Merge pull request #155 from cadenmyers13/profile-dep

sbillinge · web-flow · commit 545ab1387ed0 · 2026-02-19T17:00:15.000-08:00
deprecate: Deprecate `Profile` class and `SimpleRecipe` class
diff --git a/docs/examples/coreshellnp.py b/docs/examples/coreshellnp.py
@@ -44,8 +44,8 @@ def makeRecipe(stru1, stru2, datname):
     # Load data and add it to the profile
     parser = PDFParser()
     parser.parseFile(datname)
-    profile.loadParsedData(parser)
-    profile.setCalculationRange(xmin=1.5, xmax=45, dx=0.1)
+    profile.load_parsed_data(parser)
+    profile.set_calculation_range(xmin=1.5, xmax=45, dx=0.1)
 
     # The ProfileGenerator
     # In order to fit the core and shell phases simultaneously, we must use two
diff --git a/docs/examples/crystalpdf.py b/docs/examples/crystalpdf.py
@@ -55,8 +55,8 @@ def makeRecipe(ciffile, datname):
     # configuration steps.
     parser = PDFParser()
     parser.parseFile(datname)
-    profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax=20)
+    profile.load_parsed_data(parser)
+    profile.set_calculation_range(xmax=20)
 
     # The ProfileGenerator
     # The PDFGenerator is for configuring and calculating a PDF profile. Here,
diff --git a/docs/examples/crystalpdfall.py b/docs/examples/crystalpdfall.py
@@ -39,8 +39,8 @@ def makeProfile(datafile):
     profile = Profile()
     parser = PDFParser()
     parser.parseFile(datafile)
-    profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax=20)
+    profile.load_parsed_data(parser)
+    profile.set_calculation_range(xmax=20)
     return profile
 
 
diff --git a/docs/examples/crystalpdfobjcryst.py b/docs/examples/crystalpdfobjcryst.py
@@ -48,8 +48,8 @@ def makeRecipe(ciffile, datname):
     # structure being refined.
     parser = PDFParser()
     parser.parseFile(datname)
-    profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax=20)
+    profile.load_parsed_data(parser)
+    profile.set_calculation_range(xmax=20)
 
     # The ProfileGenerator
     # This time we use the CreateCrystalFromCIF method of pyobjcryst.crystal to
diff --git a/docs/examples/crystalpdftwodata.py b/docs/examples/crystalpdftwodata.py
@@ -48,13 +48,13 @@ def makeRecipe(ciffile, xdatname, ndatname):
     # Load data and add it to the proper Profile.
     parser = PDFParser()
     parser.parseFile(xdatname)
-    xprofile.loadParsedData(parser)
-    xprofile.setCalculationRange(xmax=20)
+    xprofile.load_parsed_data(parser)
+    xprofile.set_calculation_range(xmax=20)
 
     parser = PDFParser()
     parser.parseFile(ndatname)
-    nprofile.loadParsedData(parser)
-    nprofile.setCalculationRange(xmax=20)
+    nprofile.load_parsed_data(parser)
+    nprofile.set_calculation_range(xmax=20)
 
     # The ProfileGenerators
     # We need one of these for the x-ray data.
diff --git a/docs/examples/crystalpdftwophase.py b/docs/examples/crystalpdftwophase.py
@@ -45,8 +45,8 @@ def makeRecipe(niciffile, siciffile, datname):
     # Load data and add it to the profile
     parser = PDFParser()
     parser.parseFile(datname)
-    profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax=20)
+    profile.load_parsed_data(parser)
+    profile.set_calculation_range(xmax=20)
 
     # The ProfileGenerator
     # In order to fit two phases simultaneously, we must use two PDFGenerators.
diff --git a/docs/examples/debyemodel.py b/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.
diff --git a/docs/examples/debyemodelII.py b/docs/examples/debyemodelII.py
@@ -77,8 +77,8 @@ def makeRecipeII():
     # Change the fit ranges of the Profiles embedded within the
     # FitContributions. We want to fit one of the contributions at low
     # temperature, and one at high.
-    lowT.profile.setCalculationRange(0, 150)
-    highT.profile.setCalculationRange(400, 500)
+    lowT.profile.set_calculation_range(0, 150)
+    highT.profile.set_calculation_range(400, 500)
 
     # Vary the offset from each FitContribution separately, while keeping the
     # Debye temperatures the same. We give each offset variable a different
@@ -102,8 +102,8 @@ def plotResults(recipe):
 
     # We want to extend the fitting range to its full extent so we can get a
     # nice full plot.
-    recipe.lowT.profile.setCalculationRange(xmin="obs", xmax="obs")
-    recipe.highT.profile.setCalculationRange(xmin="obs", xmax="obs")
+    recipe.lowT.profile.set_calculation_range(xmin="obs", xmax="obs")
+    recipe.highT.profile.set_calculation_range(xmin="obs", xmax="obs")
     T = recipe.lowT.profile.x
     U = recipe.lowT.profile.y
     # We can use a FitContribution's 'evaluateEquation' method to evaluate
diff --git a/docs/examples/ellipsoidsas.py b/docs/examples/ellipsoidsas.py
@@ -39,7 +39,7 @@ def makeRecipe(datname):
     # properly and pass the metadata along.
     parser = SASParser()
     parser.parseFile(datname)
-    profile.loadParsedData(parser)
+    profile.load_parsed_data(parser)
 
     # The ProfileGenerator
     # The SASGenerator is for configuring and calculating a SAS profile. We use
diff --git a/docs/examples/nppdfcrystal.py b/docs/examples/nppdfcrystal.py
@@ -44,8 +44,8 @@ def makeRecipe(ciffile, grdata):
 
     pdfparser = PDFParser()
     pdfparser.parseFile(grdata)
-    pdfprofile.loadParsedData(pdfparser)
-    pdfprofile.setCalculationRange(xmin=0.1, xmax=20)
+    pdfprofile.load_parsed_data(pdfparser)
+    pdfprofile.set_calculation_range(xmin=0.1, xmax=20)
 
     pdfcontribution = FitContribution("pdf")
     pdfcontribution.set_profile(pdfprofile, xname="r")
diff --git a/docs/examples/nppdfobjcryst.py b/docs/examples/nppdfobjcryst.py
@@ -40,7 +40,7 @@ def makeRecipe(molecule, datname):
 
     # Load data and add it to the profile
     profile.loadtxt(datname)
-    profile.setCalculationRange(xmin=1.2, xmax=8)
+    profile.set_calculation_range(xmin=1.2, xmax=8)
 
     # The ProfileGenerator
     # Create a DebyePDFGenerator named "G".
diff --git a/docs/examples/nppdfsas.py b/docs/examples/nppdfsas.py
@@ -48,8 +48,8 @@ def makeRecipe(ciffile, grdata, iqdata):
     pdfprofile = Profile()
     pdfparser = PDFParser()
     pdfparser.parseFile(grdata)
-    pdfprofile.loadParsedData(pdfparser)
-    pdfprofile.setCalculationRange(xmin=0.1, xmax=20)
+    pdfprofile.load_parsed_data(pdfparser)
+    pdfprofile.set_calculation_range(xmin=0.1, xmax=20)
 
     pdfcontribution = FitContribution("pdf")
     pdfcontribution.set_profile(pdfprofile, xname="r")
@@ -66,7 +66,7 @@ def makeRecipe(ciffile, grdata, iqdata):
     sasprofile = Profile()
     sasparser = SASParser()
     sasparser.parseFile(iqdata)
-    sasprofile.loadParsedData(sasparser)
+    sasprofile.load_parsed_data(sasparser)
     if all(sasprofile.dy == 0):
         sasprofile.dy[:] = 1
 
diff --git a/docs/examples/simplepdf.py b/docs/examples/simplepdf.py
@@ -35,7 +35,7 @@ def makeRecipe(ciffile, datname):
     # Work directly with a custom PDFContribution to load the data
     contribution = PDFContribution("nickel")
     contribution.loadData(datname)
-    contribution.setCalculationRange(xmin=1, xmax=20, dx=0.1)
+    contribution.set_calculation_range(xmin=1, xmax=20, dx=0.1)
 
     # and the phase
     stru = Structure()
diff --git a/docs/examples/simplepdftwophase.py b/docs/examples/simplepdftwophase.py
@@ -31,7 +31,7 @@ def makeRecipe(niciffile, siciffile, datname):
     # Load data and add it to the profile
     contribution = PDFContribution("nisi")
     contribution.loadData(datname)
-    contribution.setCalculationRange(xmax=20)
+    contribution.set_calculation_range(xmax=20)
 
     stru = loadCrystal(niciffile)
     contribution.addStructure("ni", stru)
diff --git a/docs/source/extending.rst b/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.
 
diff --git a/news/profile-dep.rst b/news/profile-dep.rst
@@ -0,0 +1,29 @@
+**Added:**
+
+* Added ``load_parsed_data`` in replace of ``loadParsedData`` in ``Profile`` and ``SimpleRecipe``.
+* Added ``set_observed_profile`` in replace of ``setObservedProfile`` in ``Profile`` and ``SimpleRecipe``.
+* Added ``set_calculation_range`` in replace of ``setCalculationRange`` in ``Profile`` and ``SimpleRecipe``.
+* Added ``set_calculation_points`` in replace of ``setCalculationPoints`` in ``Profile`` and ``SimpleRecipe``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``loadParsedData`` in ``Profile`` and ``SimpleRecipe`` for removal in 4.0.0.
+* Deprecated ``setObservedProfile`` in ``Profile`` and ``SimpleRecipe`` for removal in 4.0.0.
+* Deprecated ``setCalculationRange`` in ``Profile`` and ``SimpleRecipe`` for removal in 4.0.0.
+* Deprecated ``setCalculationPoints`` in ``Profile`` and ``SimpleRecipe`` for removal in 4.0.0.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/src/diffpy/srfit/fitbase/profile.py b/src/diffpy/srfit/fitbase/profile.py
@@ -29,9 +29,40 @@
 from diffpy.srfit.fitbase.parameter import Parameter
 from diffpy.srfit.fitbase.validatable import Validatable
 from diffpy.srfit.util.observable import Observable
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
 
 # This is the roundoff tolerance for selecting bounds on arrays.
 epsilon = 1e-8
+base = "diffpy.srfit.fitbase.profile.Profile"
+removal_version = "4.0.0"
+
+loadParsedData_dep_msg = build_deprecation_message(
+    base,
+    "loadParsedData",
+    "load_parsed_data",
+    removal_version,
+)
+
+setObservedProfile_dep_msg = build_deprecation_message(
+    base,
+    "setObservedProfile",
+    "set_observed_profile",
+    removal_version,
+)
+
+setCalculationRange_dep_msg = build_deprecation_message(
+    base,
+    "setCalculationRange",
+    "set_calculation_range",
+    removal_version,
+)
+
+setCalculationPoints_dep_msg = build_deprecation_message(
+    base,
+    "setCalculationPoints",
+    "set_calculation_points",
+    removal_version,
+)
 
 
 class Profile(Observable, Validatable):
@@ -125,17 +156,28 @@ def __init__(self):
     yobs = property(lambda self: self._yobs)
     dyobs = property(lambda self: self._dyobs)
 
-    def loadParsedData(self, parser):
+    def load_parsed_data(self, parser):
         """Load parsed data from a ProfileParser.
 
         This sets the xobs, yobs, dyobs arrays as well as the metadata.
         """
         x, y, junk, dy = parser.getData()
         self.meta = dict(parser.getMetaData())
-        self.setObservedProfile(x, y, dy)
+        self.set_observed_profile(x, y, dy)
         return
 
-    def setObservedProfile(self, xobs, yobs, dyobs=None):
+    @deprecated(loadParsedData_dep_msg)
+    def loadParsedData(self, parser):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.profile.Profile.load_parsed_data
+        instead.
+        """
+        self.load_parsed_data(parser)
+        return
+
+    def set_observed_profile(self, xobs, yobs, dyobs=None):
         """Set the observed profile.
 
         Parameters
@@ -167,13 +209,25 @@ def setObservedProfile(self, xobs, yobs, dyobs=None):
 
         # Set the default calculation points
         if self.x is None:
-            self.setCalculationPoints(self._xobs)
+            self.set_calculation_points(self._xobs)
         else:
-            self.setCalculationPoints(self.x)
+            self.set_calculation_points(self.x)
 
         return
 
-    def setCalculationRange(self, xmin=None, xmax=None, dx=None):
+    @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 set_calculation_range(self, xmin=None, xmax=None, dx=None):
         """Set epsilon-inclusive calculation range.
 
         Adhere to the observed ``xobs`` points when ``dx`` is the same
@@ -274,10 +328,22 @@ def _isobs(a):
             self.dy = self.dyobs[indices]
         else:
             x1 = numpy.arange(lo, hi + epshi, step)
-            self.setCalculationPoints(x1)
+            self.set_calculation_points(x1)
         return
 
-    def setCalculationPoints(self, x):
+    @deprecated(setCalculationRange_dep_msg)
+    def setCalculationRange(self, xmin=None, xmax=None, dx=None):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.srfit.fitbase.profile.Profile.set_calculation_range
+        instead.
+        """
+        self.set_calculation_range(xmin, xmax, dx)
+        return
+
+    def set_calculation_points(self, x):
         """Set the calculation points.
 
         Parameters
@@ -295,16 +361,32 @@ def setCalculationPoints(self, x):
             x = x[x <= self.xobs[-1] + epsilon]
         self.x = x
         if self.yobs is not None:
-            self.y = rebinArray(self.yobs, self.xobs, self.x)
+            self.y = _rebin_array(self.yobs, self.xobs, self.x)
         if self.dyobs is not None:
             # work around for interpolation issue making some of these non-1
             if (self.dyobs == 1).all():
                 self.dy = numpy.ones_like(self.x)
             else:
                 # FIXME - This does not follow error propagation rules and it
                 # introduces (more) correlation between the data points.
-                self.dy = rebinArray(self.dyobs, self.xobs, self.x)
+                self.dy = _rebin_array(self.dyobs, self.xobs, self.x)
+
+        return
+
+    @deprecated(setCalculationPoints_dep_msg)
+    def setCalculationPoints(self, x):
+        """Set the calculation points.
+
+        Parameters
+        ----------
+        x
+            A non-empty numpy array containing the calculation points. If
+            xobs exists, the bounds of x will be limited to its bounds.
 
+        This will create y and dy on the specified grid if xobs, yobs and
+        dyobs exist.
+        """
+        self.set_calculation_points(x)
         return
 
     def loadtxt(self, *args, **kw):
@@ -314,7 +396,7 @@ 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.
@@ -345,7 +427,7 @@ 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):
@@ -418,7 +500,7 @@ def _validate(self):
 # End class Profile
 
 
-def rebinArray(A, xold, xnew):
+def _rebin_array(A, xold, xnew):
     """Rebin the an array by interpolating over the new x range.
 
     Parameters
diff --git a/src/diffpy/srfit/fitbase/simplerecipe.py b/src/diffpy/srfit/fitbase/simplerecipe.py
diff --git a/src/diffpy/srfit/pdf/pdfcontribution.py b/src/diffpy/srfit/pdf/pdfcontribution.py
diff --git a/tests/conftest.py b/tests/conftest.py
diff --git a/tests/test_contribution.py b/tests/test_contribution.py
diff --git a/tests/test_fitrecipe.py b/tests/test_fitrecipe.py
diff --git a/tests/test_profile.py b/tests/test_profile.py
diff --git a/tests/test_profilegenerator.py b/tests/test_profilegenerator.py
