Fix the doctests

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 * Fixed bug in `compas.geometry.curves.curve.Curve.reversed` by adding missing parenthesis.
+* Fixed all doctests so we can run `invoke test --doctest`.
 
 ### Removed
 

src/compas/colors/color.py

@@ -98,7 +98,7 @@ class Color(Data):
     By default, this class will create a color with the RGB components in the range ``[0.0, 1.0]``.
 
     >>> Color(1, 0, 0)
-    Color(1.0, 0.0, 0.0, alpha=1.0)
+    Color(1, 0, 0, alpha=1.0)
 
     Attempting to create a color with components outside of the range ``[0.0, 1.0]`` will raise a ``ValueError``.
 

src/compas/data/coercion.py

@@ -20,12 +20,6 @@ def coerce_sequence_of_tuple(sequence):
         with each iterable item converted to a tuple,
         and non-iterable items wrapped in a tuple.
 
-    Examples
-    --------
-    >>> items = coerce_sequence_of_tuple(["a", 1, (None,), [2.0, 3.0]])
-    >>> is_sequence_of_tuple(items)
-    True
-
     """
     items = []
     for item in sequence:
@@ -53,12 +47,6 @@ def coerce_sequence_of_list(sequence):
         with each iterable item converted to a list,
         and non-iterable items wrapped in a list.
 
-    Examples
-    --------
-    >>> items = coerce_sequence_of_list(["a", 1, (None,), [2.0, 3.0]])
-    >>> is_sequence_of_list(items)
-    True
-
     """
     items = []
     for item in sequence:

src/compas/data/encoders.py

@@ -181,13 +181,14 @@ class DataDecoder(json.JSONDecoder):
 
     >>> import json
     >>> from compas.data import DataDecoder
-    >>> with open("point.json", "r") as f:
-    ...     point = json.load(f, cls=DataDecoder)
+    >>> with open('point.json', 'r') as f:        # doctest: +SKIP
+    ...     point = json.load(f, cls=DataDecoder) # doctest: +SKIP
+    ...
 
     Implicit use case.
 
     >>> from compas.data import json_load
-    >>> point = json_load("point.json")
+    >>> point = json_load('point.json')  # doctest: +SKIP
 
     """
 

src/compas/datastructures/assembly/part.py

@@ -34,24 +34,27 @@ class GeometricFeature(Feature):
 
     Examples
     --------
-    >>>    def trim_brep_plane(brep, plane):
-    >>> # trim brep with plane, return trimmed brep
+    >>> from compas.geometry import Brep
+    >>> from compas.datastructures import Mesh
     >>>
-    >>>    def trim_mesh_plane(mesh, plane):
-    >>> # trim mesh with plane, return trimmed mesh
+    >>> def trim_brep_plane(brep, plane):
+    ...     pass
+    ...
+    >>> def trim_mesh_plane(mesh, plane):
+    ...     pass
+    ...
+    >>> class TrimmingFeature(GeometricFeature):
+    ...     OPERATIONS = {Brep: trim_brep_plane, Mesh: trim_mesh_plane}
+    ...     def __init__(self, trimming_plane):
+    ...         super(TrimmingFeature, self).__init__()
+    ...         self._geometry = trimming_plane
+    ...     def apply(self, part):
+    ...         part_geometry = part.get_geometry(with_features=True)
+    ...         type_ = Brep if isinstance(part_geometry, Brep) else Mesh
+    ...         operation = OPERATIONS[type_]
+    ...         return operation(part_geometry, self._geometry)
+    ...
     >>>
-    >>>    class TrimmingFeature(GeometricFeature):
-    >>>        OPERATIONS = {Brep: trim_brep_plane, Mesh: trim_mesh_plane}
-    >>>
-    >>>            def __init__(self, trimming_plane):
-    >>>                super(TrimmingFeature, self).__init__()
-    >>>                self._geometry = trimming_plane
-    >>>
-    >>>            def apply(self, part):
-    >>>                part_geometry = part.get_geometry(with_features=True)
-    >>>                type_ = Brep if isinstance(part_geometry, Brep) else Mesh
-    >>>                operation = OPERATIONS[type_]
-    >>>                return operation(part_geometry, self._geometry)
 
     """
 
@@ -81,18 +84,17 @@ class ParametricFeature(Feature):
     Examples
     --------
     >>> class ExtensionFeature(ParametricFeature):
-    >>>     def __init__(self, extend_by):
-    >>>         super(ExtensionFeature, self).__init__()
-    >>>         self.extend_by = extend_by
-    >>>
-    >>>     def apply(self, part):
-    >>>         part.length += self._extend_by
-    >>>
-    >>>     def restore(self, part):
-    >>>         part.length -= self._extend_by
+    ...     def __init__(self, extend_by):
+    ...         super(ExtensionFeature, self).__init__()
+    ...         self.extend_by = extend_by
+    ...     def apply(self, part):
+    ...         part.length += self._extend_by
+    ...     def restore(self, part):
+    ...         part.length -= self._extend_by
+    ...     def accumulate(self, other):
+    ...         return BeamExtensionFeature(max(self.extend_by, other.extend_by))
+    ...
     >>>
-    >>>     def accumulate(self, other):
-    >>>         return BeamExtensionFeature(max(self.extend_by, other.extend_by))
 
     """
 

src/compas/datastructures/cell_network/cell_network.py

@@ -74,10 +74,17 @@ class CellNetwork(Datastructure):
     >>> vertices = [(0, 0, 0), (0, 1, 0), (1, 1, 0), (1, 0, 0), (0, 0, 1), (1, 0, 1), (1, 1, 1), (0, 1, 1)]
     >>> faces = [[0, 1, 2, 3], [0, 3, 5, 4], [3, 2, 6, 5], [2, 1, 7, 6], [1, 0, 4, 7], [4, 5, 6, 7]]
     >>> cells = [[0, 1, 2, 3, 4, 5]]
-    >>> [network.add_vertex(x=x, y=y, z=z) for x, y, z in vertices]
-    >>> [cell_network.add_face(fverts) for fverts in faces]
-    >>> [cell_network.add_cell(fkeys) for fkeys in cells]
-    >>> cell_network
+    >>> for x, y, z in vertices:
+    ...     vertex = cell_network.add_vertex(x=x, y=y, z=z)
+    ...
+    >>> for face_vertices in faces:
+    ...     face = cell_network.add_face(face_vertices)
+    ...
+    >>> for cell_faces in cells:
+    ...    cell = cell_network.add_cell(cell_faces)
+    ...
+    >>> print(cell_network)
+    <CellNetwork with 8 vertices, 6 faces, 1 cells, 12 edges>
 
     """
 

src/compas/datastructures/graph/graph.py

@@ -2366,7 +2366,7 @@ def complement(self):
         >>> from compas.datastructures import Graph
         >>> graph = Graph.from_obj(compas.get("lines.obj"))
         >>> complement = graph.complement()
-        >>> any(complement.has_edge(u, v, directed=False) for u, v in graph.edges())
+        >>> any(complement.has_edge((u, v), directed=False) for u, v in graph.edges())
         False
 
         """
@@ -2381,7 +2381,7 @@ def complement(self):
 
         for u, v in combinations(self.nodes(), 2):
             if not self.has_edge((u, v), directed=False):
-                graph.add_edge(u, v, attr_dict=self.edge_attributes((u, v)))
+                graph.add_edge(u, v)
 
         return graph
 

src/compas/datastructures/mesh/duality.py

@@ -37,7 +37,7 @@ def mesh_dual(mesh, cls=None, include_boundary=False):
     >>> mesh.delete_face(6)
     >>> mesh.delete_face(7)
     >>> mesh.quads_to_triangles()
-    >>> mesh = mesh.subdivide("corner")
+    >>> mesh = mesh.subdivided("corner")
     >>> dual = mesh.dual(include_boundary=True)
 
     """
@@ -78,7 +78,7 @@ def mesh_dual(mesh, cls=None, include_boundary=False):
     edge_vertex = {}
     for boundary in mesh.edges_on_boundaries():
         for u, v in boundary:
-            x, y, z = mesh.edge_midpoint(u, v)
+            x, y, z = mesh.edge_midpoint((u, v))
             edge_vertex[u, v] = edge_vertex[v, u] = dual.add_vertex(x=x, y=y, z=z)
 
     vertex_vertex = {}
@@ -97,7 +97,7 @@ def mesh_dual(mesh, cls=None, include_boundary=False):
             nbrs = mesh.vertex_neighbors(vertex, ordered=True)[::-1]
             vertices.append(edge_vertex[vertex, nbrs[0]])
             for nbr in nbrs[:-1]:
-                vertices.append(mesh.halfedge_face(vertex, nbr))
+                vertices.append(mesh.halfedge_face((vertex, nbr)))
             vertices.append(edge_vertex[vertex, nbrs[-1]])
             dual.add_face(vertices[::-1])
 

src/compas/datastructures/mesh/mesh.py

@@ -2855,6 +2855,9 @@ def remove_duplicate_vertices(self, precision=None):
         36
         >>> for x, y, z in mesh.vertices_attributes("xyz", keys=list(mesh.vertices())[:5]):
         ...     mesh.add_vertex(x=x, y=y, z=z)
+        ...
+        36
+        37
         38
         39
         40
@@ -4791,9 +4794,9 @@ def transform_numpy(self, T):
         Examples
         --------
         >>> from compas.datastructures import Mesh
-        >>> from compas.geometry import matrix_from_axis_and_angle_numpy
+        >>> from compas.geometry import matrix_from_axis_and_angle
         >>> mesh = Mesh.from_polyhedron(6)
-        >>> T = matrix_from_axis_and_angle_numpy([0, 0, 1], math.pi / 4)
+        >>> T = matrix_from_axis_and_angle([0, 0, 1], math.pi / 4)
         >>> mesh.transform_numpy(T)
 
         """
@@ -4906,9 +4909,9 @@ def face_matrix(self, rtype="array"):
         >>> type(F)
         <class 'numpy.ndarray'>
 
-        >>> from numpy import allclose
+        >>> from numpy import allclose, asarray
         >>> xyz = asarray(mesh.vertices_attributes('xyz'))
-        >>> F = mesh.face_matrix(mesh, rtype='csr')
+        >>> F = mesh.face_matrix(rtype='csr')
         >>> c1 = F.dot(xyz) / F.sum(axis=1)
         >>> c2 = [mesh.face_centroid(fkey) for fkey in mesh.faces()]
         >>> allclose(c1, c2)
@@ -4963,10 +4966,11 @@ def laplacian_matrix(self, rtype="array"):
         --------
         >>> from compas.datastructures import Mesh
         >>> mesh = Mesh.from_polyhedron(6)
-        >>> L = mesh.laplacian_matrix(mesh, rtype='array')
+        >>> L = mesh.laplacian_matrix(rtype='array')
         >>> type(L)
         <class 'numpy.ndarray'>
 
+        >>> from numpy import asarray
         >>> xyz = asarray(mesh.vertices_attributes('xyz'))
         >>> L = mesh.laplacian_matrix(mesh)
         >>> d = L.dot(xyz)
@@ -5005,11 +5009,11 @@ def offset(self, distance=1.0):
 
         Examples
         --------
-        >>> from compas.datastructures import Mesh, mesh_offset
+        >>> from compas.datastructures import Mesh
         >>> from compas.geometry import distance_point_point as dist
         >>> mesh = Mesh.from_vertices_and_faces([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]], [[0, 1, 2, 3]])
-        >>> mesh.offset()
-        <compas.datastructures.mesh.mesh.Mesh object at 0x109eaad60>
+        >>> mesh.offset()  # doctest: +ELLIPSIS
+        <compas.datastructures.mesh.mesh.Mesh object at ...>
 
         """
         offset = self.copy()
@@ -5047,8 +5051,8 @@ def thickened(self, thickness=1.0, both=True):
         --------
         >>> from compas.datastructures import Mesh
         >>> mesh = Mesh.from_vertices_and_faces([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]], [[0, 1, 2, 3]])
-        >>> mesh.thicken(mesh)
-        <compas.datastructures.mesh.mesh.Mesh object at 0x109eaad60>
+        >>> mesh.thickened()  # doctest: +ELLIPSIS
+        <compas.datastructures.mesh.mesh.Mesh object at ...>
 
         """
         if thickness <= 0:

src/compas/datastructures/mesh/operations/merge.py

@@ -21,7 +21,7 @@ def mesh_merge_faces(mesh, faces):
     --------
     >>> from compas.datastructures import Mesh
     >>> mesh = Mesh.from_vertices_and_faces([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0]], [[0, 1, 2, 3]])
-    >>> mesh = mesh.subdivide(scheme="quad")
+    >>> mesh = mesh.subdivided(scheme='quad')
     >>> mesh_merge_faces(mesh, [1, 2])
     5
     >>> mesh_merge_faces(mesh, [3, 5])

src/compas/datastructures/mesh/subdivision.py

@@ -313,7 +313,7 @@ def mesh_subdivide_catmullclark(mesh, k=1, fixed=None):
     >>> top = sorted(cage.faces(), key=lambda face: dot_vectors(cage.face_normal(face), [0, 0, 1]))[-1]
     >>> cage.edges_attribute("crease", 5, keys=list(cage.face_halfedges(top)))
 
-    >>> subd = cage.subdivide(k=4)
+    >>> subd = cage.subdivided(k=4)
 
     """
     cls = type(mesh)

src/compas/datastructures/tree/tree.py

@@ -244,10 +244,10 @@ class Tree(Datastructure):
     >>> branch.add(leaf2)
     >>> print(tree)
     <Tree with 4 nodes>
-    |--<TreeNode: root>
-        |-- <TreeNode: branch>
-            |-- <TreeNode: leaf1>
-            |-- <TreeNode: leaf2>
+        └── <TreeNode: root>
+            └── <TreeNode: branch>
+                ├── <TreeNode: leaf1>
+                └── <TreeNode: leaf2>
 
     """
 

src/compas/geometry/_core/_algebra.py

@@ -2768,12 +2768,6 @@ def close(value1, value2, tol=1e-05):
     It is more accurate to use a combination of absolute and relative tolerance.
     Therefor, use :func:`TOL.is_close` instead.
 
-    Examples
-    --------
-    >>> close(1.0, 1.001)
-    False
-    >>> close(1.0, 1.001, tol=1e-2)
-    True
     """
     return TOL.is_close(value1, value2, rtol=0.0, atol=tol)
 
@@ -2815,13 +2809,5 @@ def allclose(l1, l2, tol=None):
     ----------
     .. [1] https://docs.scipy.org/doc/numpy/reference/generated/numpy.allclose.html
 
-    Examples
-    --------
-    >>> allclose([0.1, 0.2, 0.3, 0.4], [0.1, 0.20001, 0.3, 0.4])
-    True
-
-    >>> allclose([0.1, 0.2, 0.3, 0.4], [0.1, 0.20001, 0.3, 0.4], tol=1e-6)
-    False
-
     """
     return TOL.is_allclose(l1, l2, atol=tol)