Merge remote-tracking branch 'origin/master'

# Conflicts:
#	src/compas/numerical/solvers/ga.py

Author: andrewtliew

src/compas/com/matlab_/engine.py

@@ -27,7 +27,8 @@ def __init__(self, message=None):
 
 
 class MatlabEngine(object):
-    """Communicate with Matlab through the MATLAB engine.
+    """Communicate with Matlab through the MATLAB engine [mathworks2017a]_, [mathworks2017b]_,
+        [mathworks2017c]_, [mathworks2017d]_, [mathworks2017e]_.
 
     Attributes
     ----------
@@ -43,14 +44,6 @@ class MatlabEngine(object):
     >>> matlab.engine.isprime(37)
     True
 
-    References
-    ----------
-    * `MATLAB Engine API for Python <https://ch.mathworks.com/help/matlab/matlab-engine-for-python.html>`_
-    * `Pass Data to MATLAB from Python <https://ch.mathworks.com/help/matlab/matlab_external/pass-data-to-matlab-from-python.html>`_
-    * `Use MATLAB Arrays in Python <https://ch.mathworks.com/help/matlab/matlab_external/use-matlab-arrays-in-python.html>`_
-    * `Use MATLAB Engine Workspace in Python <https://ch.mathworks.com/help/matlab/matlab_external/use-the-matlab-engine-workspace-in-python.html>`_
-    * `Call MATLAB Functions from Python <https://ch.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-python.html>`_
-
     """
 
     def __init__(self):

src/compas/datastructures/volmesh/volmesh.py

@@ -66,8 +66,8 @@ class VolMesh(FromToData,
 
     Volumetric meshes are 3-mainfold, cellular structures.
 
-    The implementation of ``VolMesh`` is based on the notion of *x-maps* [xmaps]
-    and the concepts behind the *OpenVolumeMesh* library [ovm].
+    The implementation of ``VolMesh`` is based on the notion of *x-maps*
+    and the concepts behind the *OpenVolumeMesh* library [vci2016]_.
     In short, we add an additional entity compared to polygonal meshes,
     the *cell*, and relate cells not through *half-edges*, but through a combination
     of *half-faces* and *planes*. Each cell consists of a series of vertex pairs,
@@ -92,7 +92,7 @@ class VolMesh(FromToData,
         halffaces.
         ``self.cell[ckey][u][v] -> fkey``
     halfface : dict
-        The halffaces of the volmesh. Each halfface is represented by 
+        The halffaces of the volmesh. Each halfface is represented by
         ``self.halfface[fkey] -> vertex cycle``
     plane : dict
         The planes of the volmesh. Every plane is uniquely defined by three
@@ -104,11 +104,6 @@ class VolMesh(FromToData,
         pointing at the cells of the volmesh.
         ``self.plane[u][v][w] -> ckey``.
 
-    References
-    ----------
-    .. [xmaps] xxx
-    .. [ovm] `Open Volum Mesh <http://www.openvolumemesh.org>`_
-
     """
 
     def __init__(self):
@@ -888,5 +883,5 @@ def scale(self, factor=1.0):
 
     viewer.setup()
 
-    viewer.camera.zoom_out(5)    
+    viewer.camera.zoom_out(5)
     viewer.show()

src/compas/files/obj.py

@@ -40,7 +40,7 @@ def __init__(self, filepath, remote=False, precision=None):
 
 
 class OBJReader(object):
-    """Read the contents of an *obj* file.
+    """Read the contents of an *obj* file [Bourke]_.
 
     Parameters:
         filepath (str): Path to the file.
@@ -61,9 +61,6 @@ class OBJReader(object):
         curves2 (list): Curves
         surfaces (list): Surfaces
 
-    References:
-        http://paulbourke.net/dataformats/obj/
-
     """
 
     def __init__(self, filepath, remote=False):

src/compas/geometry/__init__.py

@@ -71,15 +71,10 @@
 
     Vector
     Point
-    Circle
     Line
-    Frame
-    Plane
     Polyline
     Polygon
     Polyhedron
-    Spline
-    Surface
 
 .. autosummary::
     :toctree: generated/
@@ -183,22 +178,14 @@
     :toctree: generated/
     :nosignatures:
 
-    angle_smallest_points
-    angle_smallest_points_xy
-    angle_smallest_points_degrees
-    angle_smallest_points_degrees_xy
-    angle_smallest_vectors
-    angle_smallest_vectors_xy
-    angle_smallest_vectors_degrees
-    angle_smallest_vectors_degrees_xy
+    angle_points
+    angle_points_xy
+    angle_vectors
+    angle_vectors_xy
     angles_points
     angles_points_xy
-    angles_points_degrees
-    angles_points_degrees_xy
     angles_vectors
     angles_vectors_xy
-    angles_vectors_degrees
-    angles_vectors_degrees_xy
 
 
 **Average**
@@ -356,7 +343,6 @@
     reflect_line_triangle
     rotate_points
     rotate_points_xy
-    rotate_points_degrees
     scale_points
     translate_lines
     translate_lines_xy

src/compas/geometry/algorithms/bestfit.py

@@ -29,7 +29,7 @@
 
 
 def bestfit_plane(points):
-    """Fit a plane to a list of (more than three) points.
+    """Fit a plane to a list of (more than three) points [Ernerfeldt2015]_.
 
     Parameters
     ----------
@@ -41,10 +41,6 @@ def bestfit_plane(points):
     plane : tuple
         Base point and normal vector (normalized).
 
-    References
-    ----------
-    http://www.ilikebigbits.com/blog/2015/3/2/plane-from-points
-
     Warning
     -------
     This method will minimize the squares of the residuals as perpendicular
@@ -210,7 +206,7 @@ def bestfit_plane_numpy4(points):
 
 
 def bestfit_circle_numpy(points):
-    """Fit a circle through a set of points.
+    """Fit a circle through a set of points [Scipya]_.
 
     Warning
     -------
@@ -233,11 +229,6 @@ def bestfit_circle_numpy(points):
 
         #
 
-
-    References
-    ----------
-    * http://scipy-cookbook.readthedocs.io/items/Least_Squares_Circle.html
-
     """
     from numpy import sqrt
     from numpy import mean

src/compas/geometry/algorithms/hull.py

@@ -25,7 +25,7 @@
 
 
 def convex_hull(points):
-    """Construct convex hull for a set of points.
+    """Construct convex hull for a set of points [githubgist_a]_.
 
     Parameters
     ----------
@@ -77,9 +77,6 @@ def convex_hull(points):
                     show_vertices = False,
                     show_edges = False)
 
-    References
-    ----------
-    * https://gist.github.com/anonymous/5184ba0bcab21d3dd19781efd3aae543
 
     """
     def _normal_face(face):
@@ -118,7 +115,7 @@ def _add_point(hull, p):
 
 
 def convex_hull_xy(points):
-    """Computes the convex hull of a set of 2D points.
+    """Computes the convex hull of a set of 2D points [wikibooks2017]_.
 
     Note
     ----
@@ -139,9 +136,6 @@ def convex_hull_xy(points):
         XY(Z) coordinates of vertices of the convex hull in counter-clockwise order,
         starting from the vertex with the lexicographically smallest coordinates.
 
-    References
-    ----------
-    * https://en.wikibooks.org/wiki/Algorithm_Implementation/Geometry/Convex_hull/Monotone_chain
 
     """
 

src/compas/geometry/algorithms/interpolation.py

@@ -22,7 +22,7 @@
 
 def discrete_coons_patch(ab, bc, dc, ad):
     """Creates a coons patch from a set of four or three boundary
-    polylines (ab, bc, dc, ad).
+    polylines (ab, bc, dc, ad) [wikipedia2017]_, [ferreol2013]_.
 
     Direction and order of polylines::
 
@@ -61,11 +61,6 @@ def discrete_coons_patch(ab, bc, dc, ad):
     --------
     * :func:`compas.datastructures.mesh_cull_duplicate_vertices`
 
-    References
-    ----------
-    * https://en.wikipedia.org/wiki/Coons_patch
-    * https://www.mathcurve.com/surfaces/patchcoons/patchcoons.shtml
-
     """
     if not ab:
         ab = [ad[0]] * len(dc)