integrate-module 0.99.0__tar.gz → 0.99.1__tar.gz

{integrate_module-0.99.0/integrate_module.egg-info → integrate_module-0.99.1}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: integrate_module
-Version: 0.99.0
+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/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 +24,31 @@ 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/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 +59,86 @@ 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 +220,7 @@ 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-0.99.1}/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-0.99.1}/integrate/integrate.py

@@ -895,6 +895,7 @@ def forward_gaaem(C=np.array(()),
     from tqdm import tqdm
 
     showInfo = kwargs.get('showInfo', 0)
+    progress_callback = kwargs.get('progress_callback', None)
     if (showInfo<0):
         disableTqdm=True
     else:
@@ -1067,7 +1068,13 @@ def forward_gaaem(C=np.array(()),
 
     # Compute forward data
     t1=time.time()
+    # Throttle callback to ~100 updates so it does not dominate runtime
+    progress_step = max(1, nd // 100)
+
     for i in tqdm(range(nd), mininterval=1, disable=disableTqdm, desc='gatdaem1d', leave=False):
+        if progress_callback and ((i + 1) % progress_step == 0 or i + 1 == nd):
+            _report_progress(progress_callback, i + 1, nd,
+                             'computing', 'Forward modeling (%d/%d soundings)' % (i + 1, nd))
         if C.ndim==1:
             # Only one model
             conductivity = C
@@ -1255,6 +1262,8 @@ def prior_data_gaaem(f_prior_h5, file_gex=None, stmfiles=None, N=0, doMakePriorC
     Ncpu = kwargs.get('Ncpu', 0)
     # of 'Nproc' is set in kwargs use it
     Ncpu = kwargs.get('Nproc', Ncpu)
+    # Pop (not get): the callback must never be pickled to worker processes
+    progress_callback = kwargs.pop('progress_callback', None)
 
     if showInfo>0:
         print('prior_data_gaaem: %s/%s -- starting' % (type, method))
@@ -1349,22 +1358,24 @@ def prior_data_gaaem(f_prior_h5, file_gex=None, stmfiles=None, N=0, doMakePriorC
         if im_height>0:
             if (showInfo>0):
                 print('Using tx_height')
-            D = ig.forward_gaaem(C=C, 
-                                 thickness=thickness, 
-                                 tx_height=tx_height, 
-                                 file_gex=file_gex, 
+            D = ig.forward_gaaem(C=C,
+                                 thickness=thickness,
+                                 tx_height=tx_height,
+                                 file_gex=file_gex,
                                  stmfiles=stmfiles,
-                                 Nhank=Nhank, 
-                                 Nfreq=Nfreq, 
-                                 parallel=parallel, **kwargs)
+                                 Nhank=Nhank,
+                                 Nfreq=Nfreq,
+                                 parallel=parallel,
+                                 progress_callback=progress_callback, **kwargs)
         else:
-            D = ig.forward_gaaem(C=C, 
-                                 thickness=thickness, 
-                                 file_gex=file_gex, 
+            D = ig.forward_gaaem(C=C,
+                                 thickness=thickness,
+                                 file_gex=file_gex,
                                  stmfiles=stmfiles,
-                                 Nhank=Nhank, 
-                                 Nfreq=Nfreq, 
-                                 parallel=parallel, **kwargs)
+                                 Nhank=Nhank,
+                                 Nfreq=Nfreq,
+                                 parallel=parallel,
+                                 progress_callback=progress_callback, **kwargs)
         if is_log:
             D = np.log10(D)
     else:
@@ -1384,14 +1395,19 @@ def prior_data_gaaem(f_prior_h5, file_gex=None, stmfiles=None, N=0, doMakePriorC
         # 1: Define a function to compute a chunk
         ## OUTSIDE
         # 2: Create chunks
-        C_chunks = np.array_split(C, Ncpu)
-        
-        if im_height>0:    
-            tx_height_chunks = np.array_split(tx_height, Ncpu)
-            
+        if progress_callback is None:
+            n_chunks = Ncpu
+        else:
+            # Finer chunking gives smoother live progress updates
+            n_chunks = min(C.shape[0], Ncpu * 4)
+        C_chunks = np.array_split(C, n_chunks)
+
+        if im_height>0:
+            tx_height_chunks = np.array_split(tx_height, n_chunks)
+
         else:
-            # create tx_height_chunks as a list of length Ncpu, where each entry is tx_height=np.array(())
-            tx_height_chunks = [np.array(())]*Ncpu
+            # create tx_height_chunks as a list of length n_chunks, where each entry is tx_height=np.array(())
+            tx_height_chunks = [np.array(())]*n_chunks
 
 
         import os
@@ -1421,7 +1437,22 @@ def prior_data_gaaem(f_prior_h5, file_gex=None, stmfiles=None, N=0, doMakePriorC
             else:
                 ctx = multiprocessing.get_context('fork')
             with ctx.Pool(processes=Ncpu) as p:
-                D_chunks = p.starmap(forward_gaaem_chunk_partial, zip(C_chunks, tx_height_chunks))
+                if progress_callback is None:
+                    D_chunks = p.starmap(forward_gaaem_chunk_partial, zip(C_chunks, tx_height_chunks))
+                else:
+                    # apply_async + ordered get() keeps chunk order for the
+                    # concatenate below while reporting per finished chunk
+                    async_results = [p.apply_async(forward_gaaem_chunk_partial, args=(Cc, th))
+                                     for Cc, th in zip(C_chunks, tx_height_chunks)]
+                    D_chunks = []
+                    n_total = C.shape[0]
+                    n_done = 0
+                    for r in async_results:
+                        D_chunk = r.get()
+                        D_chunks.append(D_chunk)
+                        n_done += D_chunk.shape[0]
+                        _report_progress(progress_callback, n_done, n_total,
+                                         'computing', 'Forward modeling (%d/%d soundings)' % (n_done, n_total))
         finally:
             if _spec_patched:
                 _main_module.__spec__ = None
@@ -1444,7 +1475,10 @@ def prior_data_gaaem(f_prior_h5, file_gex=None, stmfiles=None, N=0, doMakePriorC
     t_elapsed = t2 - t1
     if (showInfo>-1):
         print('prior_data_gaaem: Time=%5.1fs/%d soundings. %4.1fms/sounding, %3.1fit/s' % (t_elapsed, N, 1000*t_elapsed/N,N/t_elapsed))
-    
+
+    _report_progress(progress_callback, N, N,
+                     'saving', 'Saving forward data to %s' % f_prior_data_h5)
+
     # Write D to f_prior['/D1']
     with h5py.File(f_prior_data_h5, 'a') as f_prior:
         if Dname in f_prior:
@@ -1463,7 +1497,10 @@ def prior_data_gaaem(f_prior_h5, file_gex=None, stmfiles=None, N=0, doMakePriorC
         f_prior[Dname].attrs['Nfreq'] = Nfreq
 
     integrate_update_prior_attributes(f_prior_data_h5)
-    
+
+    _report_progress(progress_callback, N, N,
+                     'completed', 'Forward data saved to %s' % f_prior_data_h5)
+
     return f_prior_data_h5
 
 
@@ -1567,6 +1604,21 @@ def prior_data_identity(f_prior_h5, id=0, im=1, N=0, doMakePriorCopy=False, **kw
     return f_prior_data_h5, id
 
 # %% PRIOR MODEL GENERATORS
+def _report_progress(progress_callback, current, total, phase, status):
+    """Invoke an optional progress callback as progress_callback(current, total, info_dict).
+
+    Follows the same convention as integrate_rejection(): info_dict carries
+    'phase' and 'status' keys, and errors raised by the callback are ignored
+    so they can never break the computation.
+    """
+    if progress_callback is None:
+        return
+    try:
+        progress_callback(current, total, {'phase': phase, 'status': status})
+    except Exception:
+        pass
+
+
 def prior_model_layered(lay_dist='uniform', dz = 1, z_max = 90,
                         NLAY_min=3, NLAY_max=6, NLAY_deg=6,
                         RHO_dist='log-uniform', RHO_min=0.1, RHO_max=5000, RHO_mean=100, RHO_std=80,
@@ -1642,6 +1694,7 @@ def prior_model_layered(lay_dist='uniform', dz = 1, z_max = 90,
 
     showInfo = kwargs.get('showInfo', 0)
     f_prior_h5 = kwargs.get('f_prior_h5', '')
+    progress_callback = kwargs.get('progress_callback', None)
 
     if NLAY_max < NLAY_min:
         NLAY_max = NLAY_min
@@ -1715,7 +1768,13 @@ def prior_model_layered(lay_dist='uniform', dz = 1, z_max = 90,
     else:
         iterator = range(N)
 
+    # Throttle callback to ~100 updates so it does not dominate runtime
+    progress_step = max(1, N // 100)
+
     for i in iterator:
+        if progress_callback and ((i + 1) % progress_step == 0 or i + 1 == N):
+            _report_progress(progress_callback, i + 1, N,
+                             'generating', 'Generating prior realizations')
         n_lay = NLAY[i]
         n_boundaries = n_lay - 1
 
@@ -1739,6 +1798,8 @@ def prior_model_layered(lay_dist='uniform', dz = 1, z_max = 90,
 
     if showInfo > 0:
         print("prior_model_layered: Saving prior model to %s" % f_prior_h5)
+    _report_progress(progress_callback, N, N,
+                     'saving', 'Saving prior model to %s' % f_prior_h5)
 
     # Save to HDF5 file
     im = 0
@@ -1796,6 +1857,9 @@ def prior_model_layered(lay_dist='uniform', dz = 1, z_max = 90,
                         **save_kwargs,
                 )
 
+    _report_progress(progress_callback, N, N,
+                     'completed', 'Prior model saved to %s' % f_prior_h5)
+
     return f_prior_h5
 
 def prior_model_workbench_direct(N=100000, RHO_dist='log-uniform', z1=0, z_max= 100,
@@ -1862,6 +1926,11 @@ def prior_model_workbench_direct(N=100000, RHO_dist='log-uniform', z1=0, z_max=
 
     showInfo = kwargs.get('showInfo', 0)
     f_prior_h5 = kwargs.get('f_prior_h5', '')
+    progress_callback = kwargs.get('progress_callback', None)
+
+    # Fully vectorized: only coarse phase updates are possible
+    _report_progress(progress_callback, 0, 100,
+                     'generating', 'Generating prior realizations')
 
     if nlayers<1:
         nlayers = 30
@@ -1905,13 +1974,15 @@ def prior_model_workbench_direct(N=100000, RHO_dist='log-uniform', z1=0, z_max=
     
     if (showInfo>0):
         print("prior_model_workbench_direct: Saving prior model to %s" % f_prior_h5)
+    _report_progress(progress_callback, 80, 100,
+                     'saving', 'Saving prior model to %s' % f_prior_h5)
 
     if (showInfo>1):
         print("Saving '/M1' prior model  %s" % f_prior_h5)
     ig.save_prior_model(f_prior_h5,M_rho.astype(np.float32),
                 im=1,
                 name='Resistivity',
-                is_discrete = 0, 
+                is_discrete = 0,
                 x = z,
                 z = z,
                 delete_if_exist = True,
@@ -1919,6 +1990,8 @@ def prior_model_workbench_direct(N=100000, RHO_dist='log-uniform', z1=0, z_max=
                 showInfo=showInfo,
                 )
 
+    _report_progress(progress_callback, 100, 100,
+                     'completed', 'Prior model saved to %s' % f_prior_h5)
 
     return f_prior_h5
 
@@ -1996,6 +2069,7 @@ def prior_model_workbench(N=100000, p=2, z1=0, z_max= 100, dz=1,
 
     f_prior_h5 = kwargs.get('f_prior_h5', '')
     showInfo = kwargs.get('showInfo', 0)
+    progress_callback = kwargs.get('progress_callback', None)
     if nlayers>0:
         NLAY_min = nlayers
         NLAY_max = nlayers
@@ -2046,7 +2120,13 @@ def prior_model_workbench(N=100000, p=2, z1=0, z_max= 100, dz=1,
     M_rho_sparse = np.ones((N, nm_sparse))*np.nan
     
 
+    # Throttle callback to ~100 updates so it does not dominate runtime
+    progress_step = max(1, N // 100)
+
     for i in tqdm(range(N), mininterval=1, disable=(showInfo<0), desc='prior_workbench', leave=False):
+        if progress_callback and ((i + 1) % progress_step == 0 or i + 1 == N):
+            _report_progress(progress_callback, i + 1, N,
+                             'generating', 'Generating prior realizations')
         nlayers = NLAY[i][0]
         #print(nlayers)
         z2=z_max
@@ -2086,6 +2166,8 @@ def prior_model_workbench(N=100000, p=2, z1=0, z_max= 100, dz=1,
 
     if (showInfo>0):
         print("prior_model_workbench: Saving prior model to %s" % f_prior_h5)
+    _report_progress(progress_callback, N, N,
+                     'saving', 'Saving prior model to %s' % f_prior_h5)
 
     if (showInfo>1):
         print("Saving '/M1' prior model  %s" % f_prior_h5)
@@ -2117,13 +2199,16 @@ def prior_model_workbench(N=100000, p=2, z1=0, z_max= 100, dz=1,
     ig.save_prior_model(f_prior_h5,NLAY.astype(np.float32),
                         im=3,
                         name = 'Number of layers',
-                        is_discrete=0, 
-                        x=np.array([0]), 
+                        is_discrete=0,
+                        x=np.array([0]),
                         z=np.array([0]),
-                        force_replace=True, 
+                        force_replace=True,
                         showInfo=showInfo,
                 )
 
+    _report_progress(progress_callback, N, N,
+                     'completed', 'Prior model saved to %s' % f_prior_h5)
+
     # return the full filepath to f_prior_h5
     return f_prior_h5
 
@@ -3688,7 +3773,7 @@ def timing_plot(f_timing=''):
         plt.stackplot(N_arr, T, labels=['Prior', 'Forward', 'Rejection', 'PostStat'])
         plt.plot(N_arr, T_total[:, i_proc], 'k--')
         plt.xscale('log')
-        #plt.yscale('log')
+        plt.yscale('log')
         plt.xlabel('$N_{lookup}$')
         plt.ylabel('Time [$s$]')
         plt.title('Cumulative time, using %d processors' % Nproc_arr[i_proc])

{integrate_module-0.99.0 → integrate_module-0.99.1}/integrate/integrate_io.py

@@ -2976,7 +2976,7 @@ def get_case_data(case='DAUGAARD', loadAll=False, loadType='', filelist=None, **
     if showInfo>-1:
         print('--> Got data for case: %s' % case)
 
-    return [os.path.basename(f) for f in filelist]
+    return [f.replace('\\', '/').split('/')[-1] for f in filelist]
 
 
 

{integrate_module-0.99.0 → integrate_module-0.99.1}/integrate/integrate_query.py

@@ -414,7 +414,7 @@ def query(f_post_h5, query_dict):
 
 
 def query_plot(P, meta, ip=None, query_dict=None, f_prior_h5=None, f_post_h5=None, title=None,
-               query_text=None, interpretation=None, text_panel=False, hardcopy=False):
+               query_text=None, interpretation=None, text_panel=False, hardcopy=False, **kwargs):
     """
     Plot query results and optionally detailed model visualization for a data point.
 
@@ -455,6 +455,12 @@ def query_plot(P, meta, ip=None, query_dict=None, f_prior_h5=None, f_post_h5=Non
         Save the probability map figure. If True, saves as 'query_plot.png'.
         If a string, uses that as the filename (a '.png' extension is appended
         if the string has no extension). Default False.
+    **kwargs
+        All remaining keyword arguments are forwarded to :func:`plot_xy`, giving
+        full control over ``cmap``, ``clim``, ``uselog``, ``colorbar``,
+        ``colorbar_label``, ``plotPoints``, ``plotPoints_color``,
+        ``plotPoints_marker``, ``s``, etc.
+        ``cmap`` defaults to ``'hot_r'`` and ``clim`` defaults to ``[0, 1]``.
 
     Examples
     --------
@@ -513,11 +519,17 @@ def query_plot(P, meta, ip=None, query_dict=None, f_prior_h5=None, f_post_h5=Non
         )
 
         # Background dots so P=0 (white) areas are visible, then probability scatter
+        _cmap = kwargs.pop('cmap', 'hot_r')
+        _clim = kwargs.pop('clim', [0, 1])
+        _s = kwargs.pop('s', 1)
+        _colorbar = kwargs.pop('colorbar', True)
+        _colorbar_label = kwargs.pop('colorbar_label', 'Probability')
+        _plotPoints = kwargs.pop('plotPoints', True)
         from integrate.integrate_plot import plot_xy
         _, ax, sc = plot_xy(P, X=X, Y=Y,
-                            cmap='hot_r', clim=[0, 1],
-                            title=_title, colorbar=True, colorbar_label='Probability',
-                            ax=ax, s=1, plotPoints=True)
+                            cmap=_cmap, clim=_clim,
+                            title=_title, colorbar=_colorbar, colorbar_label=_colorbar_label,
+                            ax=ax, s=_s, plotPoints=_plotPoints, **kwargs)
         ax.set_xlabel('UTMX [m]')
         ax.set_ylabel('UTMY [m]')
 
@@ -680,7 +692,7 @@ def query_plot(P, meta, ip=None, query_dict=None, f_prior_h5=None, f_post_h5=Non
 
 
 def query_percentile_plot(percentile_values, meta, query_text=None, interpretation=None,
-                          text_panel=False, hardcopy=False):
+                          text_panel=False, hardcopy=False, **kwargs):
     """
     Plot one probability map per requested percentile as side-by-side subplots.
 
@@ -699,6 +711,14 @@ def query_percentile_plot(percentile_values, meta, query_text=None, interpretati
     hardcopy : bool or str, optional
         Save figure to disk.  True → 'query_percentile_plot.png'; a string is
         used as the filename (.png appended if no extension).
+    **kwargs
+        All remaining keyword arguments are forwarded to :func:`plot_xy`, giving
+        full control over ``cmap``, ``clim``, ``uselog``, ``colorbar``,
+        ``colorbar_label``, ``plotPoints``, ``plotPoints_color``,
+        ``plotPoints_marker``, ``s``, etc.
+        ``clim`` defaults to ``[percentile_values.min(), percentile_values.max()]``
+        so that all subplots share the same colour scale.
+        ``cmap`` defaults to ``'viridis'``.
 
     Returns
     -------
@@ -711,6 +731,10 @@ def query_percentile_plot(percentile_values, meta, query_text=None, interpretati
     X = meta.get('X')
     Y = meta.get('Y')
 
+    # Shared colour scale across all subplots unless caller overrides.
+    cmap = kwargs.pop('cmap', 'viridis')
+    clim = kwargs.pop('clim', [float(percentile_values.min()), float(percentile_values.max())])
+
     ncols = n_pct + (1 if text_panel else 0)
     width_ratios = [4] * n_pct + ([1.5] if text_panel else [])
     fig, axes = plt.subplots(1, ncols, figsize=(4.5 * n_pct + (1.5 if text_panel else 0), 5),
@@ -718,17 +742,14 @@ def query_percentile_plot(percentile_values, meta, query_text=None, interpretati
                              squeeze=False)
 
     map_axes = axes[0, :n_pct]
-    vmin = percentile_values.min()
-    vmax = percentile_values.max()
 
     from integrate.integrate_plot import plot_xy
     for k, (pct, ax) in enumerate(zip(percentiles, map_axes)):
         vals = percentile_values[:, k]
         if X is not None and Y is not None:
             _, ax, _ = plot_xy(vals, X=X, Y=Y,
-                               cmap='viridis', clim=[vmin, vmax],
-                               colorbar=True, colorbar_label='[m]',
-                               ax=ax, s=5)
+                               cmap=cmap, clim=clim,
+                               ax=ax, **kwargs)
             ax.set_xlabel('UTMX')
             if k == 0:
                 ax.set_ylabel('UTMY')

{integrate_module-0.99.0 → integrate_module-0.99.1}/integrate/integrate_rejection.py

@@ -338,8 +338,12 @@ def integrate_rejection(f_prior_h5='prior.h5',
         # Split the ip_range into Nchunks
         if Nchunks==0:
             if parallel:
-                Nchunks = Ncpu
-            else:   
+                if progress_callback is not None:
+                    # Finer chunking gives smoother live progress updates
+                    Nchunks = min(len(ip_range), Ncpu * 4)
+                else:
+                    Nchunks = Ncpu
+            else:
                 Nchunks = 1
         ip_range_shuffled = ip_range.copy()
         np.random.shuffle(ip_range_shuffled)
@@ -362,14 +366,12 @@ def integrate_rejection(f_prior_h5='prior.h5',
             use_N_best=use_N_best,
             T_N_above=_T_N_above,
             T_P_acc_level=_T_P_acc_level,
+            progress_callback=update_progress if progress_callback else None,
         )
 
 
     else:
 
-            # Extract progress_callback for non-parallel execution
-            progress_callback = kwargs.get('progress_callback', None)
-            
             i_use, T, EV, EV_post, EV_post_mean, CHI2, N_UNIQUE, ip_range = integrate_rejection_range(D=D,
                                         DATA = DATA,
                                         idx = idx,
@@ -625,9 +627,18 @@ def integrate_rejection_range(D,
         print('class_id_list',class_id_list)
         print('len(class_id_list)',len(class_id_list))
 
-    #print(ip_range)    
+    #print(ip_range)
+    # Throttle callback to ~100 updates so it does not dominate runtime
+    progress_step = max(1, nump // 100)
     #tqdm(range(nd), mininterval=1, disable=disableTqdm, desc='gatdaem1d', leave=False):
     for j in tqdm(range(len(ip_range)), disable=disableTqdm, desc='Rejection Sampling', leave=False):
+        if progress_callback and ((j + 1) % progress_step == 0 or j + 1 == nump):
+            try:
+                progress_callback(j + 1, nump,
+                                  {'phase': 'sampling',
+                                   'status': 'Rejection sampling (%d/%d data points)' % (j + 1, nump)})
+            except Exception:
+                pass
         ip = ip_range[j] # This is the index of the data point to invert
   
         t=[]
@@ -844,7 +855,7 @@ def integrate_rejection_range(D,
 
 
 
-def integrate_posterior_main(ip_chunks, D, DATA, idx, N_use, id_use, autoT, T_base, nr, Ncpu, use_N_best, T_N_above=10, T_P_acc_level=0.2):
+def integrate_posterior_main(ip_chunks, D, DATA, idx, N_use, id_use, autoT, T_base, nr, Ncpu, use_N_best, T_N_above=10, T_P_acc_level=0.2, progress_callback=None):
     """
     Coordinate parallel processing of posterior sampling across multiple chunks.
     
@@ -930,7 +941,22 @@ def integrate_posterior_main(ip_chunks, D, DATA, idx, N_use, id_use, autoT, T_ba
     try:
         with ctx.Pool(Ncpu) as p:
             # New implementation with shared memory
-            results = p.map(integrate_posterior_chunk, [(i, ip_chunks, DATA, idx,  N_use, id_use, shared_memory_refs, autoT, T_base, nr, use_N_best, T_N_above, T_P_acc_level) for i in range(len(ip_chunks))])
+            chunk_args = [(i, ip_chunks, DATA, idx,  N_use, id_use, shared_memory_refs, autoT, T_base, nr, use_N_best, T_N_above, T_P_acc_level) for i in range(len(ip_chunks))]
+            if progress_callback is None:
+                results = p.map(integrate_posterior_chunk, chunk_args)
+            else:
+                # imap_unordered yields per finished chunk, enabling live
+                # progress. Result order does not matter: each result carries
+                # its own ip_range used for aggregation below.
+                results = []
+                total_dp = sum(len(c) for c in ip_chunks)
+                done_dp = 0
+                for res in p.imap_unordered(integrate_posterior_chunk, chunk_args):
+                    results.append(res)
+                    done_dp += len(res[-1])  # last element is the chunk's ip_range
+                    progress_callback(done_dp, total_dp,
+                                      {'phase': 'sampling',
+                                       'status': 'Rejection sampling (%d/%d data points)' % (done_dp, total_dp)})
             # Old implementation where D was copied to each process
             #results = p.map(integrate_posterior_chunk, [(i, ip_chunks, D, DATA, idx,  N_use, id_use, shared_memory_refs, autoT, T_base, nr, use_N_best) for i in range(len(ip_chunks))])
     finally:

{integrate_module-0.99.0 → integrate_module-0.99.1/integrate_module.egg-info}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: integrate_module
-Version: 0.99.0
+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/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 +24,31 @@ 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/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 +59,86 @@ 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 +220,7 @@ 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-0.99.1}/integrate_module.egg-info/requires.txt

@@ -8,10 +8,12 @@ requests
 geoprior1d>=0.9
 jupyter>=1.0.0
 jupytext
+ipykernel
 pandas
 pyvista
 litellm
 streamlit
+libaarhusxyz
 
 [:platform_system == "Windows"]
 ga-aem-forward-win
@@ -19,3 +21,15 @@ ga-aem-forward-win
 [dev]
 pytest
 black
+
+[docs]
+sphinx
+nbsphinx
+sphinx-gallery
+pandoc
+myst-parser
+sphinx-rtd-theme
+furo
+
+[docs:python_version < "3.11"]
+tomli

{integrate_module-0.99.0 → integrate_module-0.99.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "integrate_module"
-version = "0.99.0"
+version = "0.99.01"
 description = "Localized probabilistic data integration"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.10"
@@ -26,12 +26,12 @@ dependencies = [
     "ga-aem-forward-win; platform_system == 'Windows'",
     "jupyter>=1.0.0",
     "jupytext",
+    "ipykernel",
     "pandas",
     "pyvista",
     "litellm",
-    "streamlit"
-    # libaarhusxyz must be installed manually (see README) — PyPI does not allow git dependencies.
-    # pip install git+https://github.com/cultpenguin/libaarhusxyz
+    "streamlit",
+    "libaarhusxyz",
 ]
 
 [project.optional-dependencies]
@@ -39,13 +39,23 @@ dev = [
     "pytest",
     "black",
 ]
+docs = [
+    "sphinx",
+    "nbsphinx",
+    "sphinx-gallery",
+    "pandoc",
+    "myst-parser",
+    "sphinx-rtd-theme",
+    "furo",
+    "tomli; python_version < '3.11'",
+]
 
 
 [project.urls]
-Homepage = "https://github.com/cultpenguin/integrate_module"
-Documentation = "https://cultpenguin.github.io/integrate_module/"
-Repository = "https://github.com/cultpenguin/integrate_module"
-Issues = "https://github.com/cultpenguin/integrate_module/issues"
+Homepage = "https://github.com/AUProbGeo/integrate_module"
+Documentation = "https://auprobgeo.github.io/integrate_module/"
+Repository = "https://github.com/AUProbGeo/integrate_module"
+Issues = "https://github.com/AUProbGeo/integrate_module/issues"
 
 [project.scripts]
 integrate = "integrate.integrate_www_cli:main"