pygeoinf 1.2.8__tar.gz → 1.3.0__tar.gz

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/PKG-INFO

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pygeoinf
-Version: 1.2.8
+Version: 1.3.0
 Summary: A package for solving geophysical inference and inverse problems
 License: BSD-3-Clause
+License-File: LICENSE
 Author: David Al-Attar and Dan Heathcote
 Requires-Python: >=3.11
 Classifier: License :: OSI Approved :: BSD License
@@ -10,12 +11,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: Cartopy (>=0.23.0,<0.24.0)
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: sphere
 Requires-Dist: joblib (>=1.5.2,<2.0.0)
 Requires-Dist: matplotlib (>=3.0.0)
 Requires-Dist: numpy (>=1.26.0)
 Requires-Dist: pyqt6 (>=6.0.0)
-Requires-Dist: pyshtools (>=4.0.0)
 Requires-Dist: scipy (>=1.16.1)
 Description-Content-Type: text/markdown
 
@@ -47,16 +48,31 @@ The library is built on a few key concepts:
 * **Optimisation Methods**: Includes Tikhonov-regularized least-squares and minimum-norm solutions.
 * **Probabilistic Modelling**: Define priors and noise models using `GaussianMeasure` objects on abstract spaces.
 * **Randomized Algorithms**: Utilizes randomized SVD and Cholesky decompositions for efficient low-rank approximations of large operators.
+* **Specialized Operator Variants**: Efficient implementations for `DiagonalSparseMatrixLinearOperator` and `NormalSumOperator`.
 * **Application-Specific Spaces**: Provides concrete `HilbertSpace` implementations for functions on a **line**, **circle**, and the **two-sphere**.
 * **High-Quality Visualisation**: Built-in plotting methods for functions on symmetric spaces, including map projections via `cartopy`.
 
+## Advanced Features
+
+* **Block Operators**: Construct complex operators from smaller components using `BlockLinearOperator`, `ColumnLinearOperator`, and `RowLinearOperator`. This is ideal for coupled inverse problems.
+* **Parallelisation**: Many expensive operations are parallelized with `joblib`, including dense matrix construction and randomized algorithms.
+
 ## Installation
 
-The package can be installed directly using pip:
+The package can be installed directly using pip. By default, this will perform a minimal installation.
 
 ```bash
+# Minimal installation
 pip install pygeoinf
 ```
+
+To include the functionality for functions on the sphere, you can install the `sphere` extra. This provides support for `pyshtools` and `Cartopy`.
+
+```bash
+# Installation with sphere-related features
+pip install pygeoinf[sphere]
+```
+
 For development, you can clone the repository and install using Poetry:
 
 ```bash
@@ -64,6 +80,7 @@ git clone https://github.com/da380/pygeoinf.git
 cd pygeoinf
 poetry install
 ```
+
 You can install all optional dependencies for development—including tools for running the test suite, 
 building the documentation, and running the Jupyter tutorials—by using the ```--with``` flag and specifying the ```dev``` group.
 
@@ -233,20 +250,30 @@ The output of the above script will look similar to the following figure:
 * NumPy
 * SciPy
 * Matplotlib
-* pyshtools (for `sphere.py`)
-* Cartopy (for plotting in `sphere.py`)
+* joblib
 
-## Future Plans
+### Optional (`sphere`)
+
+* pyshtools
+* Cartopy
+
+## Recent Updates
+
+`pygeoinf` is under active development, and recent updates have expanded its capabilities to address a broader range of geophysical problems. Key improvements include:
 
-`pygeoinf` is under active development. Current work is focused on expanding the library's capabilities to address a broader range of geophysical problems. Key areas for development include:
+* **Non-Linear Inverse Problems**: The library now supports non-linear inverse problems through the `NonLinearOperator` and `NonLinearForm` classes. This allows you to define and solve problems where the relationship between model parameters and data is non-linear. The framework includes support for Fréchet derivatives, enabling the use of gradient-based optimisation methods.
 
-* **Generalised Backus-Gilbert Methods**: Implementation of a generalised Backus-Gilbert framework for linear inference problems. The focus will be on constructing direct estimates of specific properties of interest (i.e., linear functionals of the model) from data, without needing to first solve for the full model itself.
+* **Advanced Optimisation Algorithms**: To complement the non-linear framework, `pygeoinf` now includes a suite of optimisation algorithms. You can use the custom `GradientDescent` solver or leverage the power of SciPy's optimization library with methods like 'BFGS', 'L-BFGS-B', and 'Newton-CG'. Derivative-free methods such as 'Powell' and 'Nelder-Mead' are also supported for problems where gradients are unavailable.
+
+* **Backus-Gilbert Methods**: The foundations for the Backus-Gilbert method have been implemented. While this feature is still evolving, the core components are in place for you to begin exploring this powerful inference technique.
+
+## Future Plans
 
-* **Non-linear Optimisation**: Extension of the current optimisation framework to handle non-linear inverse problems. This will involve creating a general interface where users can provide their own non-linear forward mapping, a misfit functional, and methods for computing gradients (and optionally Hessians) for use in gradient-based optimisation algorithms.
+Future development will focus on the following areas:
 
-* **Non-linear Bayesian Inference**: Development of methods for non-linear Bayesian problems. Planned approaches include linearizing the problem around the maximum a posteriori (MAP) solution to estimate posterior uncertainty, and using this linearization to construct efficient proposal distributions for Markov chain Monte Carlo (MCMC) sampling methods.
+* **Non-linear Bayesian Inference**: We plan to develop methods for non-linear Bayesian problems, including techniques for linearizing the problem around the maximum a posteriori (MAP) solution to estimate posterior uncertainty. This will also involve constructing efficient proposal distributions for Markov chain Monte Carlo (MCMC) sampling methods.
 
-* **New Geophysical Hilbert Spaces**: Addition of further `HilbertSpace` implementations tailored to specific geophysical applications. A primary focus will be on creating spaces for functions defined within a **spherical annulus** (spherical shell), which is essential for problems in global seismology and mantle tomography.
+* **New Geophysical Hilbert Spaces**: We will be adding more `HilbertSpace` implementations for specific geophysical applications. A key focus will be on creating spaces for functions defined within a **spherical annulus** (spherical shell), which is crucial for problems in global seismology and mantle tomography.
 
 
 ## Contributing

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/README.md

@@ -26,16 +26,31 @@ The library is built on a few key concepts:
 * **Optimisation Methods**: Includes Tikhonov-regularized least-squares and minimum-norm solutions.
 * **Probabilistic Modelling**: Define priors and noise models using `GaussianMeasure` objects on abstract spaces.
 * **Randomized Algorithms**: Utilizes randomized SVD and Cholesky decompositions for efficient low-rank approximations of large operators.
+* **Specialized Operator Variants**: Efficient implementations for `DiagonalSparseMatrixLinearOperator` and `NormalSumOperator`.
 * **Application-Specific Spaces**: Provides concrete `HilbertSpace` implementations for functions on a **line**, **circle**, and the **two-sphere**.
 * **High-Quality Visualisation**: Built-in plotting methods for functions on symmetric spaces, including map projections via `cartopy`.
 
+## Advanced Features
+
+* **Block Operators**: Construct complex operators from smaller components using `BlockLinearOperator`, `ColumnLinearOperator`, and `RowLinearOperator`. This is ideal for coupled inverse problems.
+* **Parallelisation**: Many expensive operations are parallelized with `joblib`, including dense matrix construction and randomized algorithms.
+
 ## Installation
 
-The package can be installed directly using pip:
+The package can be installed directly using pip. By default, this will perform a minimal installation.
 
 ```bash
+# Minimal installation
 pip install pygeoinf
 ```
+
+To include the functionality for functions on the sphere, you can install the `sphere` extra. This provides support for `pyshtools` and `Cartopy`.
+
+```bash
+# Installation with sphere-related features
+pip install pygeoinf[sphere]
+```
+
 For development, you can clone the repository and install using Poetry:
 
 ```bash
@@ -43,6 +58,7 @@ git clone https://github.com/da380/pygeoinf.git
 cd pygeoinf
 poetry install
 ```
+
 You can install all optional dependencies for development—including tools for running the test suite, 
 building the documentation, and running the Jupyter tutorials—by using the ```--with``` flag and specifying the ```dev``` group.
 
@@ -212,20 +228,30 @@ The output of the above script will look similar to the following figure:
 * NumPy
 * SciPy
 * Matplotlib
-* pyshtools (for `sphere.py`)
-* Cartopy (for plotting in `sphere.py`)
+* joblib
 
-## Future Plans
+### Optional (`sphere`)
+
+* pyshtools
+* Cartopy
+
+## Recent Updates
+
+`pygeoinf` is under active development, and recent updates have expanded its capabilities to address a broader range of geophysical problems. Key improvements include:
 
-`pygeoinf` is under active development. Current work is focused on expanding the library's capabilities to address a broader range of geophysical problems. Key areas for development include:
+* **Non-Linear Inverse Problems**: The library now supports non-linear inverse problems through the `NonLinearOperator` and `NonLinearForm` classes. This allows you to define and solve problems where the relationship between model parameters and data is non-linear. The framework includes support for Fréchet derivatives, enabling the use of gradient-based optimisation methods.
 
-* **Generalised Backus-Gilbert Methods**: Implementation of a generalised Backus-Gilbert framework for linear inference problems. The focus will be on constructing direct estimates of specific properties of interest (i.e., linear functionals of the model) from data, without needing to first solve for the full model itself.
+* **Advanced Optimisation Algorithms**: To complement the non-linear framework, `pygeoinf` now includes a suite of optimisation algorithms. You can use the custom `GradientDescent` solver or leverage the power of SciPy's optimization library with methods like 'BFGS', 'L-BFGS-B', and 'Newton-CG'. Derivative-free methods such as 'Powell' and 'Nelder-Mead' are also supported for problems where gradients are unavailable.
+
+* **Backus-Gilbert Methods**: The foundations for the Backus-Gilbert method have been implemented. While this feature is still evolving, the core components are in place for you to begin exploring this powerful inference technique.
+
+## Future Plans
 
-* **Non-linear Optimisation**: Extension of the current optimisation framework to handle non-linear inverse problems. This will involve creating a general interface where users can provide their own non-linear forward mapping, a misfit functional, and methods for computing gradients (and optionally Hessians) for use in gradient-based optimisation algorithms.
+Future development will focus on the following areas:
 
-* **Non-linear Bayesian Inference**: Development of methods for non-linear Bayesian problems. Planned approaches include linearizing the problem around the maximum a posteriori (MAP) solution to estimate posterior uncertainty, and using this linearization to construct efficient proposal distributions for Markov chain Monte Carlo (MCMC) sampling methods.
+* **Non-linear Bayesian Inference**: We plan to develop methods for non-linear Bayesian problems, including techniques for linearizing the problem around the maximum a posteriori (MAP) solution to estimate posterior uncertainty. This will also involve constructing efficient proposal distributions for Markov chain Monte Carlo (MCMC) sampling methods.
 
-* **New Geophysical Hilbert Spaces**: Addition of further `HilbertSpace` implementations tailored to specific geophysical applications. A primary focus will be on creating spaces for functions defined within a **spherical annulus** (spherical shell), which is essential for problems in global seismology and mantle tomography.
+* **New Geophysical Hilbert Spaces**: We will be adding more `HilbertSpace` implementations for specific geophysical applications. A key focus will be on creating spaces for functions defined within a **spherical annulus** (spherical shell), which is crucial for problems in global seismology and mantle tomography.
 
 
 ## Contributing

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/__init__.py

@@ -85,3 +85,70 @@ from .backus_gilbert import HyperEllipsoid
 from .nonlinear_optimisation import (
     ScipyUnconstrainedOptimiser,
 )
+
+
+__all__ = [
+    # random_matrix
+    "fixed_rank_random_range",
+    "variable_rank_random_range",
+    "random_range",
+    "random_svd",
+    "random_eig",
+    "random_cholesky",
+    "random_diagonal",
+    # hilbert_space
+    "HilbertSpace",
+    "DualHilbertSpace",
+    "EuclideanSpace",
+    "HilbertModule",
+    "MassWeightedHilbertSpace",
+    "MassWeightedHilbertModule",
+    # nonlinear_forms
+    "NonLinearForm",
+    # linear_forms
+    "LinearForm",
+    # nonlinear_operators
+    "NonLinearOperator",
+    # linear_operators
+    "LinearOperator",
+    "MatrixLinearOperator",
+    "DenseMatrixLinearOperator",
+    "SparseMatrixLinearOperator",
+    "DiagonalSparseMatrixLinearOperator",
+    "NormalSumOperator",
+    # gaussian_measure
+    "GaussianMeasure",
+    # direct_sum
+    "HilbertSpaceDirectSum",
+    "BlockStructure",
+    "BlockLinearOperator",
+    "ColumnLinearOperator",
+    "RowLinearOperator",
+    "BlockDiagonalLinearOperator",
+    # linear_solvers
+    "LinearSolver",
+    "DirectLinearSolver",
+    "LUSolver",
+    "CholeskySolver",
+    "EigenSolver",
+    "IterativeLinearSolver",
+    "ScipyIterativeSolver",
+    "CGMatrixSolver",
+    "BICGMatrixSolver",
+    "BICGStabMatrixSolver",
+    "GMRESMatrixSolver",
+    "CGSolver",
+    # forward_problem
+    "ForwardProblem",
+    "LinearForwardProblem",
+    # linear_optimisation
+    "LinearLeastSquaresInversion",
+    "LinearMinimumNormInversion",
+    # linear_bayesian
+    "LinearBayesianInversion",
+    "LinearBayesianInference",
+    # backus_gilbert
+    "HyperEllipsoid",
+    # nonlinear_optimisation
+    "ScipyUnconstrainedOptimiser",
+]

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/backus_gilbert.py

@@ -8,8 +8,6 @@ from .hilbert_space import HilbertSpace, Vector
 from .linear_operators import LinearOperator
 from .nonlinear_forms import NonLinearForm
 
-from .forward_problem import LinearForwardProblem
-from .inversion import LinearInference
 
 
 class HyperEllipsoid:

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/checks/nonlinear_operators.py

@@ -7,7 +7,7 @@ from typing import TYPE_CHECKING
 import numpy as np
 
 if TYPE_CHECKING:
-    from ..linear_operators import LinearOperator
+    pass
 
 
 class NonLinearOperatorAxiomChecks:

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/direct_sum.py

@@ -26,12 +26,10 @@ from abc import ABC, abstractmethod
 from typing import List, Any
 import numpy as np
 from scipy.linalg import block_diag
-from joblib import Parallel, delayed
 
 from .hilbert_space import HilbertSpace
 from .linear_operators import LinearOperator
 from .linear_forms import LinearForm
-from .parallel import parallel_compute_dense_matrix_from_scipy_op
 
 
 class HilbertSpaceDirectSum(HilbertSpace):

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/gaussian_measure.py

@@ -20,7 +20,7 @@ Key Features
 """
 
 from __future__ import annotations
-from typing import Callable, Optional, Any, List, TypeVar, TYPE_CHECKING
+from typing import Callable, Optional, Any, List, TYPE_CHECKING
 
 import numpy as np
 from scipy.linalg import eigh
@@ -40,6 +40,12 @@ from .direct_sum import (
 )
 
 
+# This block is only processed by type checkers, not at runtime.
+if TYPE_CHECKING:
+    from .hilbert_space import HilbertSpace
+    from .typing import Vector
+
+
 class GaussianMeasure:
     """
     Represents a Gaussian measure on a Hilbert space.

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/linear_forms.py

@@ -18,7 +18,7 @@ from .nonlinear_forms import NonLinearForm
 
 # This block only runs for type checkers, not at runtime
 if TYPE_CHECKING:
-    from .hilbert_space import HilbertSpace, EuclideanSpace, Vector
+    from .hilbert_space import HilbertSpace, Vector
     from .linear_operators import LinearOperator
 
 

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/linear_operators.py

@@ -25,7 +25,6 @@ from collections import defaultdict
 import numpy as np
 import scipy.sparse as sp
 from scipy.sparse.linalg import LinearOperator as ScipyLinOp
-from scipy.sparse import diags
 
 
 from joblib import Parallel, delayed
@@ -46,7 +45,7 @@ from .checks.linear_operators import LinearOperatorAxiomChecks
 
 # This block only runs for type checkers, not at runtime
 if TYPE_CHECKING:
-    from .hilbert_space import HilbertSpace, EuclideanSpace
+    from .hilbert_space import HilbertSpace
     from .linear_forms import LinearForm
 
 

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/nonlinear_forms.py

@@ -16,7 +16,6 @@ if TYPE_CHECKING:
     from .hilbert_space import HilbertSpace, Vector
     from .linear_forms import LinearForm
     from .linear_operators import LinearOperator
-    from .nonlinear_operators import NonLinearOperator
 
 
 class NonLinearForm:

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/nonlinear_operators.py

@@ -8,7 +8,7 @@ algebraic operations and an interface for the Frécher derivative.
 """
 
 from __future__ import annotations
-from typing import Callable, Optional, Any, TYPE_CHECKING
+from typing import Callable, Any, TYPE_CHECKING
 
 
 from .checks.nonlinear_operators import NonLinearOperatorAxiomChecks
@@ -16,7 +16,7 @@ from .checks.nonlinear_operators import NonLinearOperatorAxiomChecks
 
 # This block only runs for type checkers, not at runtime
 if TYPE_CHECKING:
-    from .hilbert_space import HilbertSpace, EuclideanSpace, Vector
+    from .hilbert_space import HilbertSpace, Vector
     from .linear_operators import LinearOperator
 
 

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/symmetric_space/sphere.py

@@ -29,10 +29,16 @@ import matplotlib.ticker as mticker
 import numpy as np
 from scipy.sparse import diags, coo_array
 
-import pyshtools as sh
-import cartopy.crs as ccrs
-import cartopy.feature as cfeature
-from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
+try:
+    import pyshtools as sh
+    import cartopy.crs as ccrs
+    import cartopy.feature as cfeature
+    from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
+except ImportError:
+    raise ImportError(
+        "pyshtools and cartopy are required for the sphere module. "
+        "Please install them with 'pip install pygeoinf[sphere]'"
+    )
 
 from pygeoinf.hilbert_space import (
     HilbertModule,
@@ -599,7 +605,9 @@ class Sobolev(SphereHelper, MassWeightedHilbertModule, AbstractInvariantSobolevS
         summation = 1.0
         l = 0
         err = 1.0
-        sobolev_func = lambda deg: (1.0 + scale**2 * deg * (deg + 1)) ** order
+
+        def sobolev_func(deg):
+            return (1.0 + scale**2 * deg * (deg + 1)) ** order
 
         while err > rtol:
             l += 1

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pygeoinf/symmetric_space/symmetric_space.py

@@ -35,7 +35,7 @@ from typing import Callable, Any, List
 import numpy as np
 from scipy.sparse import diags
 
-from pygeoinf.hilbert_space import EuclideanSpace, HilbertSpace
+from pygeoinf.hilbert_space import EuclideanSpace
 from pygeoinf.linear_operators import LinearOperator
 from pygeoinf.linear_forms import LinearForm
 from pygeoinf.gaussian_measure import GaussianMeasure

{pygeoinf-1.2.8 → pygeoinf-1.3.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pygeoinf"
-version = "1.2.8"
+version = "1.3.0"
 description = "A package for solving geophysical inference and inverse problems"
 authors = ["David Al-Attar and Dan Heathcote"]
 readme = "README.md"
@@ -10,12 +10,12 @@ license = "BSD-3-Clause"
 python = ">=3.11"
 numpy = ">=1.26.0"
 scipy = ">=1.16.1"
-pyshtools = ">=4.0.0"
 matplotlib = ">=3.0.0"
 pyqt6 = ">=6.0.0"
-Cartopy = "^0.23.0"
 joblib = "^1.5.2"
 
+[tool.poetry.extras]
+sphere = ["pyshtools", "Cartopy"]
 
 [tool.poetry.group.dev]
 optional = true
@@ -28,7 +28,22 @@ jupyter = "^1.1.1"
 furo = "^2025.7.19"
 sphinx = "<8.2"
 nbsphinx = "^0.9.7"
+pyshtools = ">=4.0.0"
+Cartopy = "^0.23.0"
+ruff = "^0.5.5"
 
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+
+# --- Added Ruff Configuration ---
+[tool.ruff]
+
+[tool.ruff.lint.per-file-ignores]
+# For any file in the "tests/" directory, ignore the lambda assignment warning (E731).
+"tests/*" = ["E731", "E741"]
+
+# For the sphere.py file, where 'l' is a common variable name for spherical
+# harmonic degree, ignore the ambiguous variable name warning (E741).
+"pygeoinf/symmetric_space/sphere.py" = ["E741"]