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

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b12eff3
Fix doc issues
paddyroddy Dec 11, 2025
82458b0
Merge branch 'main' into paddy/issue-880
paddyroddy Dec 15, 2025
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2 changes: 1 addition & 1 deletion glass/_array_api_utils.py
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Original file line number Diff line number Diff line change
@@ -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
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4 changes: 2 additions & 2 deletions glass/algorithm.py
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Expand Up @@ -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.

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10 changes: 5 additions & 5 deletions glass/fields.py
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Expand Up @@ -282,7 +282,7 @@ def discretized_cls(
return gls


@deprecated("use glass.solve_gaussian_spectra() instead")
@deprecated("use :func:`glass.solve_gaussian_spectra` instead")
def lognormal_gls(
cls: AnyArray,
shift: float = 1.0,
Expand Down Expand Up @@ -411,7 +411,7 @@ def _generate_grf(
yield hp.alm2map(alm, nside, pixwin=False, pol=False, inplace=True)


@deprecated("use glass.generate() instead")
@deprecated("use :func:`glass.generate` instead")
def generate_gaussian(
gls: AnyArray,
nside: int,
Expand All @@ -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
Expand Down Expand Up @@ -464,7 +464,7 @@ def generate_gaussian(
yield from generate(fields, gls, nside, ncorr=ncorr, rng=rng)


@deprecated("use glass.generate() instead")
@deprecated("use :func:`glass.generate` instead")
def generate_lognormal(
gls: AnyArray,
nside: int,
Expand All @@ -478,7 +478,7 @@ def generate_lognormal(

.. deprecated:: 2025.1

Use :func:`glass.generate()` instead.
Use :func:`glass.generate` instead.

Parameters
----------
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2 changes: 1 addition & 1 deletion glass/grf/_core.py
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion glass/grf/_solver.py
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion glass/lensing.py
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion glass/points.py
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Expand Up @@ -209,7 +209,7 @@ def positions_from_delta( # noqa: PLR0912, PLR0913, PLR0915
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.linear_bias` or ``'loglinear'`` for
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@paddyroddy paddyroddy Dec 11, 2025

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From reading the code, looks like it should never have been glass.loglinear @ntessore?

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@connoraird connoraird Dec 11, 2025

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If loglinear is needed than we should add :func: too?

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@paddyroddy paddyroddy Dec 11, 2025

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no, loglinear and linear are strings

:func:`glass.loglinear_bias`.
remove_monopole
If true, the monopole of the density contrast
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2 changes: 1 addition & 1 deletion glass/shells.py
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Expand Up @@ -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
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