Codecov and flake8 fix

.github/build_real.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 set -e
-pip install -e .[testing]
+pip install .[testing]

.github/test_real.sh

@@ -7,4 +7,5 @@ if [[ $IMAGE == "private" ]] && [[ $OS == "ubuntu" ]]; then
     EXTRA_FLAGS='--disallow_skipped'
 fi
 
+cd tests
 testflo -v -n 1 --coverage --coverpkg pygeo $EXTRA_FLAGS

README.md

@@ -22,7 +22,6 @@ Please cite pyGeo in any publication for which you find it useful.
 For more background, theory, and figures, see the [this paper](http://umich.edu/~mdolaboratory/pdf/Kenway2010b.pdf).
 
 G. K. W. Kenway, Kennedy, G. J., and Martins, J. R. R. A., “A CAD-Free Approach to High-Fidelity Aerostructural Optimization”, in Proceedings of the 13th AIAA/ISSMO Multidisciplinary Analysis Optimization Conference, Fort Worth, TX, 2010.
-
 ```
 @conference {Kenway:2010:C,
 	title = {A {CAD}-Free Approach to High-Fidelity Aerostructural Optimization},

examples/deform_geometry/ffd/simple_ffd.py

@@ -44,8 +44,8 @@
 f = open(filename, "w")
 f.write("\t\t1\n")
 f.write("\t\t%d\t\t%d\t\t%d\n" % (nX, nY, nZ))
-for set in [X, Y, Z]:
-    for row in set:
+for i in [X, Y, Z]:
+    for row in i:
         vals = tuple(row)
         f.write("\t%3.8f\t%3.8f\t%3.8f\t%3.8f\t%3.8f\t%3.8f\n" % vals)
 f.close()

pygeo/constraints/DVCon.py

@@ -79,32 +79,28 @@ def __init__(self, name="DVCon1"):
         self.surfaces = {}
         self.DVGeometries = {}
 
-    def setSurface(self, surf, name="default", addToDVGeo=False, DVGeoName="default", format="point-vector"):
+    def setSurface(self, surf, name="default", addToDVGeo=False, DVGeoName="default", surfFormat="point-vector"):
         """
         Set the surface DVConstraints will use to perform projections.
 
         Parameters
         ----------
         surf : pyGeo object or list
-
             This is the surface representation to use for
             projections. If available, a pyGeo surface object can be
             used OR a triagnulaed surface in the form [p0, v1, v2] can
             be used. This triangulated surface form can be supplied
             form pyADflow or from pyTrian.
 
         addToDVGeo : bool or str
-
             To embed the surface pointset in a DVGeo object,
             give the DVGeo name as a string. Otherwise, leave False
 
         name : str
-
             Name associated with the surface. Must be unique. For backward compatibility,
             the name is 'default' by default
 
         DVGeoName : str
-
             Name of the DVGeo object to set the surface to. You only
             need to set this if you're using multiple DVGeo objects
             for a problem. For backward compatibility, the name is 'default' by default
@@ -123,7 +119,7 @@ def setSurface(self, surf, name="default", addToDVGeo=False, DVGeoName="default"
             raise KeyError("Surface names must be unique. Repeated surface name: " + str(name))
 
         self.surfaces[name] = list()
-        if format == "point-vector":
+        if surfFormat == "point-vector":
             if type(surf) == list:
                 # Data from ADflow
                 p0 = np.array(surf[0])
@@ -140,7 +136,7 @@ def setSurface(self, surf, name="default", addToDVGeo=False, DVGeoName="default"
 
             p1 = p0 + v1
             p2 = p0 + v2
-        elif format == "point-point":
+        elif surfFormat == "point-point":
             if type(surf) == str:
                 # load from file
                 raise NotImplementedError
@@ -2797,7 +2793,7 @@ def addMonotonicConstraints(self, key, slope=1.0, name=None, start=0, stop=-1, c
         self.linearCon[conName] = GlobalLinearConstraint(
             conName,
             key,
-            type="monotonic",
+            conType="monotonic",
             options=options,
             lower=0,
             upper=None,

pygeo/constraints/baseConstraint.py

@@ -273,12 +273,12 @@ class GlobalLinearConstraint(object):
     constriants coupling global design variables together.
     """
 
-    def __init__(self, name, key, type, options, lower, upper, DVGeo, config):
+    def __init__(self, name, key, conType, options, lower, upper, DVGeo, config):
         # No error checking here since the calling routine should have
         # already done it.
         self.name = name
         self.key = key
-        self.type = type
+        self.type = conType
         self.lower = lower
         self.upper = upper
         self.DVGeo = DVGeo

pygeo/geo_utils/bilinear_map.py

@@ -4,14 +4,10 @@
 def getBiLinearMap(edge0, edge1, edge2, edge3):
     """Get the UV coordinates on a square defined from spacing on the edges"""
 
-    assert len(edge0) == len(
-        edge1
-    ), "Error, getBiLinearMap:\
- The len of edge0 and edge1 are not the same"
-    assert len(edge2) == len(
-        edge3
-    ), "Error, getBiLinearMap:\
- The len of edge2 and edge3 are no the same"
+    if len(edge0) != len(edge1):
+        raise ValueError("getBiLinearMap: The len of edge0 and edge1 are not the same")
+    if len(edge2) != len(edge3):
+        raise ValueError("getBiLinearMap: The len of edge2 and edge3 are no the same")
 
     N = len(edge0)
     M = len(edge2)

pygeo/geo_utils/dcel.py

@@ -452,17 +452,17 @@ def loadDCEL(self, fileName):
         self.vl = []
         self.el = []
         self.faceInfo = []
-        for i in range(nvertices):
+        for _i in range(nvertices):
             a = f.readline().split()
             self.vl.append(DCELVertex([float(a[0]), float(a[1])], np.array([float(a[2]), float(a[3]), float(a[4])])))
 
-        for i in range(nedges):
+        for _i in range(nedges):
             a = f.readline().split()
             self.el.append(DCELEdge(int(a[0]), int(a[1]), None, None, None, a[8]))
             self.el[-1].x1 = np.array([float(a[2]), float(a[3]), float(a[4])])
             self.el[-1].x2 = np.array([float(a[5]), float(a[6]), float(a[7])])
 
-        for i in range(nfaces):
+        for _i in range(nfaces):
             a = f.readline().split()
             self.faceInfo.append(a[0])
 

pygeo/geo_utils/node_edge_face.py

@@ -125,9 +125,9 @@ def setNodeValue(arr, value, nodeIndex):
     return arr
 
 
-def setEdgeValue(arr, values, dir, edgeIndex):
+def setEdgeValue(arr, values, edgeDir, edgeIndex):
 
-    if dir == -1:  # Reverse values
+    if edgeDir == -1:  # Reverse values
         values = values[::-1]
 
     if edgeIndex == 0:

pygeo/geo_utils/pointselect.py

@@ -44,24 +44,23 @@ def __init__(self, psType, *args, **kwargs):
         """
 
         if psType == "x" or psType == "y" or psType == "z":
-            assert (
-                "pt1" in kwargs and "pt2" in kwargs
-            ), "Error:, two points \
-must be specified with initialization type x,y, or z. Points are specified \
-with kwargs pt1=[x1,y1,z1],pt2=[x2,y2,z2]"
-
+            if not ("pt1" in kwargs and "pt2" in kwargs):
+                raise ValueError(
+                    "Two points must be specified with initialization type x, y, or z. "
+                    + "Points are specified with kwargs pt1=[x1,y1,z1], pt2=[x2,y2,z2]"
+                )
         elif psType == "quad":
-            assert (
-                "pt1" in kwargs and "pt2" in kwargs and "pt3" in kwargs and "pt4" in kwargs
-            ), "Error:, four points \
-must be specified with initialization type quad. Points are specified \
-with kwargs pt1=[x1,y1,z1],pt2=[x2,y2,z2],pt3=[x3,y3,z3],pt4=[x4,y4,z4]"
+            if not ("pt1" in kwargs and "pt2" in kwargs and "pt3" in kwargs and "pt4" in kwargs):
+                raise ValueError(
+                    "Four points must be specified with initialization type quad. "
+                    + "Points are specified with kwargs pt1=[x1,y1,z1], pt2=[x2,y2,z2], pt3=[x3,y3,z3], pt4=[x4,y4,z4]"
+                )
 
         elif psType == "ijkBounds":
-            assert (
-                "ijkBounds" in kwargs
-            ), "Error:, ijkBounds selection method requires a dictonary with \
-            the specific ijkBounds for each volume."
+            if not ("ijkBounds" in kwargs):
+                raise ValueError(
+                    "ijkBounds selection method requires a dictonary with the specific ijkBounds for each volume."
+                )
 
         corners = np.zeros([4, 3])
         if psType in ["x", "y", "z", "corners"]:

pygeo/geo_utils/split_quad.py

@@ -182,16 +182,10 @@ def tfi_2d(e0, e1, e2, e3):
 
         Nu = len(e0)
         Nv = len(e2)
-        assert Nu == len(e1), (
-            "Number of nodes on edge0 and edge1\
- are not the same, %d %d"
-            % (len(e0), len(e1))
-        )
-        assert Nv == len(e3), (
-            "Number of nodes on edge2 and edge3\
- are not the same, %d %d"
-            % (len(e2), len(e3))
-        )
+        if Nu != len(e1):
+            raise ValueError(f"Number of nodes on edge0 and edge1 are not the same: {len(e0)} {len(e1)}")
+        if Nv != len(e3):
+            raise ValueError(f"Number of nodes on edge2 and edge3 are not the same: {len(e2)} {len(e3)}")
 
         U = np.linspace(0, 1, Nu)
         V = np.linspace(0, 1, Nv)

pygeo/parameterization/DVGeo.py

@@ -76,13 +76,19 @@ class DVGeometry(object):
       >>>
     """
 
-    def __init__(self, fileName, complex=False, child=False, faceFreeze=None, name=None, *args, **kwargs):
+    def __init__(self, fileName, isComplex=False, child=False, faceFreeze=None, name=None, *args, **kwargs):
 
         self.DV_listGlobal = OrderedDict()  # Global Design Variable List
         self.DV_listLocal = OrderedDict()  # Local Design Variable List
         self.DV_listSectionLocal = OrderedDict()  # Local Normal Design Variable List
         self.DV_listSpanwiseLocal = OrderedDict()  # Local Normal Design Variable List
 
+        # FIXME: for backwards compatibility we still allow the argument complex=True/False
+        # which we now check in kwargs and overwrite
+        if "complex" in kwargs:
+            isComplex = kwargs.pop("complex")
+            warnings.warn("The keyword argument 'complex' is deprecated, use 'isComplex' instead.")
+
         # Coefficient rotation matrix dict for Section Local variables
         self.coefRotM = {}
 
@@ -97,7 +103,7 @@ def __init__(self, fileName, complex=False, child=False, faceFreeze=None, name=N
         self.updated = {}
         self.masks = None
         self.finalized = False
-        self.complex = complex
+        self.complex = isComplex
         if self.complex:
             self.dtype = "D"
         else:
@@ -362,7 +368,7 @@ def addRefAxis(
 
                 curveSymm = copy.deepcopy(curve)
                 curveSymm.reverse()
-                for coef in curveSymm.coef:
+                for _coef in curveSymm.coef:
                     curveSymm.coef[:, index] = -curveSymm.coef[:, index]
                 self.axis[name] = {
                     "curve": curve,
@@ -417,7 +423,7 @@ def addRefAxis(
             nVol = len(v)
             volOrd = [v.pop(0)]
             faceLink = self.FFD.topo.faceLink
-            for iter in range(nVol):
+            for _iter in range(nVol):
                 for vInd, i in enumerate(v):
                     for pInd, j in enumerate(volOrd):
                         if faceLink[i, faceCol] == faceLink[j, faceCol + 1]:
@@ -4220,8 +4226,8 @@ def sectionFrame(self, sectionIndex, sectionTransform, sectionLink, ivol=0, orie
 
             # Need to initialize coefRotM to identity matrix for case with no
             # global design variables
-            for slice in rolledlIndex[i, :, :]:
-                for coef in slice:
+            for j in rolledlIndex[i, :, :]:
+                for coef in j:
                     self.coefRotM[coef] = np.eye(3)
 
         return nSections

pygeo/parameterization/DVGeoAxi.py

@@ -1,3 +1,4 @@
+import warnings
 import numpy as np
 from scipy import sparse
 from collections import OrderedDict
@@ -29,8 +30,14 @@ class _AxiTransform(object):
         into the x,z plane and use z as the rotational axis
     """
 
-    def __init__(self, pts, center, collapse_into, complex=False):
-        self.complex = complex
+    def __init__(self, pts, center, collapse_into, isComplex=False, **kwargs):
+        # FIXME: for backwards compatibility we still allow the argument complex=True/False
+        # which we now check in kwargs and overwrite
+        if "complex" in kwargs:
+            isComplex = kwargs.pop("complex")
+            warnings.warn("The keyword argument 'complex' is deprecated, use 'isComplex' instead.")
+
+        self.complex = isComplex
 
         self.c_plane = collapse_into
         self.n_points = pts.shape[0]
@@ -193,11 +200,17 @@ class DVGeometryAxi(DVGeometry):
       >>>
     """
 
-    def __init__(self, fileName, center, collapse_into, complex=False, child=False, *args, **kwargs):
+    def __init__(self, fileName, center, collapse_into, isComplex=False, child=False, *args, **kwargs):
 
         self.axiTransforms = OrderedDict()  # TODO: Why is this ordered?
 
-        super(DVGeometryAxi, self).__init__(fileName, complex, child, *args, **kwargs)
+        # FIXME: for backwards compatibility we still allow the argument complex=True/False
+        # which we now check in kwargs and overwrite
+        if "complex" in kwargs:
+            isComplex = kwargs.pop("complex")
+            warnings.warn("The keyword argument 'complex' is deprecated, use 'isComplex' instead.")
+
+        super().__init__(fileName, isComplex=isComplex, child=child, *args, **kwargs)
 
         self.center = center
         self.collapse_into = collapse_into