deprecate Profile.setObservedProfile and SimpleRecipe.setObservedProfile

Author: cadenmyers13

docs/examples/debyemodel.py

@@ -93,7 +93,7 @@ def makeRecipe():
     # data into the profile.
     xydy = numpy.array(data.split(), dtype=float).reshape(-1, 3)
     x, y, dy = xydy.T
-    profile.setObservedProfile(x, y, dy)
+    profile.set_observed_profile(x, y, dy)
 
     # The FitContribution
     # The FitContribution associates the profile with the Debye function.

docs/source/extending.rst

@@ -185,7 +185,7 @@ customized Profile is the ``SASProfile`` class in the
 
 The ``__init__`` method sets the ``xobs``, ``yobs`` and ``dyobs`` attributes of
 the ``SASProfile`` to the associated arrays within the ``_datainfo`` attribute.
-The ``setObservedProfile`` method is overloaded to modify the ``_datainfo``
+The ``set_observed_profile`` method is overloaded to modify the ``_datainfo``
 arrays when their corresponding attributes are modified. This keeps the arrays
 in sync.
 

src/diffpy/srfit/fitbase/profile.py

@@ -43,6 +43,13 @@
     removal_version,
 )
 
+setObservedProfile_dep_msg = build_deprecation_message(
+    base,
+    "setObservedProfile",
+    "set_observed_profile",
+    removal_version,
+)
+
 
 class Profile(Observable, Validatable):
     """Observed and calculated profile container.
@@ -142,7 +149,7 @@ def load_parsed_data(self, parser):
         """
         x, y, junk, dy = parser.getData()
         self.meta = dict(parser.getMetaData())
-        self.setObservedProfile(x, y, dy)
+        self.set_observed_profile(x, y, dy)
         return
 
     @deprecated(loadParsedData_dep_msg)
@@ -156,7 +163,7 @@ def loadParsedData(self, parser):
         self.load_parsed_data(parser)
         return
 
-    def setObservedProfile(self, xobs, yobs, dyobs=None):
+    def set_observed_profile(self, xobs, yobs, dyobs=None):
         """Set the observed profile.
 
         Parameters
@@ -194,6 +201,18 @@ def setObservedProfile(self, xobs, yobs, dyobs=None):
 
         return
 
+    @deprecated(setObservedProfile_dep_msg)
+    def setObservedProfile(self, xobs, yobs, dyobs=None):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.srfit.fitbase.profile.Profile.set_observed_profile
+        instead.
+        """
+        self.set_observed_profile(xobs, yobs, dyobs)
+        return
+
     def setCalculationRange(self, xmin=None, xmax=None, dx=None):
         """Set epsilon-inclusive calculation range.
 
@@ -335,7 +354,7 @@ def loadtxt(self, *args, **kw):
         enforced. The first two arrays returned by numpy.loadtxt are
         assumed to be x and y. If there is a third array, it is assumed
         to by dy. Any other arrays are ignored. These are passed to
-        setObservedProfile.
+        set_observed_profile.
 
         Raises ValueError if the call to numpy.loadtxt returns fewer
         than 2 arrays.
@@ -366,7 +385,7 @@ def loadtxt(self, *args, **kw):
         if len(cols) > 2:
             dy = cols[2]
 
-        self.setObservedProfile(x, y, dy)
+        self.set_observed_profile(x, y, dy)
         return x, y, dy
 
     def savetxt(self, fname, **kwargs):

src/diffpy/srfit/fitbase/simplerecipe.py

@@ -30,6 +30,13 @@
     removal_version,
 )
 
+setObservedProfile_dep_msg = build_deprecation_message(
+    base,
+    "setObservedProfile",
+    "set_observed_profile",
+    removal_version,
+)
+
 
 class SimpleRecipe(FitRecipe):
     """SimpleRecipe class.
@@ -138,7 +145,7 @@ def loadParsedData(self, parser):
         """
         return self.load_parsed_data(parser)
 
-    def setObservedProfile(self, xobs, yobs, dyobs=None):
+    def set_observed_profile(self, xobs, yobs, dyobs=None):
         """Set the observed profile.
 
         Parameters
@@ -158,6 +165,17 @@ def setObservedProfile(self, xobs, yobs, dyobs=None):
         """
         return self.profile.setObservedProfile(xobs, yobs, dyobs)
 
+    @deprecated(setObservedProfile_dep_msg)
+    def setObservedProfile(self, xobs, yobs, dyobs=None):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.srfit.fitbase.simplerecipe.SimpleRecipe.set_observed_profile
+        instead.
+        """
+        return self.set_observed_profile(xobs, yobs, dyobs)
+
     def setCalculationRange(self, xmin=None, xmax=None, dx=None):
         """Set epsilon-inclusive calculation range.
 
@@ -213,7 +231,7 @@ def loadtxt(self, *args, **kw):
         enforced. The first two arrays returned by numpy.loadtxt are
         assumed to be x and y. If there is a third array, it is assumed
         to by dy. Any other arrays are ignored. These are passed to
-        setObservedProfile.
+        set_observed_profile.
 
          Raises ValueError if the call to numpy.loadtxt returns fewer
         than 2 arrays.

tests/conftest.py

@@ -152,7 +152,7 @@ def build_recipe_one_contribution():
     profile = Profile()
     x = linspace(0, pi, 10)
     y = sin(x)
-    profile.setObservedProfile(x, y)
+    profile.set_observed_profile(x, y)
     contribution = FitContribution("c1")
     contribution.set_profile(profile)
     contribution.set_equation("A*sin(k*x + c)")
@@ -170,14 +170,14 @@ def build_recipe_two_contributions():
     profile1 = Profile()
     x = linspace(0, pi, 10)
     y1 = sin(x)
-    profile1.setObservedProfile(x, y1)
+    profile1.set_observed_profile(x, y1)
     contribution1 = FitContribution("c1")
     contribution1.set_profile(profile1)
     contribution1.set_equation("A*sin(k*x + c)")
 
     profile2 = Profile()
     y2 = 0.5 * sin(2 * x)
-    profile2.setObservedProfile(x, y2)
+    profile2.set_observed_profile(x, y2)
     contribution2 = FitContribution("c2")
     contribution2.set_profile(profile2)
     contribution2.set_equation("B*sin(m*x + d)")

tests/test_contribution.py

@@ -101,7 +101,7 @@ def testInteraction(self):
         # create some data
         xobs = arange(0, 10, 0.5)
         yobs = xobs
-        profile.setObservedProfile(xobs, yobs)
+        profile.set_observed_profile(xobs, yobs)
 
         # Make sure this is where it's supposed to be
         self.assertTrue(gen.profile.xobs is xobs)
@@ -123,11 +123,11 @@ def testReplacements(self):
         xobs = arange(0, 10, 0.5)
         yobs = xobs
         profile = self.profile
-        profile.setObservedProfile(xobs, yobs)
+        profile.set_observed_profile(xobs, yobs)
         xobs2 = arange(0, 10, 0.8)
         yobs2 = 0.5 * xobs2
         profile2 = Profile()
-        profile2.setObservedProfile(xobs2, yobs2)
+        profile2.set_observed_profile(xobs2, yobs2)
         gen = self.gen
 
         # Validate equations
@@ -217,7 +217,7 @@ def testResidual(noObserversInGlobalBuilders):
     # Let's create some data)
     xobs = arange(0, 10, 0.5)
     yobs = xobs
-    profile.setObservedProfile(xobs, yobs)
+    profile.set_observed_profile(xobs, yobs)
 
     # Check our fitting equation.
     assert np.array_equal(fc._eq(), gen(xobs))
@@ -249,7 +249,7 @@ def testResidual(noObserversInGlobalBuilders):
     assert fc._reseq._value is None
     xobs = arange(0, 10, 0.5)
     yobs = 9 * sin(xobs)
-    profile.setObservedProfile(xobs, yobs)
+    profile.set_observed_profile(xobs, yobs)
     assert fc._eq._value is None
     assert fc._reseq._value is None
 

tests/test_fitrecipe.py

@@ -41,7 +41,7 @@ def setUp(self):
         self.profile = Profile()
         x = linspace(0, pi, 10)
         y = sin(x)
-        self.profile.setObservedProfile(x, y)
+        self.profile.set_observed_profile(x, y)
 
         # Set up the FitContribution
         self.fitcontribution = FitContribution("cont")
@@ -258,7 +258,7 @@ def testPrintFitHook(capturestdout):
     profile = Profile()
     x = linspace(0, pi, 10)
     y = sin(x)
-    profile.setObservedProfile(x, y)
+    profile.set_observed_profile(x, y)
 
     # Set up the FitContribution
     fitcontribution = FitContribution("cont")
@@ -306,7 +306,7 @@ def test_add_contribution(capturestdout):
     profile = Profile()
     x = linspace(0, pi, 10)
     y = sin(x)
-    profile.setObservedProfile(x, y)
+    profile.set_observed_profile(x, y)
 
     # Set up the FitContribution
     fitcontribution = FitContribution("cont")

tests/test_profile.py

@@ -43,16 +43,52 @@ def testInit(self):
         self.assertEqual(profile.meta, {})
         return
 
+    def test_set_observed_profile(self):
+        """Test the set_observed_profile method."""
+        # Make a profile with defined dy
+
+        x = arange(0, 10, 0.1)
+        y = x
+        dy = x
+
+        prof = self.profile
+        prof.set_observed_profile(x, y, dy)
+
+        self.assertTrue(array_equal(x, prof.xobs))
+        self.assertTrue(array_equal(y, prof.yobs))
+        self.assertTrue(array_equal(dy, prof.dyobs))
+
+        # Make a profile with undefined dy
+        x = arange(0, 10, 0.1)
+        y = x
+        dy = None
+
+        self.profile.set_observed_profile(x, y, dy)
+
+        self.assertTrue(array_equal(x, prof.xobs))
+        self.assertTrue(array_equal(y, prof.yobs))
+        self.assertTrue(array_equal(ones_like(prof.xobs), prof.dyobs))
+
+        # Get the ranged profile to make sure its the same
+        self.assertTrue(array_equal(x, prof.x))
+        self.assertTrue(array_equal(y, prof.y))
+        self.assertTrue(array_equal(ones_like(prof.xobs), prof.dy))
+
+        return
+
     def testSetObservedProfile(self):
-        """Test the setObservedProfile method."""
+        """Test the deprecated setObservedProfile method.
+
+        Remove this test when setObservedProfile is removed in 4.0.0.
+        """
         # Make a profile with defined dy
 
         x = arange(0, 10, 0.1)
         y = x
         dy = x
 
         prof = self.profile
-        prof.setObservedProfile(x, y, dy)
+        prof.set_observed_profile(x, y, dy)
 
         self.assertTrue(array_equal(x, prof.xobs))
         self.assertTrue(array_equal(y, prof.yobs))
@@ -88,7 +124,7 @@ def testSetCalculationRange(self):
         self.assertRaises(AttributeError, prof.setCalculationRange, 0, 5)
         self.assertRaises(AttributeError, prof.setCalculationRange, 0, 5, 0.2)
         # assign data
-        prof.setObservedProfile(x, y, dy)
+        prof.set_observed_profile(x, y, dy)
         # Test normal execution w/o arguments
         self.assertTrue(array_equal(x, prof.x))
         self.assertTrue(array_equal(y, prof.y))
@@ -172,7 +208,7 @@ def testSetCalculationPoints(self):
         self.assertTrue(array_equal(xcalc, prof.x))
 
         # Add the data. This should change the bounds of the calculation array.
-        prof.setObservedProfile(x, y, dy)
+        prof.set_observed_profile(x, y, dy)
         self.assertTrue(array_equal(arange(3, 10.1, 0.2), prof.x))
 
         return
@@ -183,7 +219,7 @@ def test_savetxt(self):
         self.assertRaises(SrFitError, prof.savetxt, "foo")
         xobs = arange(-2, 3.01, 0.25)
         yobs = xobs**2
-        prof.setObservedProfile(xobs, yobs)
+        prof.set_observed_profile(xobs, yobs)
         prof.ycalc = yobs.copy()
         fp = io.BytesIO()
         prof.savetxt(fp)