update citations for html (#132)

Linked to
mesh-adaptation/docs#50

should be evaluated in combination with:
mesh-adaptation/docs#50
mesh-adaptation/animate#160
mesh-adaptation/goalie#232

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

demos/lineal_spring.py

@@ -230,5 +230,5 @@ def update_boundary_displacement(t):
 #
 # .. rubric:: References
 #
-# .. bibliography:: demo_references.bib
+# .. bibliography::
 #    :filter: docname in docnames

demos/monge_ampere1.py

@@ -195,5 +195,5 @@ def ring_monitor(mesh):
 #
 # .. rubric:: References
 #
-# .. bibliography:: demo_references.bib
+# .. bibliography::
 #    :filter: docname in docnames

demos/monge_ampere_3d.py

@@ -3,7 +3,7 @@
 
 # In this demo we demonstrate that the  Monge-Ampère mesh movement
 # can also be applied to 3D meshes. We employ the `sinatan3` function
-# from :cite:`park2019` to introduce an interesting pattern.
+# from :cite:`Park:2019` to introduce an interesting pattern.
 
 from firedrake import *
 
@@ -98,5 +98,5 @@ def monitor(mesh):
 #
 # .. rubric:: References
 #
-# .. bibliography:: demo_references.bib
+# .. bibliography::
 #    :filter: docname in docnames

movement/monge_ampere.py

@@ -46,7 +46,7 @@ def MongeAmpereMover(mesh, monitor_function, method="relaxation", **kwargs):
     :class:`~.MongeAmpereMover_Relaxation`. If the argument is set to `"quasi_newton"`
     then it is solved in its elliptic form using a quasi-Newton method in
     :class:`~.MongeAmpereMover_QuasiNewton`. Descriptions of both methods may be found in
-    :cite:`MCB:18`.
+    :cite:`McRae:2018`.
 
     The physical mesh coordinates :math:`\mathbf{x}` are updated according to
 
@@ -109,7 +109,7 @@ class MongeAmpereMover_Base(PrimeMover, metaclass=abc.ABCMeta):
 
     Currently implemented subclasses: :class:`~.MongeAmpereMover_Relaxation` and
     :class:`~.MongeAmpereMover_QuasiNewton`. Descriptions of both methods may be found in
-    :cite:`MCB:18`.
+    :cite:`McRae:2018`.
     """
 
     def __init__(self, mesh, monitor_function, **kwargs):
@@ -366,7 +366,7 @@ class MongeAmpereMover_Relaxation(MongeAmpereMover_Base):
         = m(\mathbf{x})\det(\mathbf{I} + \mathbf{H}(\phi)) - \theta,
 
     where :math:`\tau` is the pseudo-time variable. Forward Euler is used for the
-    pseudo-time integration (see :cite:`MCB:18` for details).
+    pseudo-time integration (see :cite:`McRae:2018` for details).
 
     This approach typically takes tens or hundreds of iterations to converge, but each
     iteration is relatively cheap.
@@ -424,7 +424,7 @@ def pseudotimestepper(self):
         """
         Setup the pseudo-timestepper for the relaxation method.
 
-        Forward Euler is used for the pseudo-time integration (see :cite:`MCB:18` for
+        Forward Euler is used for the pseudo-time integration (see :cite:`McRae:2018` for
         details). The pseudo-timestep may be set through the `pseudo_timestep` keyword
         argument to the constructor.
 
@@ -555,7 +555,7 @@ class MongeAmpereMover_QuasiNewton(MongeAmpereMover_Base):
     :math:`\phi` with respect to :math:`\boldsymbol{\xi}`.
 
     In this mesh mover, the elliptic Monge-Ampère equation is solved using a quasi-Newton
-    method (see :cite:`MCB:18` for details).
+    method (see :cite:`McRae:2018` for details).
 
     This approach typically takes fewer than ten iterations to converge, but each
     iteration is relatively expensive.

movement/spring.py

@@ -16,7 +16,7 @@ def SpringMover(*args, method="lineal", **kwargs):
     """
     Movement of a ``mesh`` is determined by reinterpreting it as a structure of stiff
     beams and solving an associated discrete linear elasticity problem. (See
-    :cite:`FDK+:98` for details.)
+    :cite:`Farhat:1998` for details.)
 
     :arg mesh: the physical mesh to be moved
     :type mesh: :class:`firedrake.mesh.MeshGeometry`
@@ -237,7 +237,7 @@ class SpringMover_Lineal(SpringMover_Base):
     Movement of a ``mesh`` is determined by reinterpreting it as a structure of stiff
     beams and solving an associated discrete linear elasticity problem.
 
-    We consider the 'lineal' case, as described in :cite:`FDK+:98`.
+    We consider the 'lineal' case, as described in :cite:`Farhat:1998`.
     """
 
     @PETSc.Log.EventDecorator()
@@ -285,7 +285,7 @@ class SpringMover_Torsional(SpringMover_Lineal):
     Movement of a ``mesh`` is determined by reinterpreting it as a structure of stiff
     beams and solving an associated discrete linear elasticity problem.
 
-    We consider the 'torsional' case, as described in :cite:`FDK+:98`.
+    We consider the 'torsional' case, as described in :cite:`Farhat:1998`.
     """
 
     def __init__(self, *args, **kwargs):