample_logl
+from integrate.integrate import prior_data
+from integrate.integrate import prior_data_gaaem
+from integrate.integrate import prior_data_identity
+from integrate.integrate import forward_gaaem
+from integrate.integrate import synthetic_case
+from integrate.integrate import prior_model_layered
+from integrate.integrate import prior_model_workbench
+from integrate.integrate import prior_model_workbench_direct
+from integrate.integrate import posterior_cumulative_thickness
+#from integrate.integrate import integrate_rejection_multi  
+from integrate.integrate import use_parallel
+from integrate.integrate import kl_divergence
+from integrate.integrate import entropy
+from integrate.integrate import class_id_to_idx
+from integrate.integrate import is_notebook
+from integrate.integrate import get_hypothesis_probability
+from integrate.integrate import sample_posterior_multiple_hypotheses
+from integrate.integrate import timing_compute
+from integrate.integrate import timing_plot
+#from integrate.integrate import compute_P_obs_from_log
+#from integrate.integrate import rescale_P_obs_temperature
+#from integrate.integrate import Pobs_to_datagrid
+
+# Import matplotlib backend setup
+from integrate.integrate_plot import setup_matplotlib_backend
+
+from integrate.integrate_io import copy_prior
+from integrate.integrate_io import load_prior
+from integrate.integrate_io import load_prior_data
+from integrate.integrate_io import save_prior_data
+from integrate.integrate_io import load_prior_model
+from integrate.integrate_io import save_prior_model
+from integrate.integrate_io import load_data
+from integrate.integrate_io import get_geometry
+from integrate.integrate_io import extract_feature_at_elevation
+from integrate.integrate_io import get_discrete_classes
+from integrate.integrate_io import get_number_of_datasets
+from integrate.integrate_io import get_number_of_data
+from integrate.integrate_io import read_gex
+from integrate.integrate_io import read_gex_workbench
+from integrate.integrate_io import gex_to_stm
+from integrate.integrate_io import get_gex_file_from_data
+from integrate.integrate_io import write_stm_files
+from integrate.integrate_io import post_to_csv
+from integrate.integrate_io import copy_hdf5_file
+from integrate.integrate_io import hdf5_scan
+from integrate.integrate_io import get_case_data
+from integrate.integrate_io import save_data_gaussian
+from integrate.integrate_io import xyz_to_h5
+from integrate.integrate_io import save_data_multinomial
+from integrate.integrate_io import write_data_gaussian  # Deprecated - use save_data_gaussian
+from integrate.integrate_io import write_data_multinomial  # Deprecated - use save_data_multinomial
+from integrate.integrate_io import check_data
+from integrate.integrate_io import merge_prior
+from integrate.integrate_io import merge_data
+from integrate.integrate_io import merge_posterior
+from integrate.integrate_io import filter_prior
+from integrate.integrate_io import read_usf
+from integrate.integrate_io import read_usf_mul
+from integrate.integrate_io import test_read_usf
+from integrate.integrate_io import hdf5_info
+from integrate.integrate_io import read_borehole
+from integrate.integrate_io import write_borehole
+
+from integrate.integrate_plot import plot_geometry
+from integrate.integrate_plot import plot_profile
+from integrate.integrate_plot import plot_profile_continuous
+from integrate.integrate_plot import plot_profile_discrete
+from integrate.integrate_plot import plot_cumulative_probability_profile
+from integrate.integrate_plot import plot_T_EV
+from integrate.integrate_plot import plot_data_xy
+from integrate.integrate_plot import plot_data
+from integrate.integrate_plot import plot_data_prior_post
+from integrate.integrate_plot import plot_data_prior
+from integrate.integrate_plot import plot_prior_stats
+from integrate.integrate_plot import plot_post_stats
+from integrate.integrate_plot import plot_feature_2d
+from integrate.integrate_plot import plot_posterior_cumulative_thickness
+from integrate.integrate_plot import h5_get_clim_cmap
+from integrate.integrate_plot import get_colormap_and_limits
+from integrate.integrate_plot import plot_xy
+from integrate.integrate_plot import find_points_along_line_segments
+from integrate.integrate_plot import plot_boreholes
+
+# Import from borehole module
+from integrate.integrate_borehole import compute_P_obs_discrete
+from integrate.integrate_borehole import compute_P_obs_discrete as Pobs_discrete_compute
+from integrate.integrate_borehole import welllog_compute_P_obs_class_mode
+from integrate.integrate_borehole import rescale_P_obs_temperature
+from integrate.integrate_borehole import rescale_P_obs_temperature as Pobs_rescale_temperature
+from integrate.integrate_borehole import Pobs_to_datagrid
+from integrate.integrate_borehole import get_weight_from_position
+from integrate.integrate_borehole import prior_data_borehole
+from integrate.integrate_borehole import prior_data_borehole_class_mode
+from integrate.integrate_borehole import prior_data_borehole_class_layer
+from integrate.integrate_borehole import save_borehole_data
+
+# Import query functions
+from integrate.integrate_query import query
+from integrate.integrate_query import query_probability
+from integrate.integrate_query import query_percentile
+from integrate.integrate_query import query_plot
+from integrate.integrate_query import query_percentile_plot
+from integrate.integrate_query import save_query
+from integrate.integrate_query import load_query
+from integrate.integrate_query import get_prior_model_info
+from integrate.integrate_query import prior_describe
+from integrate.integrate_query import query_from_text
+from integrate.integrate_query import title_from_json
+from integrate.integrate_query import query_test_llm
+
+# Import gex module functions
+from integrate.gex import read_gex as read_gex2
+from integrate.gex import describe_gex as describe_gex2
+
+
+# REMOVE CLI IMPORTS - These cause circular dependencies
+# from . import integrate_cli
+# from . import integrate_timing
+