update citations for html (#232)

Linked to
mesh-adaptation/docs#50

should be evaluated in combination with:
mesh-adaptation/docs#50
mesh-adaptation/animate#160
mesh-adaptation/movement#132

Locally the main warning remaining after all the PRs should be about
'duplicate_citations', though all citations should still render.

demos/gray_scott.py

@@ -160,5 +160,5 @@ def qoi():
 #
 # .. rubric:: References
 #
-# .. bibliography:: demo_references.bib
+# .. bibliography::
 #    :filter: docname in docnames

demos/point_discharge2d.py

@@ -9,7 +9,7 @@
 #
 # Consider the same steady-state advection-diffusion test case as in the
 # motivation for the Goalie manual: the "point discharge with diffusion"
-# test case from :cite:`RCJ:14`. In this test case, we solve
+# test case from :cite:`Riadh:2014`. In this test case, we solve
 #
 # .. math::
 #   \left\{\begin{array}{rl}
@@ -39,11 +39,11 @@ def get_function_spaces(mesh):
 
 
 # Point sources are difficult to represent in numerical models. Here we
-# follow :cite:`WBHP:22` in using a Gaussian approximation. Let
+# follow :cite:`Wallwork:2022` in using a Gaussian approximation. Let
 # :math:`(x_0,y_0)=(2,5)` denote the point source location and
 # :math:`r=0.05606388` be a radius parameter, which has been calibrated
 # so that the finite element approximation is as close as possible to the
-# analytical solution, in some sense (see :cite:`WBHP:22` for details). ::
+# analytical solution, in some sense (see :cite:`Wallwork:2022` for details). ::
 
 
 def source(mesh):
@@ -210,3 +210,9 @@ def qoi():
 # metric-based mesh adaptation to the point discharge test case considered here.
 #
 # This tutorial can be dowloaded as a `Python script <point_discharge2d.py>`__.
+#
+#
+# .. rubric:: References
+#
+# .. bibliography::
+#    :filter: docname in docnames

demos/solid_body_rotation.py

@@ -234,5 +234,5 @@ def qoi():
 #
 # .. rubric:: References
 #
-# .. bibliography:: demo_references.bib
+# .. bibliography::
 #    :filter: docname in docnames

goalie/go_mesh_seq.py

@@ -72,9 +72,9 @@ def get_enriched_mesh_seq(self, enrichment_method="p", num_enrichments=1):
 
         The following global enrichment methods are supported:
         * h-refinement (``enrichment_method='h'``) - refine each mesh element
-          uniformly in each direction;
+        uniformly in each direction;
         * p-refinement (``enrichment_method='p'``) - increase the function space
-          polynomial order by one globally.
+        polynomial order by one globally.
 
         :kwarg enrichment_method: the method for enriching the mesh sequence
         :type enrichment_method: :class:`str`
@@ -179,8 +179,8 @@ def indicate_errors(
             space(s) as arguments to the error indicator
             :class:`firedrake.function.Function`
         :returns: solution and indicator data objects
-        :rtype1: :class:`~.AdjointSolutionData
-        :rtype2: :class:`~.IndicatorData
+        :rtype1: :class:`~.AdjointSolutionData`
+        :rtype2: :class:`~.IndicatorData`
         """
         solver_kwargs = solver_kwargs or {}
         default_enrichment_kwargs = {"enrichment_method": "p", "num_enrichments": 1}
@@ -353,8 +353,8 @@ def fixed_point_iteration(
             space(s) as arguments to the error indicator
             :class:`firedrake.function.Function`
         :returns: solution and indicator data objects
-        :rtype1: :class:`~.AdjointSolutionData
-        :rtype2: :class:`~.IndicatorData
+        :rtype1: :class:`~.AdjointSolutionData`
+        :rtype2: :class:`~.IndicatorData`
         """
         # TODO #124: adaptor no longer needs solution and indicator data to be passed
         #            explicitly

goalie/math.py

@@ -9,7 +9,7 @@ def bessi0(x):
     """
     Modified Bessel function of the first kind.
 
-    Code taken from :cite:`VVP+:92`.
+    Code taken from :cite:`Vetterling:1992`.
     """
     if isinstance(x, np.ndarray):
         if np.isclose(x, 0).any():

goalie/mesh_seq.py

@@ -272,14 +272,14 @@ def get_solver(self):
 
         Signature for the function to be returned:
         ```
-        :arg index: the subinterval index
-        :type index: :class:`int`
-        :arg ic: map from fields to the corresponding initial condition components
-        :type ic: :class:`dict` with :class:`str` keys and
-            :class:`firedrake.function.Function` values
-        :return: map from fields to the corresponding solutions
-        :rtype: :class:`dict` with :class:`str` keys and
-            :class:`firedrake.function.Function` values
+            :arg index: the subinterval index
+            :type index: :class:`int`
+            :arg ic: map from fields to the corresponding initial condition components
+            :type ic: :class:`dict` with :class:`str` keys and
+                :class:`firedrake.function.Function` values
+            :return: map from fields to the corresponding solutions
+            :rtype: :class:`dict` with :class:`str` keys and
+                :class:`firedrake.function.Function` values
         ```
 
         :returns: the function for obtaining the solver