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Merge branch 'docs' of https://github.com/simpeg/simpeg into feat/docs-deploy

Browse Source 
# Conflicts:
#	SimPEG/Utils/meshutils.py
#	docs/api_Utils.rst
#	docs/conf.py
#	docs/flow/index.rst
This commit is contained in:
Rowan Cockett
2016-05-29 19:18:36 -07:00
parent bc073e49b5 756b738ef2
commit 18f98b2ecd
17 changed files with 123 additions and 66 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.travis.yml
+4 -1
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@@ -24,6 +24,7 @@ env:
- TEST_DIR=tests/examples
- TEST_DIR=tests/em/fdem/inverse/adjoint
- TEST_DIR=tests/em/fdem/forward
- TEST_DIR=tests/docs
# Setup anaconda
before_install:
@@ -35,7 +36,7 @@ before_install:
# Install packages
install:
- conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose vtk
- conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose vtk sphinx
- pip install nose-cov python-coveralls
- git clone https://github.com/rowanc1/pymatsolver.git
@@ -46,8 +47,10 @@ install:
# Run test
script:
# test docs
- nosetests $TEST_DIR --with-cov --cov SimPEG --cov-config .coveragerc -v -s
# Calculate coverage
after_success:
- coveralls --config_file .coveragerc
SimPEG/EM/FDEM/ProblemFDEM.py
+5
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@@ -31,6 +31,7 @@ class BaseFDEMProblem(BaseEMProblem):
if using the H-J formulation (:code:`Problem3D_j` or :code:`Problem3D_h`). Note that here, :math:`\mathbf{s_m}` is an integrated quantity.
The problem performs the elimination so that we are solving the system for \\\(\\\mathbf{e},\\\mathbf{b},\\\mathbf{j} \\\) or \\\(\\\mathbf{h}\\\)
"""
surveyPair = SurveyFDEM
@@ -444,6 +445,7 @@ class Problem3D_j(BaseFDEMProblem):
\mathbf{h} = \\frac{1}{i \omega} \mathbf{M_{\mu}^e}^{-1} \\left(-\mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{j} + \mathbf{M^e} \mathbf{s_m} \\right)
and solve for \\\(\\\mathbf{j}\\\) using
.. math ::
@@ -608,9 +610,11 @@ class Problem3D_h(BaseFDEMProblem):
.. math::
\mathbf{A} = \mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{C} + i \omega \mathbf{M_{\mu}^e}
:param float freq: Frequency
:rtype: scipy.sparse.csr_matrix
:return: A
"""
MeMu = self.MeMu
@@ -653,6 +657,7 @@ class Problem3D_h(BaseFDEMProblem):
:param float freq: Frequency
:rtype: numpy.ndarray
:return: RHS (nE, nSrc)
"""
s_m, s_e = self.getSourceTerm(freq)
SimPEG/Maps.py
+6 -6
View File
@@ -41,8 +41,8 @@ class IdentityMap(object):
If this is a meshless mapping (i.e. nP is defined independently)
the shape will be the the shape (nP,nP).
:rtype: (int,int)
:return: shape of the operator as a tuple
:rtype: tuple
:return: shape of the operator as a tuple (int,int)
"""
if self._nP is not None:
return (self.nP, self.nP)
@@ -86,7 +86,7 @@ class IdentityMap(object):
The derivative of the transformation.
:param numpy.array m: model
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: derivative of transformed model
"""
@@ -216,7 +216,7 @@ class ExpMap(IdentityMap):
def deriv(self, m):
"""
:param numpy.array m: model
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: derivative of transformed model
The *transform* changes the model into the physical property.
@@ -366,7 +366,7 @@ class SurjectVertical1D(IdentityMap):
def deriv(self, m):
"""
:param numpy.array m: model
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: derivative of transformed model
"""
repNum = self.mesh.vnC[:self.mesh.dim-1].prod()
@@ -427,7 +427,7 @@ class Surject2Dto3D(IdentityMap):
def deriv(self, m):
"""
:param numpy.array m: model
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: derivative of transformed model
"""
inds = self * np.arange(self.nP)
SimPEG/Mesh/BaseMesh.py
+18 -16
View File
@@ -7,8 +7,8 @@ class BaseMesh(object):
BaseMesh does all the counting you don't want to do.
BaseMesh should be inherited by meshes with a regular structure.
:param numpy.array,list n: number of cells in each direction (dim, )
:param numpy.array,list x0: Origin of the mesh (dim, )
:param numpy.array n: (or list) number of cells in each direction (dim, )
:param numpy.array x0: (or list) Origin of the mesh (dim, )
"""
@@ -34,8 +34,8 @@ class BaseMesh(object):
"""
Origin of the mesh
:rtype: numpy.array (dim, )
:return: x0
:rtype: numpy.array
:return: x0, (dim, )
"""
return self._x0
@@ -116,8 +116,8 @@ class BaseMesh(object):
"""
Total number of edges in each direction
:rtype: numpy.array (dim, )
:return: [nEx, nEy, nEz]
:rtype: numpy.array
:return: [nEx, nEy, nEz], (dim, )
.. plot::
:include-source:
@@ -173,8 +173,8 @@ class BaseMesh(object):
"""
Total number of faces in each direction
:rtype: numpy.array (dim, )
:return: [nFx, nFy, nFz]
:rtype: numpy.array
:return: [nFx, nFy, nFz], (dim, )
.. plot::
:include-source:
@@ -200,8 +200,8 @@ class BaseMesh(object):
"""
Face Normals
:rtype: numpy.array (sum(nF), dim)
:return: normals
:rtype: numpy.array
:return: normals, (sum(nF), dim)
"""
if self.dim == 2:
nX = np.c_[np.ones(self.nFx), np.zeros(self.nFx)]
@@ -218,8 +218,8 @@ class BaseMesh(object):
"""
Edge Tangents
:rtype: numpy.array (sum(nE), dim)
:return: normals
:rtype: numpy.array
:return: normals, (sum(nE), dim)
"""
if self.dim == 2:
tX = np.c_[np.ones(self.nEx), np.zeros(self.nEx)]
@@ -236,8 +236,9 @@ class BaseMesh(object):
Given a vector, fV, in cartesian coordinates, this will project it onto the mesh using the normals
:param numpy.array fV: face vector with shape (nF, dim)
:rtype: numpy.array with shape (nF, )
:return: projected face vector
:rtype: numpy.array
:return: projected face vector, (nF, )
"""
assert isinstance(fV, np.ndarray), 'fV must be an ndarray'
assert len(fV.shape) == 2 and fV.shape[0] == self.nF and fV.shape[1] == self.dim, 'fV must be an ndarray of shape (nF x dim)'
@@ -248,8 +249,9 @@ class BaseMesh(object):
Given a vector, eV, in cartesian coordinates, this will project it onto the mesh using the tangents
:param numpy.array eV: edge vector with shape (nE, dim)
:rtype: numpy.array with shape (nE, )
:return: projected edge vector
:rtype: numpy.array
:return: projected edge vector, (nE, )
"""
assert isinstance(eV, np.ndarray), 'eV must be an ndarray'
assert len(eV.shape) == 2 and eV.shape[0] == self.nE and eV.shape[1] == self.dim, 'eV must be an ndarray of shape (nE x dim)'
SimPEG/Mesh/CylMesh.py
+6 -6
View File
@@ -68,8 +68,8 @@ class CylMesh(BaseTensorMesh, BaseRectangularMesh, InnerProducts, CylView):
"""
Number of x-faces in each direction
:rtype: numpy.array (dim, )
:return: vnFx
:rtype: numpy.array
:return: vnFx, (dim, )
"""
return self.vnC
@@ -78,8 +78,8 @@ class CylMesh(BaseTensorMesh, BaseRectangularMesh, InnerProducts, CylView):
"""
Number of y-edges in each direction
:rtype: numpy.array (dim, )
:return: vnEy or None if dim < 2
:rtype: numpy.array
:return: vnEy or None if dim < 2, (dim, )
"""
nNx = self.nNx if self.isSymmetric else self.nNx - 1
return np.r_[nNx, self.nCy, self.nNz]
@@ -89,8 +89,8 @@ class CylMesh(BaseTensorMesh, BaseRectangularMesh, InnerProducts, CylView):
"""
Number of z-edges in each direction
:rtype: numpy.array (dim, )
:return: vnEz or None if nCy > 1
:rtype: numpy.array
:return: vnEz or None if nCy > 1, (dim, )
"""
if self.isSymmetric:
return np.r_[self.nNx, self.nNy, self.nCz]
SimPEG/Mesh/InnerProducts.py
+7 -7
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@@ -16,7 +16,7 @@ class InnerProducts(object):
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: M, the inner product matrix (nF, nF)
"""
return self._getInnerProduct('F', prop=prop, invProp=invProp, invMat=invMat, doFast=doFast)
@@ -27,7 +27,7 @@ class InnerProducts(object):
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: M, the inner product matrix (nE, nE)
"""
return self._getInnerProduct('E', prop=prop, invProp=invProp, invMat=invMat, doFast=doFast)
@@ -39,7 +39,7 @@ class InnerProducts(object):
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: M, the inner product matrix (nE, nE)
"""
assert projType in ['F', 'E'], "projType must be 'F' for faces or 'E' for edges"
@@ -121,7 +121,7 @@ class InnerProducts(object):
Given u, dMdmu returns (nF, nC*nA)
:param np.ndarray u: vector that multiplies dMdmu
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: dMdmu, the derivative of the inner product matrix for a certain u
"""
return self._getInnerProductDeriv(prop, 'F', doFast=doFast, invProp=invProp, invMat=invMat)
@@ -133,7 +133,7 @@ class InnerProducts(object):
:param bool doFast: do a faster implementation if available.
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: dMdm, the derivative of the inner product matrix (nE, nC*nA)
"""
return self._getInnerProductDeriv(prop, 'E', doFast=doFast, invProp=invProp, invMat=invMat)
@@ -145,7 +145,7 @@ class InnerProducts(object):
:param bool doFast: do a faster implementation if available.
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: dMdm, the derivative of the inner product matrix (nE, nC*nA)
"""
fast = None
@@ -169,7 +169,7 @@ class InnerProducts(object):
:param numpy.array v: vector to multiply (required in the general implementation)
:param list P: list of projection matrices
:param str projType: 'F' for faces 'E' for edges
:rtype: scipy.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: dMdm, the derivative of the inner product matrix (n, nC*nA)
"""
assert projType in ['F', 'E'], "projType must be 'F' for faces or 'E' for edges"
SimPEG/Mesh/TreeMesh.py
+1 -1
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@@ -1875,7 +1875,7 @@ class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
:param numpy.ndarray locs: Location of points to interpolate to
:param str locType: What to interpolate (see below)
:rtype: scipy.sparse.csr.csr_matrix
:rtype: scipy.sparse.csr_matrix
:return: M, the interpolation matrix
locType can be::
SimPEG/Utils/meshutils.py
+7 -8
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@@ -104,18 +104,17 @@ def closestPoints(mesh, pts, gridLoc='CC'):
def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
"""
Extracts Core Mesh from Global mesh
Extracts Core Mesh from Global mesh
:param numpy.ndarray xyzlim: 2D array [ndim x 2]
:param simpeg.Mesh.BaseMesh mesh: The mesh
:param numpy.ndarray xyzlim: 2D array [ndim x 2]
:param simpeg.Mesh.BaseMesh mesh: The mesh
This function ouputs::
This function ouputs::
- actind: corresponding boolean index from global to core
- meshcore: core SimPEG mesh
Warning: 1D and 2D has not been tested
- actind: corresponding boolean index from global to core
- meshcore: core SimPEG mesh
Warning: 1D and 2D has not been tested
"""
from SimPEG import Mesh
if mesh.dim == 1:
docs/api_ForwardProblem.rst
+2 -2
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@@ -67,13 +67,13 @@ The API
Problem
-------
.. automodule:: SimPEG.Problem
.. autoclass:: SimPEG.Problem
:members:
:undoc-members:
Survey
------
.. automodule:: SimPEG.Survey
.. autoclass:: SimPEG.Survey
:members:
:undoc-members:
docs/api_InnerProducts.rst
+1 -1
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@@ -266,6 +266,6 @@ These are computed for each of the 8 projections, horizontally concatenated, and
The API
-------
.. automodule:: SimPEG.Mesh.InnerProducts
.. autoclass:: SimPEG.Mesh.InnerProducts
:members:
:undoc-members:
docs/api_Inversion.rst
+3 -3
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@@ -3,7 +3,7 @@
InvProblem
**********
.. automodule:: SimPEG.InvProblem
.. autoclass:: SimPEG.InvProblem
:show-inheritance:
:members:
:undoc-members:
@@ -12,7 +12,7 @@ InvProblem
Inversion
*********
.. automodule:: SimPEG.Inversion
.. autoclass:: SimPEG.Inversion
:show-inheritance:
:members:
:undoc-members:
@@ -20,7 +20,7 @@ Inversion
Directives
**********
.. automodule:: SimPEG.Directives
.. autoclass:: SimPEG.Directives
:show-inheritance:
:members:
:undoc-members:
docs/api_Mesh.rst
+1 -1
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@@ -188,6 +188,6 @@ other types of meshes in this SimPEG framework.
The API
=======
.. automodule:: SimPEG.Mesh.BaseMesh
.. autoclass:: SimPEG.Mesh.BaseMesh
:members:
:undoc-members:
docs/api_MeshCode.rst
+7 -10
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@@ -3,34 +3,31 @@
Tensor Mesh
===========
.. automodule:: SimPEG.Mesh.TensorMesh
:show-inheritance:
.. autoclass:: SimPEG.Mesh.TensorMesh
:members:
:undoc-members:
:show-inheritance:
Cylindrical Mesh
================
.. automodule:: SimPEG.Mesh.CylMesh
:show-inheritance:
.. autoclass:: SimPEG.Mesh.CylMesh
:members:
:undoc-members:
:show-inheritance:
Tree Mesh
=========
.. autoclass:: SimPEG.Mesh.TreeMesh.TreeMesh
:show-inheritance:
:members:
:undoc-members:
:show-inheritance:
Curvilinear Mesh
================
.. automodule:: SimPEG.Mesh.CurvilinearMesh
:show-inheritance:
.. autoclass:: SimPEG.Mesh.CurvilinearMesh
:members:
:undoc-members:
:show-inheritance:
docs/api_Solver.rst
+2
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@@ -46,6 +46,8 @@ The API
=======
.. autofunction:: SimPEG.Utils.SolverUtils.SolverWrapD
:noindex:
.. autofunction:: SimPEG.Utils.SolverUtils.SolverWrapI
:noindex:
docs/api_Utils.rst
+2 -2
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@@ -51,7 +51,6 @@ Interpolation Utilities
Counter Utilities
=================
.. code-block:: python
:linenos:
@@ -73,7 +72,6 @@ Counter Utilities
c.counter.summary()
.. code-block:: text
:linenos:
@@ -83,6 +81,8 @@ Counter Utilities
Times: mean sum
MyClass.MySecondMethod : 1.70e-06, 5.10e-04, 300x
The API
-------
docs/conf.py
+8 -2
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@@ -28,7 +28,7 @@ sys.path.append('../')
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'matplotlib.sphinxext.plot_directive']
extensions = ['sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'matplotlib.sphinxext.plot_directive']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
@@ -129,7 +129,7 @@ except Exception, e:
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_static_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
@@ -229,6 +229,12 @@ man_pages = [
# If true, show URL addresses after external links.
#man_show_urls = False
# Intersphinx
intersphinx_mapping = {'python': ('http://docs.python.org/2', None),
'numpy': ('http://docs.scipy.org/doc/numpy/', None),
'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
'matplotlib': ('http://matplotlib.sourceforge.net/', None)}
# -- Options for Texinfo output ------------------------------------------------
tests/docs/test_docs.py
+43
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@@ -0,0 +1,43 @@
import subprocess
import unittest
import os
class Doc_Test(unittest.TestCase):
@property
def path_to_docs(self):
dirname, filename = os.path.split(os.path.abspath(__file__))
return os.path.sep.join(dirname.split(os.path.sep)[:-2] + ['docs'])
def test_html(self):
doctrees_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['doctrees'])
html_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['html'])
check = subprocess.call(["sphinx-build", "-nW", "-b", "html", "-d",
"%s"%(doctrees_path) ,
"%s"%(self.path_to_docs),
"%s"%(html_path)])
assert check == 0
# def test_latex(self):
# doctrees_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['doctrees'])
# latex_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['latex'])
# check = subprocess.call(["sphinx-build", "-nW", "-b", "latex", "-d",
# "%s"%(doctrees_path),
# "%s"%(self.path_to_docs),
# "%s"%(latex_path)])
# assert check == 0
# def test_linkcheck(self):
# doctrees_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build']+['doctrees'])
# link_path = os.path.sep.join(self.path_to_docs.split(os.path.sep) + ['_build'])
# check = subprocess.call(["sphinx-build", "-nW", "-b", "linkcheck", "-d",
# "%s"%(doctrees_path),
# "%s"%(self.path_to_docs),
# "%s"%(link_path)])
# assert check == 0
if __name__ == '__main__':
unittest.main()