integrate-module 0.99.9__tar.gz → 1.0.0__tar.gz

{integrate_module-0.99.9/integrate_module.egg-info → integrate_module-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: integrate_module
-Version: 0.99.9
+Version: 1.0.0
 Summary: Localized probabilistic data integration
 Author-email: Thomas Mejer Hansen <tmeha@geo.au.dk>
 License: MIT
@@ -10,7 +10,7 @@ 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
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
@@ -23,6 +23,7 @@ Requires-Dist: requests
 Requires-Dist: geoprior1d>=0.9
 Requires-Dist: shapely
 Requires-Dist: ga-aem-forward-win; platform_system == "Windows"
+Requires-Dist: simpeg>=0.25
 Requires-Dist: jupyter>=1.0.0
 Requires-Dist: jupytext
 Requires-Dist: ipykernel
@@ -35,6 +36,7 @@ Requires-Dist: uvicorn[standard]
 Requires-Dist: python-fasthtml
 Requires-Dist: openpyxl
 Requires-Dist: httpx
+Requires-Dist: threadpoolctl
 Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: black; extra == "dev"
@@ -48,12 +50,8 @@ Requires-Dist: shapely; extra == "examples"
 Provides-Extra: docs
 Requires-Dist: sphinx; 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: ghp-import; extra == "docs"
-Requires-Dist: tomli; python_version < "3.11" and extra == "docs"
 Provides-Extra: jax-cuda
 Requires-Dist: jax[cuda13]; extra == "jax-cuda"
 Dynamic: license-file
@@ -64,14 +62,15 @@ Dynamic: license-file
 [![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/)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/AUProbGeo/integrate_module/blob/main/examples/gallery/10_getting_started/integrate_getting_started.ipynb)
 
 This repository contains the INTEGRATE Python module for localized probabilistic data integration in geophysics.
 
 
 ## Installation
 
-Assuming you already have Python 3.10+ installed:
+Assuming you already have Python 3.11+ installed:
 
     pip install integrate_module
 
@@ -89,7 +88,7 @@ On Linux/macOS, you will need to install GA-AEM manually.
 
     # Create virtual environment in .venv/ inside the module root
     cd path/to/integrate_module
-    uv venv .venv --python 3.11
+    uv venv .venv --python 3.13
 
     # Activate
     source .venv/bin/activate      # Linux/macOS
@@ -157,7 +156,7 @@ To also install the packages needed to build the Sphinx documentation, use the `
 
 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 create --name integrate python=3.13 numpy pandas matplotlib scipy tqdm requests h5py psutil
     conda activate integrate
     pip install integrate_module
     
@@ -166,7 +165,7 @@ Create a Conda environment (called integrate) and install the required modules:
 
 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 create --name integrate python=3.12 numpy pandas matplotlib scipy tqdm requests h5py psutil
     conda activate integrate
     pip install -e .
 
@@ -227,7 +226,7 @@ First install Homebrew, then run:
 
 ## Alternative EM forward backends (anemone, SimPEG)
 
-GA-AEM is the default TDEM forward modeller. Two pure-Python alternatives can be
+GA-AEM is the default TDEM forward modeller. Two alternatives can be
 selected with `method=` in `ig.forward_em()` / `ig.prior_data_em()` (or via the
 `EM_FORWARD_METHOD` environment variable):
 
@@ -235,9 +234,11 @@ selected with `method=` in `ig.forward_em()` / `ig.prior_data_em()` (or via the
     ig.prior_data_em(f_prior_h5, file_gex=gex, method='anemone')   # PyTorch, GPU-capable
     ig.prior_data_em(f_prior_h5, file_gex=gex, method='simpeg')    # SimPEG 1D layered TDEM
 
-* **anemone** (`pip install "integrate[anemone]"`): see `ANEMONE_VS_GAAEM_VS_AI.md`.
-* **SimPEG** (`pip install "integrate[simpeg]"`, or `uv pip install -e ../simpeg` from a
-  checkout): `ig.forward_simpeg()` / `ig.prior_data_simpeg()`. The `.gex` low-pass filters
+* **anemone** (PyTorch, GPU-capable): not on PyPI yet. Install it from a local checkout
+  with `pip install -e path/to/anemone`, plus a `torch` build for your hardware. See the
+  install guide in `doc/install.rst`.
+* **SimPEG**: installed with `integrate_module` (core dependency, `simpeg>=0.25`).
+  Use `ig.forward_simpeg()` / `ig.prior_data_simpeg()`. The `.gex` low-pass filters
   and gate integration are applied by INTEGRATE on top of SimPEG's
   `Simulation1DLayered`; agreement with GA-AEM is ~1 % (LM) / ~0.2 % (HM) on Daugaard tTEM,
   see `SIMPEG_VS_GAAEM.md`.
@@ -248,7 +249,7 @@ The `main` branch is the most stable, with less frequent updates but larger chan
 
 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/>`_.
+An extra set of tests and examples are located in the `experimental` submodule repository: 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

{integrate_module-0.99.9 → integrate_module-1.0.0}/README.md

@@ -4,14 +4,15 @@
 [![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/)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/AUProbGeo/integrate_module/blob/main/examples/gallery/10_getting_started/integrate_getting_started.ipynb)
 
 This repository contains the INTEGRATE Python module for localized probabilistic data integration in geophysics.
 
 
 ## Installation
 
-Assuming you already have Python 3.10+ installed:
+Assuming you already have Python 3.11+ installed:
 
     pip install integrate_module
 
@@ -29,7 +30,7 @@ On Linux/macOS, you will need to install GA-AEM manually.
 
     # Create virtual environment in .venv/ inside the module root
     cd path/to/integrate_module
-    uv venv .venv --python 3.11
+    uv venv .venv --python 3.13
 
     # Activate
     source .venv/bin/activate      # Linux/macOS
@@ -97,7 +98,7 @@ To also install the packages needed to build the Sphinx documentation, use the `
 
 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 create --name integrate python=3.13 numpy pandas matplotlib scipy tqdm requests h5py psutil
     conda activate integrate
     pip install integrate_module
     
@@ -106,7 +107,7 @@ Create a Conda environment (called integrate) and install the required modules:
 
 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 create --name integrate python=3.12 numpy pandas matplotlib scipy tqdm requests h5py psutil
     conda activate integrate
     pip install -e .
 
@@ -167,7 +168,7 @@ First install Homebrew, then run:
 
 ## Alternative EM forward backends (anemone, SimPEG)
 
-GA-AEM is the default TDEM forward modeller. Two pure-Python alternatives can be
+GA-AEM is the default TDEM forward modeller. Two alternatives can be
 selected with `method=` in `ig.forward_em()` / `ig.prior_data_em()` (or via the
 `EM_FORWARD_METHOD` environment variable):
 
@@ -175,9 +176,11 @@ selected with `method=` in `ig.forward_em()` / `ig.prior_data_em()` (or via the
     ig.prior_data_em(f_prior_h5, file_gex=gex, method='anemone')   # PyTorch, GPU-capable
     ig.prior_data_em(f_prior_h5, file_gex=gex, method='simpeg')    # SimPEG 1D layered TDEM
 
-* **anemone** (`pip install "integrate[anemone]"`): see `ANEMONE_VS_GAAEM_VS_AI.md`.
-* **SimPEG** (`pip install "integrate[simpeg]"`, or `uv pip install -e ../simpeg` from a
-  checkout): `ig.forward_simpeg()` / `ig.prior_data_simpeg()`. The `.gex` low-pass filters
+* **anemone** (PyTorch, GPU-capable): not on PyPI yet. Install it from a local checkout
+  with `pip install -e path/to/anemone`, plus a `torch` build for your hardware. See the
+  install guide in `doc/install.rst`.
+* **SimPEG**: installed with `integrate_module` (core dependency, `simpeg>=0.25`).
+  Use `ig.forward_simpeg()` / `ig.prior_data_simpeg()`. The `.gex` low-pass filters
   and gate integration are applied by INTEGRATE on top of SimPEG's
   `Simulation1DLayered`; agreement with GA-AEM is ~1 % (LM) / ~0.2 % (HM) on Daugaard tTEM,
   see `SIMPEG_VS_GAAEM.md`.
@@ -188,7 +191,7 @@ The `main` branch is the most stable, with less frequent updates but larger chan
 
 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/>`_.
+An extra set of tests and examples are located in the `experimental` submodule repository: 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

{integrate_module-0.99.9 → integrate_module-1.0.0}/integrate/__init__.py

@@ -21,6 +21,7 @@ from integrate.integrate_rejection import compute_hypothesis_probability
 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 data_set
 from integrate.integrate import logl_T_est
 from integrate.integrate import lu_post_sample_logl
 from integrate.integrate import prior_data
@@ -35,6 +36,8 @@ from integrate.anemone_forward import gex_to_anemone_system
 from integrate.simpeg_forward import forward_simpeg
 from integrate.simpeg_forward import prior_data_simpeg
 from integrate.em_system import gex_to_em_system
+from integrate.sr2_gex import gex_apply_sr2
+from integrate.sr2_gex import sr2_effective_current
 from integrate.integrate import synthetic_case
 from integrate.integrate import prior_model_layered
 from integrate.integrate import prior_model_workbench