gh-880: Fix inconsistencies in the documentation rendering (#889)

Author: paddyroddy

glass/_array_api_utils.py

@@ -1,6 +1,6 @@
 """
 Array API Utilities for glass.
-============================
+==============================
 
 This module provides utility functions and classes for working with multiple array
 backends in the glass project, including NumPy, JAX, and array-api-strict. It includes

glass/algorithm.py

@@ -234,15 +234,15 @@ def cov_nearest(
 
     Divides *cov* along rows and columns by the square root of the
     diagonal, then computes the nearest valid correlation matrix using
-    :func:`nearcorr`, before scaling rows and columns back.  The
+    :func:`glass.nearcorr`, before scaling rows and columns back.  The
     diagonal of the input is hence unchanged.
 
     Parameters
     ----------
     cov
         A square matrix (or a stack of matrices).
     tol
-        Tolerance for convergence, see :func:`nearcorr`.
+        Tolerance for convergence, see :func:`glass.nearcorr`.
     niter
         Maximum number of iterations.
 

glass/fields.py

@@ -424,7 +424,7 @@ def generate_gaussian(
 
     .. deprecated:: 2025.1
 
-       Use :func:`glass.generate()` instead.
+       Use :func:`glass.generate` instead.
 
     A generator that iteratively samples HEALPix maps of Gaussian random fields
     with the given angular power spectra ``gls`` and resolution parameter
@@ -478,7 +478,7 @@ def generate_lognormal(
 
     .. deprecated:: 2025.1
 
-       Use :func:`glass.generate()` instead.
+       Use :func:`glass.generate` instead.
 
     Parameters
     ----------

glass/grf/_core.py

@@ -164,7 +164,7 @@ def compute(
 
     See Also
     --------
-    glass.grf.solve: Iterative solver for non-band-limited spectra.
+    :func:`glass.grf.solve`: Iterative solver for non-band-limited spectra.
 
     """
     if t2 is None:

glass/grf/_solver.py

@@ -77,7 +77,7 @@ def solve(  # noqa: PLR0912, PLR0913
 
     See Also
     --------
-    glass.grf.compute : Direct computation for band-limited spectra.
+    :func:`glass.grf.compute`: Direct computation for band-limited spectra.
 
     """
     if t2 is None:

glass/lensing.py

@@ -618,7 +618,7 @@ def deflect(
     Apply deflections to positions.
 
     .. deprecated:: >2025.2
-       Use :func:`displace` instead.
+       Use :func:`glass.displace` instead.
 
     Takes an array of :term:`deflection` values and applies them
     to the given positions.

glass/points.py

@@ -162,7 +162,7 @@ def positions_from_delta(  # noqa: PLR0912, PLR0913, PLR0915
     bias: float | FloatArray | None = None,
     vis: FloatArray | None = None,
     *,
-    bias_model: str | Callable[..., Any] = "linear",
+    bias_model: Callable[..., Any] = linear_bias,
     remove_monopole: bool = False,
     batch: int = 1_000_000,
     rng: np.random.Generator | None = None,
@@ -207,10 +207,8 @@ def positions_from_delta(  # noqa: PLR0912, PLR0913, PLR0915
         Visibility map for the observed points. This is multiplied with
         the full sky number count map, and must hence be of compatible shape.
     bias_model
-        The bias model to apply. If a string, refers to a function in
-        the :mod:`~glass.points` module, e.g. ``'linear'`` for
-        :func:`glass.linear_bias()` or ``'glass.loglinear'`` for
-        :func:`glass.loglinear_bias`.
+        The bias model to apply. For examples, :func:`glass.linear_bias`
+        or :func:`glass.loglinear_bias`.
     remove_monopole
         If true, the monopole of the density contrast
         after biasing is fixed to zero.
@@ -239,13 +237,9 @@ def positions_from_delta(  # noqa: PLR0912, PLR0913, PLR0915
     if rng is None:
         rng = np.random.default_rng(42)
 
-    # get the bias model
-    if isinstance(bias_model, str):
-        bias_model_callable = globals()[f"{bias_model}_bias"]
-    elif not callable(bias_model):
-        raise TypeError("bias_model must be string or callable")
-    else:
-        bias_model_callable = bias_model
+    # ensure bias_model is a function
+    if not callable(bias_model):
+        raise TypeError("bias_model must be callable")
 
     # broadcast inputs to common shape of extra dimensions
     inputs: list[tuple[float | FloatArray, int]] = [(ngal, 0), (delta, 1)]
@@ -263,11 +257,7 @@ def positions_from_delta(  # noqa: PLR0912, PLR0913, PLR0915
     # iterate the leading dimensions
     for k in np.ndindex(dims):
         # compute density contrast from bias model, or copy
-        n = (
-            np.copy(delta[k])
-            if bias is None
-            else bias_model_callable(delta[k], bias[k])
-        )
+        n = np.copy(delta[k]) if bias is None else bias_model(delta[k], bias[k])
 
         # remove monopole if asked to
         if remove_monopole:

glass/shells.py

@@ -609,7 +609,7 @@ def partition(
     where :math:`\lambda` is a multiplier to enforce the integral
     constraints.
 
-    The :func:`glass.partition()` function implements a number of methods to
+    The :func:`glass.partition` function implements a number of methods to
     obtain a solution:
 
     If ``method="nnls"`` (the default), obtain a partition from a

tests/benchmarks/test_points.py

@@ -28,7 +28,7 @@
     ("bias", "bias_model"),
     [
         (None, lambda x: x),
-        (0.8, "linear"),
+        (0.8, glass.linear_bias),
     ],
 )
 @pytest.mark.parametrize("remove_monopole", [True, False])
@@ -38,7 +38,7 @@ def test_positions_from_delta(  # noqa: PLR0913
     generator_consumer: GeneratorConsumer,
     xpb: ModuleType,
     bias: float,
-    bias_model: str | Callable[[int], int],
+    bias_model: Callable[[int], int],
     remove_monopole: bool,  # noqa: FBT001
 ) -> None:
     """Benchmarks for glass.positions_from_delta."""

tests/core/test_points.py

@@ -249,7 +249,7 @@ def test_positions_from_delta(  # noqa: PLR0915
 
     # test TypeError
 
-    with pytest.raises(TypeError, match="bias_model must be string or callable"):
+    with pytest.raises(TypeError, match="bias_model must be callable"):
         next(glass.positions_from_delta(ngal, delta, bias, vis, bias_model=0))