Merge pull request #167 from stevenhua0320/deprecate-symmetryutilities-3

chore: deprecate method in symmetryutilities

Author: sbillinge

news/deprecate-symmetryutilities-3.rst

@@ -0,0 +1,27 @@
+**Added:**
+
+* Added ``equal_positions`` method in ``symmetryutilities.py``
+* Added ``expand_position`` method in ``symmetryutilities.py``
+* Added ``null_space`` method in ``symmetryutilities.py``
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``equalPositions`` method in ``symmetryutilities.py`` for removal in version 4.0.0
+* Deprecated ``expandPosition`` method in ``symmetryutilities.py`` for removal in version 4.0.0
+* Deprecated ``nullSpace`` method in ``symmetryutilities.py`` for removal in version 4.0.0
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/structure/symmetryutilities.py

@@ -60,6 +60,24 @@
     "nearest_site_index",
     removal_version,
 )
+equalPositions_deprecation_msg = build_deprecation_message(
+    base,
+    "equalPositions",
+    "equal_positions",
+    removal_version,
+)
+expandPosition_deprecation_msg = build_deprecation_message(
+    base,
+    "expandPosition",
+    "expand_position",
+    removal_version,
+)
+nullSpace_deprecation_msg = build_deprecation_message(
+    base,
+    "nullSpace",
+    "null_space",
+    removal_version,
+)
 
 # Constants ------------------------------------------------------------------
 
@@ -299,7 +317,17 @@ def nearest_site_index(sites, xyz):
     return nearindex
 
 
+@deprecated(equalPositions_deprecation_msg)
 def equalPositions(xyz0, xyz1, eps):
+    """'diffpy.structure.equalPositions' is deprecated and will be
+    removed in version 4.0.0.
+
+    Please use 'diffpy.structure.equal_positions' instead.
+    """
+    return equal_positions(xyz0, xyz1, eps)
+
+
+def equal_positions(xyz0, xyz1, eps):
     """Equality of two coordinates with optional tolerance.
 
     Parameters
@@ -319,7 +347,17 @@ def equalPositions(xyz0, xyz1, eps):
     return numpy.all(dxyz <= eps)
 
 
+@deprecated(expandPosition_deprecation_msg)
 def expandPosition(spacegroup, xyz, sgoffset=[0, 0, 0], eps=None):
+    """'diffpy.structure.expandPosition' is deprecated and will be
+    removed in version 4.0.0.
+
+    Please use 'diffpy.structure.expand_position' instead.
+    """
+    return expand_position(spacegroup, xyz, sgoffset, eps)
+
+
+def expand_position(spacegroup, xyz, sgoffset=[0, 0, 0], eps=None):
     """Obtain unique equivalent positions and corresponding operations.
 
     Parameters
@@ -358,7 +396,7 @@ def expandPosition(spacegroup, xyz, sgoffset=[0, 0, 0], eps=None):
             if positions:
                 nearpos = positions[nearest_site_index(positions, pos)]
                 # is it an equivalent position?
-                if equalPositions(nearpos, pos, eps):
+                if equal_positions(nearpos, pos, eps):
                     # tpl should map to the same list as nearpos
                     site_symops[tpl] = site_symops[pos2tuple(nearpos)]
                     pos_is_new = False
@@ -372,7 +410,17 @@ def expandPosition(spacegroup, xyz, sgoffset=[0, 0, 0], eps=None):
     return positions, pos_symops, multiplicity
 
 
+@deprecated(nullSpace_deprecation_msg)
 def nullSpace(A):
+    """'diffpy.structure.nullSpace' is deprecated and will be removed in
+    version 4.0.0.
+
+    Please use 'diffpy.structure.null_space' instead.
+    """
+    return null_space(A)
+
+
+def null_space(A):
     """Null space of matrix A."""
     from numpy import linalg
 
@@ -588,7 +636,7 @@ def _findNullSpace(self):
         R0 = self.invariants[0].R
         Rdiff = [(symop.R - R0) for symop in self.invariants]
         Rdiff = numpy.concatenate(Rdiff, axis=0)
-        self.null_space = nullSpace(Rdiff)
+        self.null_space = null_space(Rdiff)
         if self.null_space.size == 0:
             return
         # reverse sort rows of null_space rows by absolute value
@@ -649,7 +697,7 @@ def _findUSpace(self):
                 Ucj2 = numpy.dot(R, numpy.dot(Ucj, R.T))
                 for i, kl in i6kl:
                     R6z[i, j] += Ucj2[kl]
-        Usp6 = nullSpace(R6zall)
+        Usp6 = null_space(R6zall)
         # normalize Usp6 by its maximum component
         mxcols = numpy.argmax(numpy.fabs(Usp6), axis=1)
         mxrows = numpy.arange(len(mxcols))
@@ -716,7 +764,7 @@ def positionFormula(self, pos, xyzsymbols=("x", "y", "z")):
         # find pos in eqxyz
         idx = nearest_site_index(self.eqxyz, pos)
         eqpos = self.eqxyz[idx]
-        if not equalPositions(eqpos, pos, self.eps):
+        if not equal_positions(eqpos, pos, self.eps):
             return {}
         # any rotation matrix should do fine
         R = self.symops[idx][0].R
@@ -768,7 +816,7 @@ def UFormula(self, pos, Usymbols=stdUsymbols):
         # find pos in eqxyz
         idx = nearest_site_index(self.eqxyz, pos)
         eqpos = self.eqxyz[idx]
-        if not equalPositions(eqpos, pos, self.eps):
+        if not equal_positions(eqpos, pos, self.eps):
             return {}
         # any rotation matrix should do fine
         R = self.symops[idx][0].R

tests/test_symmetryutilities.py

@@ -27,13 +27,18 @@
     GeneratorSite,
     SymmetryConstraints,
     _Position2Tuple,
+    equal_positions,
+    equalPositions,
+    expand_position,
     expandPosition,
     is_constant_formula,
     is_space_group_latt_parms,
     isconstantFormula,
     isSpaceGroupLatPar,
     nearest_site_index,
     nearestSiteIndex,
+    null_space,
+    nullSpace,
     position_difference,
     positionDifference,
     pruneFormulaDictionary,
@@ -127,6 +132,17 @@ def test_expandPosition(self):
         self.assertEqual(4, pmult)
         return
 
+    def test_expand_position(self):
+        """Check expand_position()"""
+        # ok again Ni example
+        fcc = GetSpaceGroup(225)
+        pos, pops, pmult = expand_position(fcc, [0, 0, 0])
+        self.assertTrue(numpy.all(pos[0] == 0.0))
+        self.assertEqual(4, len(pos))
+        self.assertEqual(192, sum([len(line) for line in pops]))
+        self.assertEqual(4, pmult)
+        return
+
     def test_pruneFormulaDictionary(self):
         """Check pruneFormulaDictionary()"""
         fmdict = {"x": "3*y-0.17", "y": "0", "z": "0.13"}
@@ -152,6 +168,12 @@ def test_is_constant_formula(self):
         self.assertTrue(is_constant_formula("+13/ 9"))
         return
 
+    def test_equalPositions(self):
+        """Check equalPositions()"""
+        self.assertTrue(equalPositions([0.1, 0.2, 0.3], [0.1, 0.2, 0.3], 1.0e-5))
+        self.assertTrue(equalPositions([0.1 + 0.5e-5, 0.2 + 0.5e-5, 0.3 + 0.5e-5], [0.1, 0.2, 0.3], 1.0e-5))
+        self.assertFalse(equalPositions([0.2, 0.2, 0.3], [0.1, 0.2, 0.3], 1.0e-5))
+
 
 # End of class TestRoutines
 
@@ -704,5 +726,85 @@ def test_nearest_site_index(sites, xyz, expected):
     assert actual == expected
 
 
+@pytest.mark.parametrize(
+    "xyz0, xyz1, eps, expected",
+    [
+        pytest.param([0.1, 0.2, 0.3], [0.1, 0.2, 0.3], 1.0e-5, True),  # C1: same position
+        pytest.param(
+            [0.1 + 0.5e-5, 0.2 + 0.5e-5, 0.3 + 0.5e-5], [0.1, 0.2, 0.3], 1.0e-5, True
+        ),  # C2: same position with some tolerance
+        pytest.param([0.2, 0.2, 0.3], [0.1, 0.2, 0.3], 1.0e-5, False),  # C3: different positions
+    ],
+)
+def test_equal_positions(xyz0, xyz1, eps, expected):
+    """Check equalPositions."""
+    actual = equal_positions(xyz0, xyz1, eps)
+    assert actual == expected
+
+
+@pytest.mark.parametrize(
+    "A, expected_dim",
+    [
+        pytest.param(  # C1: full-rank 2x2 matrix
+            [[1.0, 0.0], [0.0, 1.0]],
+            0,
+        ),
+        pytest.param(  # C2: Nullspace has dim 1
+            [[1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 2.0]],
+            1,
+        ),
+        pytest.param(  # C3: Nullspace has dim 2
+            [[1.0, 2.0, 3.0], [2.0, 4.0, 6.0], [0.0, 0.0, 0.0]],
+            2,
+        ),
+        pytest.param(  # C4: Nullspace has dim 2
+            [[0.0, 0.0], [0.0, 0.0]],
+            2,
+        ),
+    ],
+)
+def test_nullSpace(A, expected_dim):
+    """Check nullSpace returns an orthonormal basis on supported square
+    matrices."""
+    A = numpy.asarray(A, dtype=float)
+    actual = nullSpace(A)
+
+    assert actual.shape == (expected_dim, A.shape[1])
+    assert numpy.allclose(A @ actual.T, numpy.zeros((A.shape[0], expected_dim)), atol=1e-12)
+    assert numpy.allclose(actual @ actual.T, numpy.eye(expected_dim), atol=1e-12)
+
+
+@pytest.mark.parametrize(
+    "A, expected_dim",
+    [
+        pytest.param(  # C1: full-rank 2x2 matrix
+            [[1.0, 0.0], [0.0, 1.0]],
+            0,
+        ),
+        pytest.param(  # C2: Nullspace has dim 1
+            [[1.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 2.0]],
+            1,
+        ),
+        pytest.param(  # C3: Nullspace has dim 2
+            [[1.0, 2.0, 3.0], [2.0, 4.0, 6.0], [0.0, 0.0, 0.0]],
+            2,
+        ),
+        pytest.param(  # C4: Nullspace has dim 2
+            [[0.0, 0.0], [0.0, 0.0]],
+            2,
+        ),
+    ],
+)
+def test_null_space(A, expected_dim):
+    """Check null_space returns an orthonormal basis on supported square
+    matrices."""
+    A = numpy.asarray(A, dtype=float)
+    actual = null_space(A)
+
+    assert actual.shape == (expected_dim, A.shape[1])
+    assert numpy.allclose(A @ actual.T, numpy.zeros((A.shape[0], expected_dim)), atol=1e-12)
+    assert numpy.allclose(actual @ actual.T, numpy.eye(expected_dim), atol=1e-12)
+
+
 if __name__ == "__main__":
     unittest.main()