liesel-gam 0.1.0a3__tar.gz → 0.1.1__tar.gz

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/.gitignore

@@ -185,3 +185,5 @@ notebooks/multivariate/test_tx_optim.ipynb
 /doctests
 notebooks/univariate/test_ps_nosmooth.ipynb
 notebooks/univariate/test_ps_smooth_constant_prior.ipynb
+notebooks/univariate/test_ps_vi.ipynb
+notebooks/univariate/test_ps_with_optim.ipynb

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: liesel_gam
-Version: 0.1.0a3
+Version: 0.1.1
 Summary: Functionality for Generalized Additive Models in Liesel
 Author: Johannes Brachem
 License-File: LICENSE
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: <3.14,>=3.13
 Requires-Dist: formulaic>=1.2.1
 Requires-Dist: liesel>=0.4.2
+Requires-Dist: plotnine>=0.14.5
 Requires-Dist: smoothcon>=0.0.9
 Description-Content-Type: text/markdown
 
@@ -97,6 +98,13 @@ You can also install the development version from GitHub via pip:
 pip install git+https://github.com/liesel-devs/liesel_gam.git
 ```
 
+Since liesel-GAM interfaces with R via `ryp` under the hood,
+you also need the R packages `{arrow}` and `{svglite}` to be available on your system:
+
+```bash
+Rscript -e "install.packages(c('arrow', 'svglite'))"
+```
+
 ## Contents
 
 - [Short usage illustration](https://github.com/liesel-devs/liesel_gam?tab=readme-ov-file#illustrations)

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/README.md

@@ -80,6 +80,13 @@ You can also install the development version from GitHub via pip:
 pip install git+https://github.com/liesel-devs/liesel_gam.git
 ```
 
+Since liesel-GAM interfaces with R via `ryp` under the hood,
+you also need the R packages `{arrow}` and `{svglite}` to be available on your system:
+
+```bash
+Rscript -e "install.packages(c('arrow', 'svglite'))"
+```
+
 ## Contents
 
 - [Short usage illustration](https://github.com/liesel-devs/liesel_gam?tab=readme-ov-file#illustrations)

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/docs/source/index.rst

@@ -13,6 +13,14 @@ The library can be installed from PYPI:
 
     $ pip install liesel_gam
 
+Since liesel-GAM interfaces with R via ``ryp`` under the hood,
+you also need the R packages ``{arrow}`` and ``{svglite}`` to be available on your system:
+
+.. code:: bash
+
+    $ Rscript -e "install.packages(c('arrow', 'svglite'))"
+
+
 Demo Notebooks
 ---------------
 
@@ -44,7 +52,7 @@ Relevant Literature
 --------------------
 
 Fahrmeier et al. (2013) is a textbook that introduces structured additive
-regression concepts form the ground up. Wood (2017) is another seminal textbook on
+regression concepts from the ground up. Wood (2017) is another seminal textbook on
 generalized additive models. The R package mgcv provides many basis functions and
 penalty matrices that we use in ``liesel_gam``.
 
@@ -70,6 +78,7 @@ regression.
 
 
 
+
 API Reference
 -------------
 
@@ -182,6 +191,16 @@ Other
     ~liesel_gam.demo_data_ta
     ~liesel_gam.LinearConstraintEVD
 
+.. rubric:: In/Out
+
+.. autosummary::
+    :toctree: generated
+    :caption: In/Out
+    :nosignatures:
+
+    ~liesel_gam.io.read_bnd
+    ~liesel_gam.io.polygon_is_closed
+
 Experimental
 ***************
 
@@ -197,6 +216,14 @@ future.
     ~liesel_gam.experimental.BSplineApprox
 
 
+.. toctree::
+   :hidden:
+   :caption: Help
+   :maxdepth: 1
+
+   troubleshooting
+
+
 Acknowledgements and Funding
 --------------------------------
 

liesel_gam-0.1.1/docs/source/troubleshooting.md

@@ -0,0 +1,21 @@
+# Troubleshooting
+
+## Problems with interfacing to R / Problems with ryp
+
+We use the Python package [`ryp`](https://github.com/Wainberg/ryp) to interface to R.
+It uses the R installation pointed to by the environment variable `R_HOME`, or if
+`R_HOME` is not defined by running `R HOME`. If you encounter problems with the
+interface to R, it may be a solution to set the `R_HOME` environment variable manually.
+
+Here, as an example, we set `R_HOME` to an R installation in a conda environment:
+
+```bash
+export R_HOME=conda/envs/r-renv/lib/R
+```
+
+In some cases, you may also need to explicitly append the R library to the environment
+variable `LD_LIBRARY_PATH`:
+
+```bash
+export LD_LIBRARY_PATH="$R_HOME/lib:$LD_LIBRARY_PATH"
+```

liesel_gam-0.1.1/docs/source/troubleshooting.rst

@@ -0,0 +1,2 @@
+.. include:: troubleshooting.md
+   :parser: myst_parser.sphinx_

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/docs/source/welcome.md

@@ -1,5 +1,5 @@
 This title is short and catchy, but does not convey the full range of models covered
-by this library. We could also say:
+by this Python library. We could also say:
 
 - Bayesian Generalized Additive Models for **Location, Scale, and Shape** (and beyond)
 - Bayesian **Structured Additive Distributional Regression**
@@ -15,8 +15,8 @@ formulas, known to many from the formula syntax in R.
 
 Some technical highlights:
 
-- Express Bayesian models as probabilistic graphical models via [liesel.model](https://github.com/liesel-devs/liesel)
-- Build custom MCMC algorithms using Gibbs samplers, Hamiltonian Monte Carlo (HMC),
+- Express Bayesian models as probabilistic graphical models in Python via [liesel.model](https://github.com/liesel-devs/liesel)
+- Build custom MCMC algorithms in Python, including Gibbs samplers, Hamiltonian Monte Carlo (HMC),
   the iteratively reweighted least squares sampler (IWLS), and more via
    [liesel.goose](https://github.com/liesel-devs/liesel)
 - Speed up models using just-in-time compilation and automatic differentiation via [JAX](https://docs.jax.dev/en/latest/), since Liesel builds on JAX.

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/pyproject.toml

@@ -8,6 +8,7 @@ dependencies = [
     "formulaic>=1.2.1",
     "liesel>=0.4.2",
     "smoothcon>=0.0.9",
+    "plotnine>=0.14.5"
 ]
 authors = [{ name = "Johannes Brachem" }]
 keywords = ["statistics", "machine-learning"]

liesel_gam-0.1.1/src/liesel_gam/__about__.py

@@ -0,0 +1 @@
+__version__ = "0.1.1"

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/src/liesel_gam/__init__.py

@@ -1,6 +1,7 @@
 import os
 
 from . import experimental as experimental
+from . import io as io
 from .__about__ import __version__ as __version__
 from .basis import Basis as Basis
 from .basis import LinBasis as LinBasis

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/src/liesel_gam/basis.py

@@ -19,11 +19,11 @@ ArrayLike = jax.typing.ArrayLike
 
 
 def make_callback(function, output_shape, dtype, m: int = 0):
-    if len(output_shape):
-        k = output_shape[-1]
+    k = output_shape[-1] if len(output_shape) else None
 
     def fn(x, **basis_kwargs):
         n = jnp.shape(jnp.atleast_1d(x))[0]
+
         if len(output_shape) == 2:
             shape = (n - m, k)
         elif len(output_shape) == 1:
@@ -35,11 +35,17 @@ def make_callback(function, output_shape, dtype, m: int = 0):
                 "Return shape of 'basis_fn(value)' must"
                 f" have <= 2 dimensions, got {output_shape}"
             )
-        result_shape = jax.ShapeDtypeStruct(shape, dtype)
-        result = jax.pure_callback(
-            function, result_shape, x, vmap_method="sequential", **basis_kwargs
+
+        sig = jax.ShapeDtypeStruct(shape, dtype)
+
+        # ordered=True enforces sequencing of callback executions
+        return jax.experimental.io_callback(
+            function,
+            sig,
+            x,
+            ordered=True,
+            **basis_kwargs,
         )
-        return result
 
     return fn
 
@@ -55,12 +61,13 @@ class Basis(UserVar):
     """
     General basis for a structured additive term.
 
-    The ``Basis`` class wraps either a provided observation variable or a raw array and
-    a basis-generation function. It constructs an internal calculation node that
-    produces the basis (design) matrix used by smooth terms. The basis function may be
-    executed via a callback that does not need to be jax-compatible (the default,
-    potentially slow) with a jax-compatible function that is included in
-    just-in-time-compilation (when ``use_callback=False``).
+    The ``Basis`` class wraps an observation variable (or an array) and a
+    basis-generation function. It constructs an internal calculation node that produces
+    the basis (design) matrix by computing ``basis_fn(value)``. The basis function may
+    be executed via a callback, in which case it does not need to be jax-compatible.
+    This is the default, but it is potentially very slow, if the value of the basis
+    needs to be recomputed during estimation. We recommend it only for bases that remain
+    static during estimation.
 
     Parameters
     ----------
@@ -139,10 +146,9 @@ class Basis(UserVar):
     ... )
     Basis(name="B(x)")
 
-    Implementing a fixed basis matrix (without using the basis function). This is
-    not recommended, because it means you cannot simply supply new covariate values
-    to :meth:`liesel.model.Model.predict` for evaluating the basis matrix for
-    predictions.
+    Implementing a fixed basis matrix (without using the basis function). This is not
+    recommended, because it means you cannot simply supply new covariate values to
+    :meth:`liesel.model.Model.predict` for evaluating the basis matrix for predictions.
 
     >>> from liesel.contrib.splines import equidistant_knots, basis_matrix
     >>> import liesel_gam as gam

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/src/liesel_gam/constraint.py

@@ -82,11 +82,12 @@ class LinearConstraintEVD:
         AtA = A.T @ A
         evals, evecs = jnp.linalg.eigh(AtA)
 
-        if evecs[0, 0] < 0:
-            evecs = -evecs
+        signs = jnp.sign(evecs[0, :])
+        signs = jnp.where(signs == 0, 1.0, signs)
+        evecs = evecs * signs
 
         rank = jnp.linalg.matrix_rank(AtA)
-        Abar = evecs[:-rank]
+        Abar = evecs[:, :-rank].T
 
         A_stacked = jnp.r_[A, Abar]
         C_stacked = jnp.linalg.inv(A_stacked)

liesel_gam-0.1.1/src/liesel_gam/io.py

@@ -0,0 +1,132 @@
+import logging
+from pathlib import Path
+
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+
+def read_bnd(
+    filename: str | Path,
+    delimiter: str = ",",
+) -> dict[str, np.typing.NDArray]:
+    """
+    Reads a .bnd file with geographical information, returns a polys dictionary.
+
+    Parameters
+    ----------
+    filename
+        Filename.
+    delimiter
+        Delimiter
+
+    Notes
+    -----
+    The expected file format looks like this::
+
+        "A", 66
+        25.6422, -17.8037
+        25.6477, -17.7607
+        ...
+        "B", 192
+        27.276, -17.0096
+        27.6848, -17.1684
+        ...
+
+    Where the lines ``"A",66`` and ``"B",192`` are header lines that indicate the region
+    label, and the number of following lines that define the polygon for the respective
+    region. In this case, the region labelled ``"A"`` is defined by the following 66
+    lines, and the region labelled ``"B"`` is defined by the following 192 lines.
+    """
+    polygons = {}
+
+    with open(filename) as f:
+        while True:
+            header = f.readline()
+            if not header:
+                break  # EOF
+
+            header = header.strip()
+            if not header:
+                continue  # skip empty lines
+
+            parts = header.split(delimiter)
+            if len(parts) != 2:
+                raise ValueError(f"Invalid header line: {header}")
+
+            label, n_points = parts
+            label = label.strip().strip("\"'")
+
+            try:
+                n_points_int = int(n_points)
+            except ValueError as e:
+                raise ValueError(f"Invalid number of points in header: {header}") from e
+
+            coords = []
+            for _ in range(n_points_int):
+                line = f.readline()
+                if not line:
+                    raise ValueError("Unexpected end of file while reading coordinates")
+
+                line = line.strip()
+                if not line:
+                    raise ValueError("Unexpected empty line while reading coordinates")
+
+                xy = line.split(delimiter)
+                if len(xy) != 2:
+                    raise ValueError(f"Invalid coordinate line: {line}")
+
+                x, y = map(float, xy)
+                coords.append([x, y])
+
+            polygons[label] = np.array(coords, dtype=float)
+
+    for label, poly in polygons.items():
+        if not polygon_is_closed(poly):
+            msg = (
+                f"Polygon of region with label '{label}' does not appear to be closed "
+                "(first and last point are not equal)."
+            )
+            logger.warning(msg)
+
+    return polygons
+
+
+def polygon_is_closed(
+    poly: np.typing.ArrayLike,
+    *,
+    atol: float = 1e-12,
+    rtol: float = 0.0,
+    require_min_points: bool = True,
+) -> bool:
+    """
+    Validate that a polygon is closed: first vertex equals last vertex (within
+    tolerance).
+
+    Parameters
+    ----------
+    poly : array-like, shape (n, 2)
+        Polygon vertices.
+    atol, rtol : float
+        Absolute / relative tolerances used by np.allclose.
+    require_min_points : bool
+        If True, require at least 4 points for a closed polygon (first==last + >=3
+        distinct vertices).
+
+    Returns
+    -------
+        True if closed, else False.
+    """
+    arr = np.asarray(poly, dtype=float)
+
+    if arr.ndim != 2 or arr.shape[1] != 2:
+        raise ValueError(f"Expected shape (n, 2), got {arr.shape}")
+
+    n = arr.shape[0]
+    if n == 0:
+        return False
+
+    if require_min_points and n < 4:
+        return False
+
+    return np.allclose(arr[0], arr[-1], atol=atol, rtol=rtol)

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/src/liesel_gam/term_builder.py

@@ -62,7 +62,10 @@ class TermBuilder:
         Defines the default inference specification for terms created by this builder.
         Note that this inference is only used for the coefficient variables
         of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for the
-        scale variables (:attr:`.StrctTerm.scale`).
+        scale variables (:attr:`.StrctTerm.scale`). The default
+        ``gs.MCMCSpec(gs.IWLSKernel.untuned)`` is an iteratively-reweighted least
+        squares kernel without step size tuning, see
+        :meth:`liesel.goose.IWLSKernel.untuned`.
     default_scale_fn
         A function or :class:`.VarIGPrior` object that defines the default scale
         for structured additive terms initialized by this builder. If this is a
@@ -72,11 +75,13 @@ class TermBuilder:
         ``var ~ InverseGamma(concentration, scale)``, with concentration and scale
         given by the :class:`.VarIGPrior` object. For most terms, this
         will mean that a fitting Gibbs sampler can be automatically set up for
-        ``var``. The exceptions to this rule are :meth:`.ta`, :meth:`.tf`, and
+        ``var``. The exceptions to this rule are :meth:`.tf` and
         :meth:`.tx`. Note that, if you supply a custom default scale function, you
         should make sure that the ``inference`` attribute of your custom scale
         is defined, otherwise your custom scale may not be included in MCMC
-        sampling.
+        sampling. The default is ``VarIGPrior(1.0, 0.005)``, which leads to an
+        inverse Gamma prior on the level of the variance parameter, i.e.
+        :math:`\tau^2 \sim \operatorname{InverseGamma}(1.0, 0.005)`.
 
     See Also
     --------
@@ -441,8 +446,10 @@ class TermBuilder:
             prior.
         inference
             An optional :class:`liesel.goose.MCMCSpec` instance (or other valid
-            inference object). If omitted, the term's default inference specification
-            is used.
+            inference object).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         context
             Dictionary of additional Python objects that should be made available to
             formulaic when constructing the design matrix. Gets passed to
@@ -571,13 +578,31 @@ class TermBuilder:
         formula
             Right-hand side of a model formula, as understood by formulaic_. Most of
             formulaic's grammar_ is supported. See notes for details.
-        prior
-            An optional prior for this term's coefficient. The default is a constant
-            prior.
+        scale
+            Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
+
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
+            - If you pass a ``float``, this will be taken as the constant value of
+              the scale, and the scale will not be estimated as part of the model
+              without further action.
+            - If you pass a :class:`liesel.model.Var`, this will be used as the scale.
+              Make sure to define the ``inference`` attribute of your custom
+              scale variable (or a latent, transformed version of it).
+            - If you pass a :class:`.VarIGPrior`, a scale variable will be set up for
+              you using :class:`.ScaleIG`. This means, the scale will be
+              :math:`\tau`, with an iverse Gamma prior on its square, i.e.
+              :math:`\tau^2 \\sim \\operatorname{InverseGamma}(a, b)`, where a and b
+              are taken from the :class:`.VarIGPrior` object. A fitting Gibbs kernel
+              will be set up automatically to sample :math:`\tau^2` in this case,
+              see :class:`.ScaleIG` for details.
         inference
             An optional :class:`liesel.goose.MCMCSpec` instance (or other valid
-            inference object). If omitted, the term's default inference specification
-            is used.
+            inference object).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         context
             Dictionary of additional Python objects that should be made available to
             formulaic when constructing the design matrix. Gets passed to
@@ -692,6 +717,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -710,6 +738,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty_order
             Order of the penalty.
         knots
@@ -816,6 +847,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -834,6 +868,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty_order
             Order of the penalty.
         knots
@@ -940,6 +977,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -958,6 +998,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty_order
             Order of the penalty.
         knots
@@ -1066,6 +1109,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1084,6 +1130,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         basis_degree
             Degree of the polynomials used in the B-spline basis function. Default is 3
             for cubic B-splines.
@@ -1196,6 +1245,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1214,6 +1266,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         basis_degree
             Degree of the polynomials used in the B-spline basis function. Default is 3
             for cubic B-splines.
@@ -1338,6 +1393,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1356,6 +1414,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         basis_degree
             Degree of the polynomials used in the B-spline basis function. Default is 3
             for cubic B-splines.
@@ -1477,6 +1538,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1495,6 +1559,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         basis_degree
             Degree of the polynomials used in the B-spline basis function. Default is 3
             for cubic B-splines.
@@ -1602,6 +1669,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1620,6 +1690,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty
             Custom penalty matrix to use. Default is an iid penalty.
         factor_scale
@@ -1717,6 +1790,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1735,6 +1811,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty
             Custom penalty matrix to use. Default is an iid penalty.
         factor_scale
@@ -1920,6 +1999,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -1938,6 +2020,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         polys
             Dictionary of arrays. The keys of the dict are the region labels. The
             corresponding values define the region by defining polygons. The
@@ -2095,6 +2180,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -2113,6 +2201,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         use_callback
             If *True*, the basis function is evaluated using a Python callback,
             which means that it does not have to be jit-compatible via JAX. This also
@@ -2239,6 +2330,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -2257,6 +2351,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         kernel_name
             Selects the kernel / covariance function to use.
         linear_trend
@@ -2367,6 +2464,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -2385,6 +2485,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty_order
             Order of the penalty. Quote from mgcv: "The default is to set this to the
             smallest value satisfying ``2*penalty_order > d+1`` where ``d`` is the
@@ -2494,6 +2597,9 @@ class TermBuilder:
         scale
             Scale parameter passed to the coefficient prior, :attr:`.StrctTerm.scale`.
 
+            - If ``"default"``, the scale will be initialized according to the default
+              scale function defined for this :class:`.TermBuilder` instance.
+              Please refer to the TermBuilder documentation for more information.
             - If you pass a ``float``, this will be taken as the constant value of
               the scale, and the scale will not be estimated as part of the model
               without further action.
@@ -2512,6 +2618,9 @@ class TermBuilder:
             Note that this inference is only used for the coefficient variables
             of the terms created by this builder (:attr:`.StrctTerm.coef`), *not* for
             the scale variables (:attr:`.StrctTerm.scale`).
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         penalty_order
             Order of the penalty. Quote from mgcv: "The default is to set this to the
             smallest value satisfying ``2*penalty_order > d+1`` where ``d`` is the
@@ -2695,7 +2804,7 @@ class TermBuilder:
         Includes only the tensor product interaction. Corresponds to ``mgcv::ti``.
 
         .. warning::
-            This method remove any default gibbs samplers and replace them with
+            This method removes any default gibbs samplers and replaces them with
             ``scales_inference`` on log level, since the full conditional for the
             variance parameters is not known in closed form for an anisotropic
             tensor product.
@@ -2711,6 +2820,9 @@ class TermBuilder:
             in the notation used in :class:`.StrctTensorProdTerm`.
         inference
             Inference specification for this term's coefficient.
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         scales_inference
             If ``"default"``, uses the default inference passed to the TermBuilder
             upon initialization.
@@ -2885,7 +2997,7 @@ class TermBuilder:
         Corresponds to ``mgcv::te``.
 
         .. warning::
-            This method remove any default gibbs samplers and replace them with
+            This method removes any default gibbs samplers and replaces them with
             ``scales_inference`` on log level, since the full conditional for the
             variance parameters is not known in closed form for an anisotropic
             tensor product.
@@ -2901,6 +3013,9 @@ class TermBuilder:
             in the notation used in :class:`.StrctTensorProdTerm`.
         inference
             Inference specification for this term's coefficient.
+            The default (``"default"``) uses the :class:`.TermBuilder`'s default
+            inference specification defined during initialization. Please refer to
+            the TermBuilder documentation for more information.
         scales_inference
             If ``"default"``, uses the default inference passed to the TermBuilder
             upon initialization.

{liesel_gam-0.1.0a3 → liesel_gam-0.1.1}/uv.lock

@@ -853,6 +853,7 @@ source = { editable = "." }
 dependencies = [
     { name = "formulaic" },
     { name = "liesel" },
+    { name = "plotnine" },
     { name = "smoothcon" },
 ]
 
@@ -878,6 +879,7 @@ dev = [
 requires-dist = [
     { name = "formulaic", specifier = ">=1.2.1" },
     { name = "liesel", specifier = ">=0.4.2" },
+    { name = "plotnine", specifier = ">=0.14.5" },
     { name = "smoothcon", specifier = ">=0.0.9" },
 ]
 

liesel_gam-0.1.0a3/src/liesel_gam/__about__.py

@@ -1 +0,0 @@
-__version__ = "0.1.0-a3"