Tweak documentation (#991)

* Update index syntax * Account for missing FIPY_DISPLAY_MATRIX environment variable * Fix parameter syntax * Don't ignore things that no longer exist
usnistgov · Jan 10, 2024 · 9239820 · 9239820
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diff --git a/.gitignore b/.gitignore
@@ -6,7 +6,6 @@
 FiPy.egg-info
 MANIFEST.in
 dist/
-documentation/_build/
 generated/
 *.logamgx
 *.dump.gz

diff --git a/examples/cahnHilliard/tanh1D.py b/examples/cahnHilliard/tanh1D.py
@@ -127,7 +127,7 @@
 If we are running interactively, we create a viewer to see the results
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var, datamin=0., datamax=1.0)

diff --git a/examples/convection/exponential1D/cylindricalMesh1D.py b/examples/convection/exponential1D/cylindricalMesh1D.py
@@ -90,7 +90,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var)

diff --git a/examples/convection/exponential1D/cylindricalMesh1DNonUniform.py b/examples/convection/exponential1D/cylindricalMesh1DNonUniform.py
@@ -92,7 +92,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var)

diff --git a/examples/convection/exponential1D/mesh1D.py b/examples/convection/exponential1D/mesh1D.py
@@ -88,7 +88,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var)

diff --git a/examples/convection/exponential1DSource/mesh1D.py b/examples/convection/exponential1DSource/mesh1D.py
@@ -85,7 +85,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var)

diff --git a/examples/convection/exponential2D/cylindricalMesh2D.py b/examples/convection/exponential2D/cylindricalMesh2D.py
@@ -92,7 +92,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var)

diff --git a/examples/convection/exponential2D/cylindricalMesh2DNonUniform.py b/examples/convection/exponential2D/cylindricalMesh2DNonUniform.py
@@ -90,7 +90,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=var)

diff --git a/examples/diffusion/circle.py b/examples/diffusion/circle.py
@@ -41,7 +41,7 @@
 Using this mesh, we can construct a solution variable
 
 .. index::
-   object: fipy.variables.cellVariable.CellVariable
+   pair: object; fipy.variables.cellVariable.CellVariable
 
 >>> phi = CellVariable(name = "solution variable",
 ...                    mesh = mesh,
@@ -63,8 +63,8 @@
 We set up a transient diffusion equation
 
 .. index::
-   object: fipy.terms.transientTerm.TransientTerm
-   object: fipy.terms.implicitDiffusionTerm.DiffusionTerm
+   pair: object; fipy.terms.transientTerm.TransientTerm
+   pair: object; fipy.terms.implicitDiffusionTerm.DiffusionTerm
 
 >>> D = 1.
 >>> eq = TransientTerm() == DiffusionTerm(coeff=D)
@@ -98,7 +98,7 @@
 another application, we could export tab-separated-values with
 
 .. index::
-   object: fipy.viewers.tsvViewer.TSVViewer
+   pair: object; fipy.viewers.tsvViewer.TSVViewer
 
 ::
 
@@ -124,7 +124,7 @@
 ...                              mesh=mesh) # doctest: +GMSH
 
 .. index::
-    module: scipy
+    pair: module; scipy
     single: sqrt; arcsin; cos
 
 >>> x0 = radius * numerix.cos(numerix.arcsin(y)) # doctest: +GMSH

diff --git a/examples/diffusion/circleQuad.py b/examples/diffusion/circleQuad.py
@@ -42,7 +42,7 @@
 Using this mesh, we can construct a solution variable
 
 .. index::
-   object: fipy.variables.cellVariable.CellVariable
+   pair: object; fipy.variables.cellVariable.CellVariable
 
 >>> phi = CellVariable(name = "solution variable",
 ...                    mesh = mesh,
@@ -64,8 +64,8 @@
 We set up a transient diffusion equation
 
 .. index::
-   object: fipy.terms.transientTerm.TransientTerm
-   object: fipy.terms.implicitDiffusionTerm.DiffusionTerm
+   pair: object; fipy.terms.transientTerm.TransientTerm
+   pair: object; fipy.terms.implicitDiffusionTerm.DiffusionTerm
 
 >>> D = 1.
 >>> eq = TransientTerm() == DiffusionTerm(coeff=D)
@@ -97,7 +97,7 @@
 another application, we could export tab-separated-values with
 
 .. index::
-   object: fipy.viewers.tsvViewer.TSVViewer
+   pair: object; fipy.viewers.tsvViewer.TSVViewer
 
 ::
 
@@ -123,7 +123,7 @@
 ...                              mesh=mesh) # doctest: +GMSH
 
 .. index::
-    module: scipy
+    pair: module; scipy
     single: sqrt; arcsin; cos
 
 >>> x0 = radius * numerix.cos(numerix.arcsin(y)) # doctest: +GMSH

diff --git a/examples/diffusion/mesh1D.py b/examples/diffusion/mesh1D.py
@@ -114,7 +114,7 @@
 viewers and the dimension of the mesh.
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> phiAnalytical = CellVariable(name="analytical value",
 ...                              mesh=mesh)

diff --git a/examples/diffusion/mesh20x20.py b/examples/diffusion/mesh20x20.py
@@ -48,7 +48,7 @@
 We create a viewer to see the results
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=phi, datamin=0., datamax=1.)

diff --git a/examples/diffusion/mesh20x20Coupled.py b/examples/diffusion/mesh20x20Coupled.py
@@ -48,7 +48,7 @@
 We create a viewer to see the results
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=phi, datamin=0., datamax=1.)

diff --git a/examples/diffusion/nthOrder/input4thOrder1D.py b/examples/diffusion/nthOrder/input4thOrder1D.py
@@ -88,7 +88,7 @@
 If the problem is run interactively, we can view the result:
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=(var, analytical))

diff --git a/examples/flow/stokesCavity.py b/examples/flow/stokesCavity.py
@@ -214,7 +214,7 @@
 Set up the viewers,
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=(pressure, xVelocity, yVelocity, velocity),

diff --git a/examples/levelSet/electroChem/gold.py b/examples/levelSet/electroChem/gold.py
@@ -27,7 +27,7 @@
 more complex mesh.
 
 .. index::
-   module: gmsh
+   pair: module; gmsh
 
 There are a few differences between the gold superfill model presented
 in this example and in :mod:`examples.levelSet.electroChem.simpleTrenchSystem`.

diff --git a/examples/levelSet/electroChem/howToWriteAScript.py b/examples/levelSet/electroChem/howToWriteAScript.py
@@ -80,7 +80,7 @@
 Build the mesh:
 
 .. index::
-   module: fipy.tools.parser
+   pair: module; fipy.tools.parser
 
 >>> from fipy.tools.parser import parse
 >>> numberOfElements = parse('--numberOfElements', action='store',

diff --git a/examples/levelSet/electroChem/leveler.py b/examples/levelSet/electroChem/leveler.py
@@ -26,7 +26,7 @@
 construct the mesh.
 
 .. index::
-   module: gmsh
+   pair: module; gmsh
 
 This example models the case when suppressor, accelerator and leveler
 additives are present in the electrolyte. The suppressor is

diff --git a/examples/levelSet/electroChem/simpleTrenchSystem.py b/examples/levelSet/electroChem/simpleTrenchSystem.py
@@ -54,7 +54,7 @@
 complex meshes requiring the :command:`gmsh` software.
 
 .. index::
-   module: gmsh
+   pair: module; gmsh
 
 .. this is kind of nasty, but reST tables can't handle what we need, particularly decimal alignment
 

diff --git a/examples/phase/anisotropyOLD.py b/examples/phase/anisotropyOLD.py
@@ -172,7 +172,7 @@
 the phase and temperature fields
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     phaseViewer = Viewer(vars=phase)

diff --git a/examples/phase/binary.py b/examples/phase/binary.py
@@ -470,7 +470,7 @@ def deltaChemPot(phase, C, T):
 >>> sharp.setValue(Cl, where=x >= L * fraction)
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=(phase, C, sharp),

diff --git a/examples/phase/binaryCoupled.py b/examples/phase/binaryCoupled.py
@@ -457,7 +457,7 @@ def deltaChemPot(phase, C, T):
 ...                                   [ 1. / C[0],      -1. / C[1]]])
 
 .. index::
-   module: scipy
+   pair: module; scipy
 
 >>> try:
 ...     from scipy.optimize import fsolve # doctest: +SCIPY
@@ -481,7 +481,7 @@ def deltaChemPot(phase, C, T):
 >>> sharp.setValue(Cl, where=x >= L * fraction)
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=(phase, C, sharp),

diff --git a/examples/phase/impingement/mesh20x20.py b/examples/phase/impingement/mesh20x20.py
@@ -5,7 +5,7 @@
 with different initial conditions and a 2D mesh:
 
 .. index::
-   module: fipy.tools.parser
+   pair: module; fipy.tools.parser
 
 >>> from fipy.tools.parser import parse
 
@@ -158,7 +158,7 @@
 by the phase
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> if __name__ == '__main__':
 ...     phaseViewer = Viewer(vars=phase, datamin=0., datamax=1.)
@@ -227,7 +227,7 @@
 We save the variables to disk.
 
 .. index::
-   module: fipy.tools.dump
+   pair: module; fipy.tools.dump
 
 >>> (f, filename) = dump.write({'phase' : phase, 'theta' : theta}, extension = '.gz')
 

diff --git a/examples/phase/impingement/mesh40x1.py b/examples/phase/impingement/mesh40x1.py
@@ -173,7 +173,7 @@
 and orientation variables.
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 .. index::
    single: :math:`\pi`

diff --git a/examples/phase/quaternary.py b/examples/phase/quaternary.py
@@ -345,7 +345,7 @@
 If we're running interactively, we create a viewer
 
 .. index::
-   module: viewers
+   pair: module; viewers
 
 >>> if __name__ == '__main__':
 ...     viewer = Viewer(vars=([phase]

diff --git a/examples/phase/simple.py b/examples/phase/simple.py
@@ -78,7 +78,7 @@
 If we are running interactively, we'll want a viewer to see the results
 
 .. index::
-   module: fipy.viewers
+   pair: module; fipy.viewers
 
 >>> from fipy import input
 >>> if __name__ == '__main__':
@@ -465,7 +465,7 @@
 thickness
 
 .. index::
-   module: scipy
+   pair: module; scipy
 
 >>> try:
 ...     def tanhResiduals(p, y, x, t):

diff --git a/examples/updating/update0_1to1_0.py b/examples/updating/update0_1to1_0.py
@@ -138,7 +138,7 @@
 or
 
 .. index::
-   module: fipy.numerix
+   pair: module; fipy.numerix
 
 >>> axis = 0
 >>> x = mesh.getCellCenters()[:, axis]

diff --git a/fipy/terms/abstractConvectionTerm.py b/fipy/terms/abstractConvectionTerm.py
@@ -66,7 +66,8 @@ def __init__(self, coeff=1.0, var=None):
 
         Parameters
         ----------
-        coeff : The `Term`'s coefficient value.
+        coeff : :class:`~fipy.variables.meshVariable.MeshVariable`
+            The :class:`~fipy.terms.term.Term`'s coefficient value.
         """
         if self.__class__ is _AbstractConvectionTerm:
             raise AbstractBaseClassError

diff --git a/fipy/viewers/matplotlibViewer/matplotlibSparseMatrixViewer.py b/fipy/viewers/matplotlibViewer/matplotlibSparseMatrixViewer.py
@@ -46,7 +46,7 @@ def plot(self, matrix, RHSvector, log='auto'):
         import tempfile
         import os
 
-        if "print" in os.environ['FIPY_DISPLAY_MATRIX'].lower().split():
+        if "print" in os.environ.get('FIPY_DISPLAY_MATRIX', '').lower().split():
             print("-"*75)
             print(self.title)
             print("-"*75)

diff --git a/fipy/viewers/matplotlibViewer/matplotlibStreamViewer.py b/fipy/viewers/matplotlibViewer/matplotlibStreamViewer.py
@@ -52,7 +52,7 @@ def __init__(self, vars, title=None, log=False, limits={}, axes=None, figaspect=
             desired aspect ratio of figure. If arg is a number, use that aspect
             ratio. If arg is `auto`, the aspect ratio will be determined from
             the Variable's mesh.
-        density : float or (float, float), optional
+        density : float or tuple of float, optional
             Controls the closeness of streamlines.  When ``density = 1``,
             the domain is divided into a 30x30 grid.  *density* linearly
             scales this grid.  Each cell in the grid can have, at most, one