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Tweak documentation #991

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merged 4 commits into from
Jan 10, 2024
Merged

Tweak documentation #991

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c1f0b08
Update index syntax
guyer Oct 10, 2023
d0369ae
Account for missing FIPY_DISPLAY_MATRIX environment variable
guyer Dec 22, 2022
6f3bf7e
Fix parameter syntax
guyer Oct 10, 2023
79653ef
Don't ignore things that no longer exist
guyer Jan 9, 2024
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1 change: 0 additions & 1 deletion .gitignore
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Expand Up @@ -6,7 +6,6 @@
FiPy.egg-info
MANIFEST.in
dist/
documentation/_build/
generated/
*.logamgx
*.dump.gz
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2 changes: 1 addition & 1 deletion examples/cahnHilliard/tanh1D.py
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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)
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2 changes: 1 addition & 1 deletion examples/convection/exponential1D/cylindricalMesh1D.py
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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)
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2 changes: 1 addition & 1 deletion examples/convection/exponential1D/cylindricalMesh1DNonUniform.py
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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)
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2 changes: 1 addition & 1 deletion examples/convection/exponential1D/mesh1D.py
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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)
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2 changes: 1 addition & 1 deletion examples/convection/exponential1DSource/mesh1D.py
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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)
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2 changes: 1 addition & 1 deletion examples/convection/exponential2D/cylindricalMesh2D.py
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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)
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2 changes: 1 addition & 1 deletion examples/convection/exponential2D/cylindricalMesh2DNonUniform.py
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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)
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10 changes: 5 additions & 5 deletions examples/diffusion/circle.py
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Using this mesh, we can construct a solution variable

.. index::
object: fipy.variables.cellVariable.CellVariable
pair: object; fipy.variables.cellVariable.CellVariable
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What is this supposed to do? When I go to the documentation, I'm not seeing anything to click on or anything at that point in the documentation.

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If you look in the index for fipy.variables.cellVariable.CellVariable, there's a link back to https://pages.nist.gov/fipy/en/tweak_documentation/generated/examples.diffusion.circleQuad.html#index-0.

It's probably stupid. I did it a long time ago and was just bringing the syntax up-to-date.


>>> phi = CellVariable(name = "solution variable",
... mesh = mesh,
Expand All @@ -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)
Expand Down Expand Up @@ -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

::

Expand All @@ -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
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10 changes: 5 additions & 5 deletions examples/diffusion/circleQuad.py
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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,
Expand All @@ -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)
Expand Down Expand Up @@ -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

::

Expand All @@ -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
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2 changes: 1 addition & 1 deletion examples/diffusion/mesh1D.py
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viewers and the dimension of the mesh.

.. index::
module: fipy.viewers
pair: module; fipy.viewers

>>> phiAnalytical = CellVariable(name="analytical value",
... mesh=mesh)
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2 changes: 1 addition & 1 deletion examples/diffusion/mesh20x20.py
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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.)
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2 changes: 1 addition & 1 deletion examples/diffusion/mesh20x20Coupled.py
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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.)
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2 changes: 1 addition & 1 deletion examples/diffusion/nthOrder/input4thOrder1D.py
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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))
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2 changes: 1 addition & 1 deletion examples/flow/stokesCavity.py
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Set up the viewers,

.. index::
module: fipy.viewers
pair: module; fipy.viewers

>>> if __name__ == '__main__':
... viewer = Viewer(vars=(pressure, xVelocity, yVelocity, velocity),
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2 changes: 1 addition & 1 deletion examples/levelSet/electroChem/gold.py
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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`.
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2 changes: 1 addition & 1 deletion examples/levelSet/electroChem/howToWriteAScript.py
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Build the mesh:

.. index::
module: fipy.tools.parser
pair: module; fipy.tools.parser

>>> from fipy.tools.parser import parse
>>> numberOfElements = parse('--numberOfElements', action='store',
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2 changes: 1 addition & 1 deletion examples/levelSet/electroChem/leveler.py
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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
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2 changes: 1 addition & 1 deletion examples/levelSet/electroChem/simpleTrenchSystem.py
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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

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2 changes: 1 addition & 1 deletion examples/phase/anisotropyOLD.py
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Expand Up @@ -172,7 +172,7 @@
the phase and temperature fields

.. index::
module: fipy.viewers
pair: module; fipy.viewers

>>> if __name__ == '__main__':
... phaseViewer = Viewer(vars=phase)
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2 changes: 1 addition & 1 deletion examples/phase/binary.py
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Expand Up @@ -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),
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4 changes: 2 additions & 2 deletions examples/phase/binaryCoupled.py
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Expand Up @@ -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
Expand All @@ -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),
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6 changes: 3 additions & 3 deletions examples/phase/impingement/mesh20x20.py
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with different initial conditions and a 2D mesh:

.. index::
module: fipy.tools.parser
pair: module; fipy.tools.parser

>>> from fipy.tools.parser import parse

Expand Down Expand Up @@ -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.)
Expand Down Expand Up @@ -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')

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2 changes: 1 addition & 1 deletion examples/phase/impingement/mesh40x1.py
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and orientation variables.

.. index::
module: fipy.viewers
pair: module; fipy.viewers

.. index::
single: :math:`\pi`
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2 changes: 1 addition & 1 deletion examples/phase/quaternary.py
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If we're running interactively, we create a viewer

.. index::
module: viewers
pair: module; viewers

>>> if __name__ == '__main__':
... viewer = Viewer(vars=([phase]
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4 changes: 2 additions & 2 deletions examples/phase/simple.py
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Expand Up @@ -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__':
Expand Down Expand Up @@ -465,7 +465,7 @@
thickness

.. index::
module: scipy
pair: module; scipy

>>> try:
... def tanhResiduals(p, y, x, t):
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2 changes: 1 addition & 1 deletion examples/updating/update0_1to1_0.py
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Expand Up @@ -138,7 +138,7 @@
or

.. index::
module: fipy.numerix
pair: module; fipy.numerix

>>> axis = 0
>>> x = mesh.getCellCenters()[:, axis]
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3 changes: 2 additions & 1 deletion fipy/terms/abstractConvectionTerm.py
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion fipy/viewers/matplotlibViewer/matplotlibSparseMatrixViewer.py
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion fipy/viewers/matplotlibViewer/matplotlibStreamViewer.py
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Expand Up @@ -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
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