Flumpy: Don't allow converting 1D vectors to vec2/3 (cctbx#648)

Previously, a size (3,) array would have erroneously converted
to a 0x3 length vec3.

This is now explicitly forbidden; you must pass at least a (0, 3)
multidimensional array.

Fixes cctbx#439.

newsfragments/439.bugfix

@@ -0,0 +1 @@
+``flumpy``: Fix case where incorrect ``flex.vec2``, ``flex.vec3`` could be generated.

src/dxtbx/boost_python/flumpy.cc

@@ -520,6 +520,13 @@ py::object vec_from_numpy(py::array np_array) {
 
   static_assert(VecType<int>::fixed_size == 2 || VecType<int>::fixed_size == 3,
                 "Only vec2/vec3 supported");
+
+  // Only accept arrays that have a dimension higher than 1 - we want
+  // numpy.array([1,2,3]) to fail but numpy.array([[1,2,3]]) to work
+  if (np_array.ndim() == 1) {
+    throw std::invalid_argument("Array for conversion to vec must be multidimensional");
+  }
+
   // Only accept arrays whose last dimension is the size of this object
   if (np_array.shape(np_array.ndim() - 1) != VecType<int>::fixed_size) {
     throw std::invalid_argument("Input array last dimension is not size "

tests/test_flumpy.py

@@ -136,7 +136,7 @@ def test_reverse_numeric_2d(flex_numeric):
 
 
 def test_numeric_4d(flex_numeric):
-    #  Check that we can think fourth-dimnesionally
+    # Check that we can think fourth-dimensionally
     grid = flex.grid(1, 9, 8, 5)
     fo = flex_numeric(grid)
     assert fo.nd() == 4
@@ -402,3 +402,11 @@ def test_int_long_degeneracy():
     npo[0] = 42
     assert all(fo[x] == npo[x] for x in range(4))
     assert fo[0] == 42
+
+
+def test_single_entry_vec_from_numpy():
+    with pytest.raises(ValueError):
+        flumpy.vec_from_numpy(np.array([2.0, 3.0, 4.0]))
+    ao = flumpy.vec_from_numpy(np.array([[2.0, 3.0, 4.0]]))
+    assert len(ao) == 1
+    assert ao[0] == pytest.approx([2.0, 3.0, 4.0])