diffpy.srfit 3.3.0rc2__tar.gz → 3.3.1rc0__tar.gz

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.srfit
-Version: 3.3.0rc2
+Version: 3.3.1rc0
 Summary: Generalized code base for modeling problems.
 Author-email: Christopher Farrow <farrowch@gmail.com>, Pavol Juhas <pavol.juhas@gmail.com>, Caden Myers <cjm2304@columbia.edu>, "Simon J. L. Billinge" <sbillinge@ucsb.edu>
 Maintainer-email: Caden Myers <cjm2304@columbia.edu>, "Simon J. L. Billinge" <sbillinge@ucsb.edu>
@@ -86,16 +86,16 @@ target function being optimized can be specified by the user according to the
 data available.
 
 Within the diffpy.srfit framework, any parameter used in describing the
-structure of a material can be passed as a refinable variable to the global
+model can be passed as a refinable variable to the global
 optimizer.  Once parameters are declared as variables they can easily be turned
 "on" or "off", i.e. fixed or allowed to vary. Additionally, variables may be
 constrained to obey mathematical relationships with other parameters or
-variables used in the structural model. Restraints can be applied to
+variables used in the model. Restraints can be applied to
 variables, which adds a penalty to the refinement process commensurate with the
 deviation from the known value or range. The cost function can also be
-customized by the user. If the refinement contains multiple models, each model
+customized by the user. If the refinement contains multiple ``physics" models, each model
 can have its own cost function which will be properly weighted and combined to
-obtain the total cost function. Additionally, diffpy.srfit is designed to be
+obtain the total cost function. Additionally, ``diffpy.srfit`` is designed to be
 extensible, allowing the user to integrate external calculators to perform
 co-refinements with other techniques.
 
@@ -134,7 +134,11 @@ If you use diffpy.srfit in a scientific publication, we would like you to cite t
 Installation
 ------------
 
-The preferred method is to use `Miniconda Python
+The best way to install ``diffpy.srfit`` is as part of the ``diffpy.cmi`` package.  Please
+see https://github.com/diffpy/diffpy.cmi for installation information.
+
+If for some reason you want to install the ``diffpy.srfit`` library on its own,
+the preferred method is to use `Miniconda Python
 <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
 and install from the "conda-forge" channel of Conda packages.
 
@@ -150,27 +154,6 @@ The following creates and activates a new environment named ``diffpy.srfit_env``
 
 The output should print the latest version displayed on the badges above.
 
-This will install the minimal `diffpy.srfit` installation.  It will often be used
-as along with other packages for manipulating and computing crystal structures
-and so on.  We also therefore recommend installing the following:
-
-* ``diffpy.structure`` - crystal structure container and parsers,
-  https://github.com/diffpy/diffpy.structure
-* ``pyobjcryst`` - Crystal and Molecule storage, rigid units, bond
-  length and bond angle restraints, https://github.com/diffpy/pyobjcryst
-
-Optimizations involving pair distribution functions PDF or bond valence
-sums require
-
-* ``diffpy.srreal`` - python library for PDF calculation,
-  https://github.com/diffpy/diffpy.srreal
-
-Optimizations involving small angle scattering or shape characteristic
-functions from the diffpy.srfit.sas module require
-
-* ``sas`` - module for calculation of P(R) in small-angle scattering
-  from the SasView project, http://www.sasview.org
-
 Fallback Installation
 ---------------------
 

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/README.rst

@@ -50,16 +50,16 @@ target function being optimized can be specified by the user according to the
 data available.
 
 Within the diffpy.srfit framework, any parameter used in describing the
-structure of a material can be passed as a refinable variable to the global
+model can be passed as a refinable variable to the global
 optimizer.  Once parameters are declared as variables they can easily be turned
 "on" or "off", i.e. fixed or allowed to vary. Additionally, variables may be
 constrained to obey mathematical relationships with other parameters or
-variables used in the structural model. Restraints can be applied to
+variables used in the model. Restraints can be applied to
 variables, which adds a penalty to the refinement process commensurate with the
 deviation from the known value or range. The cost function can also be
-customized by the user. If the refinement contains multiple models, each model
+customized by the user. If the refinement contains multiple ``physics" models, each model
 can have its own cost function which will be properly weighted and combined to
-obtain the total cost function. Additionally, diffpy.srfit is designed to be
+obtain the total cost function. Additionally, ``diffpy.srfit`` is designed to be
 extensible, allowing the user to integrate external calculators to perform
 co-refinements with other techniques.
 
@@ -98,7 +98,11 @@ If you use diffpy.srfit in a scientific publication, we would like you to cite t
 Installation
 ------------
 
-The preferred method is to use `Miniconda Python
+The best way to install ``diffpy.srfit`` is as part of the ``diffpy.cmi`` package.  Please
+see https://github.com/diffpy/diffpy.cmi for installation information.
+
+If for some reason you want to install the ``diffpy.srfit`` library on its own,
+the preferred method is to use `Miniconda Python
 <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
 and install from the "conda-forge" channel of Conda packages.
 
@@ -114,27 +118,6 @@ The following creates and activates a new environment named ``diffpy.srfit_env``
 
 The output should print the latest version displayed on the badges above.
 
-This will install the minimal `diffpy.srfit` installation.  It will often be used
-as along with other packages for manipulating and computing crystal structures
-and so on.  We also therefore recommend installing the following:
-
-* ``diffpy.structure`` - crystal structure container and parsers,
-  https://github.com/diffpy/diffpy.structure
-* ``pyobjcryst`` - Crystal and Molecule storage, rigid units, bond
-  length and bond angle restraints, https://github.com/diffpy/pyobjcryst
-
-Optimizations involving pair distribution functions PDF or bond valence
-sums require
-
-* ``diffpy.srreal`` - python library for PDF calculation,
-  https://github.com/diffpy/diffpy.srreal
-
-Optimizations involving small angle scattering or shape characteristic
-functions from the diffpy.srfit.sas module require
-
-* ``sas`` - module for calculation of P(R) in small-angle scattering
-  from the SasView project, http://www.sasview.org
-
 Fallback Installation
 ---------------------
 

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/pyproject.toml

@@ -53,7 +53,7 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-srfit = "diffpy.srfit.app:main"
+diffpy-srfit = "diffpy.srfit.srfit_app:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/src/diffpy/srfit/pdf/pdfparser.py

@@ -22,8 +22,13 @@ See the class documentation for more information.
 
 __all__ = ["PDFParser"]
 
+import re
+from pathlib import Path
+
 from diffpy.srfit.fitbase.profileparser import ProfileParser
 
+_FLOAT_RX = r"[-+]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][-+]?\d+)?"
+
 
 class PDFParser(ProfileParser):
     """Parser for PDF diffraction pattern data.
@@ -31,7 +36,11 @@ class PDFParser(ProfileParser):
     PDFgetX and PDFgetN write their header as plain ``name = value``
     pairs, including ``stype = X`` or ``stype = N`` for the scattering
     type, so this class parses files identically to ``ProfileParser``
-    and only sets ``_format`` to identify PDF data.
+    for those. Some facilities instead prepend a
+    free-text instrument comment, so this class also falls back to
+    scanning that comment for the scattering type, ``qmin``, ``qmax``,
+    ``qdamp``, and ``qbroad`` when they are not already present as
+    ``name = value`` pairs.
 
     Attributes
     ----------
@@ -85,6 +94,10 @@ class PDFParser(ProfileParser):
         The minimum scattering vector (float).
     qmax
         The maximum scattering vector (float).
+    qdamp
+        The Q-resolution damping factor (float).
+    qbroad
+        The Q-resolution broadening factor (float).
 
     These, along with any other ``name = value`` pairs in the header,
     may appear in the metadata dictionary.
@@ -92,5 +105,66 @@ class PDFParser(ProfileParser):
 
     _format = "PDF"
 
+    def _parse_metadata(self, filename):
+        """Return the metadata read from a PDFgetX or PDFgetN header.
+
+        This calls ``ProfileParser``'s ``name = value`` based parsing
+        first, then falls back to scanning the free-text instrument
+        comments some facilities prepend to their files for the
+        scattering type and Q-resolution parameters that
+        such comments are not already covered by a ``name = value``
+        pair.
+
+        Parameters
+        ----------
+        filename : str or Path
+            The name of the file to parse.
+
+        Returns
+        -------
+        dict
+            The metadata read from the file header.
+        """
+        metadata = super()._parse_metadata(filename)
+        self._parse_comment_metadata(Path(filename).read_text(), metadata)
+        return metadata
+
+    @staticmethod
+    def _parse_comment_metadata(header_text, metadata):
+        """Fill in stype, qmin, qmax, qdamp, and qbroad from free-text
+        instrument comments, without overwriting values already found
+        by the ``name = value`` based parsing.
+
+        Parameters
+        ----------
+        header_text : str
+            The full text of the file being parsed.
+        meta : dict
+            The metadata dictionary to update in place.
+
+        Returns
+        -------
+        dict
+            The updated metadata dictionary.
+        """
+        if "stype" not in metadata:
+            if re.search(r"(x-?ray|PDFgetX)", header_text, re.I):
+                metadata["stype"] = "X"
+            elif re.search(r"(neutron|PDFgetN)", header_text, re.I):
+                metadata["stype"] = "N"
+        regexes = {
+            "qmin": r"\bqmin *= *(%s)\b" % _FLOAT_RX,
+            "qmax": r"\bqmax *= *(%s)\b" % _FLOAT_RX,
+            "qdamp": r"\b(?:qdamp|qsig) *= *(%s)\b" % _FLOAT_RX,
+            "qbroad": r"\b(?:qbroad|qalp) *= *(%s)\b" % _FLOAT_RX,
+        }
+        for key, pattern in regexes.items():
+            if key in metadata:
+                continue
+            res = re.search(pattern, header_text, re.I)
+            if res:
+                metadata[key] = float(res.group(1))
+        return metadata
+
 
 # End of PDFParser

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/src/diffpy.srfit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.srfit
-Version: 3.3.0rc2
+Version: 3.3.1rc0
 Summary: Generalized code base for modeling problems.
 Author-email: Christopher Farrow <farrowch@gmail.com>, Pavol Juhas <pavol.juhas@gmail.com>, Caden Myers <cjm2304@columbia.edu>, "Simon J. L. Billinge" <sbillinge@ucsb.edu>
 Maintainer-email: Caden Myers <cjm2304@columbia.edu>, "Simon J. L. Billinge" <sbillinge@ucsb.edu>
@@ -86,16 +86,16 @@ target function being optimized can be specified by the user according to the
 data available.
 
 Within the diffpy.srfit framework, any parameter used in describing the
-structure of a material can be passed as a refinable variable to the global
+model can be passed as a refinable variable to the global
 optimizer.  Once parameters are declared as variables they can easily be turned
 "on" or "off", i.e. fixed or allowed to vary. Additionally, variables may be
 constrained to obey mathematical relationships with other parameters or
-variables used in the structural model. Restraints can be applied to
+variables used in the model. Restraints can be applied to
 variables, which adds a penalty to the refinement process commensurate with the
 deviation from the known value or range. The cost function can also be
-customized by the user. If the refinement contains multiple models, each model
+customized by the user. If the refinement contains multiple ``physics" models, each model
 can have its own cost function which will be properly weighted and combined to
-obtain the total cost function. Additionally, diffpy.srfit is designed to be
+obtain the total cost function. Additionally, ``diffpy.srfit`` is designed to be
 extensible, allowing the user to integrate external calculators to perform
 co-refinements with other techniques.
 
@@ -134,7 +134,11 @@ If you use diffpy.srfit in a scientific publication, we would like you to cite t
 Installation
 ------------
 
-The preferred method is to use `Miniconda Python
+The best way to install ``diffpy.srfit`` is as part of the ``diffpy.cmi`` package.  Please
+see https://github.com/diffpy/diffpy.cmi for installation information.
+
+If for some reason you want to install the ``diffpy.srfit`` library on its own,
+the preferred method is to use `Miniconda Python
 <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
 and install from the "conda-forge" channel of Conda packages.
 
@@ -150,27 +154,6 @@ The following creates and activates a new environment named ``diffpy.srfit_env``
 
 The output should print the latest version displayed on the badges above.
 
-This will install the minimal `diffpy.srfit` installation.  It will often be used
-as along with other packages for manipulating and computing crystal structures
-and so on.  We also therefore recommend installing the following:
-
-* ``diffpy.structure`` - crystal structure container and parsers,
-  https://github.com/diffpy/diffpy.structure
-* ``pyobjcryst`` - Crystal and Molecule storage, rigid units, bond
-  length and bond angle restraints, https://github.com/diffpy/pyobjcryst
-
-Optimizations involving pair distribution functions PDF or bond valence
-sums require
-
-* ``diffpy.srreal`` - python library for PDF calculation,
-  https://github.com/diffpy/diffpy.srreal
-
-Optimizations involving small angle scattering or shape characteristic
-functions from the diffpy.srfit.sas module require
-
-* ``sas`` - module for calculation of P(R) in small-angle scattering
-  from the SasView project, http://www.sasview.org
-
 Fallback Installation
 ---------------------
 

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/src/diffpy.srfit.egg-info/SOURCES.txt

@@ -98,7 +98,9 @@ tests/test_literals.py
 tests/test_objcrystparset.py
 tests/test_parameter.py
 tests/test_parameterset.py
-tests/test_pdf.py
+tests/test_pdfcontribution.py
+tests/test_pdfgenerator.py
+tests/test_pdfparser.py
 tests/test_profile.py
 tests/test_profilegenerator.py
 tests/test_profileparser.py
@@ -114,6 +116,7 @@ tests/test_weakrefcallable.py
 tests/testdata/LaMnO3.stru
 tests/testdata/ni-q27r100-neutron.gr
 tests/testdata/ni.cif
+tests/testdata/nom-mno-neutron.gr
 tests/testdata/results.res
 tests/testdata/sas_ascii_test_1.txt
 tests/testdata/sas_ellipsoid_testdata.txt

diffpy_srfit-3.3.1rc0/src/diffpy.srfit.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+diffpy-srfit = diffpy.srfit.srfit_app:main

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/tests/test_constraint.py

@@ -60,10 +60,17 @@ class TestConstraint(unittest.TestCase):
         return
 
 
-class TestConstraint_deprecated(unittest.TestCase):
+# ----------------------------------------------------------------------------
+# Constraint.constrain and Parameter.setConst are deprecated in favor of
+# Constraint.add_constraint and Parameter.set_constant. The old names must
+# still work and forward to the new implementation.
 
-    def testConstraint(self):
-        """Test the Constraint class."""
+
+class TestConstraintDeprecated(unittest.TestCase):
+
+    def test_constrain_deprecated(self):
+        """Test the deprecated Constraint.constrain and
+        Parameter.setConst methods."""
         p1 = Parameter("p1", 1)
         p2 = Parameter("p2", 2)
 

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/tests/test_fitrecipe.py

@@ -340,62 +340,6 @@ def test_convert_bounds_to_restraints():
     assert r.scaled is True
 
 
-def testPrintFitHook(capturestdout):
-    "check output from default PrintFitHook."
-    recipe = FitRecipe("recipe")
-    recipe.fithooks[0].verbose = 0
-
-    # Set up the Profile
-    profile = Profile()
-    x = linspace(0, pi, 10)
-    y = sin(x)
-    profile.set_observed_profile(x, y)
-
-    # Set up the FitContribution
-    fitcontribution = FitContribution("cont")
-    fitcontribution.set_profile(profile)
-    fitcontribution.set_equation("A*sin(k*x + c)")
-    fitcontribution.A.set_value(1)
-    fitcontribution.k.set_value(1)
-    fitcontribution.c.set_value(0)
-
-    recipe.addContribution(fitcontribution)
-
-    recipe.add_variable(fitcontribution.c)
-    recipe.add_soft_bounds("c", lower_bound=5)
-    (pfh,) = recipe.getFitHooks()
-    out = capturestdout(recipe.scalar_residual)
-    assert "" == out
-    pfh.verbose = 1
-    out = capturestdout(recipe.scalar_residual)
-    assert out.strip().isdigit()
-    assert "\nRestraints:" not in out
-    pfh.verbose = 2
-    out = capturestdout(recipe.scalar_residual)
-    assert "\nResidual:" in out
-    assert "\nRestraints:" in out
-    assert "\nVariables" not in out
-    pfh.verbose = 3
-    out = capturestdout(recipe.scalarResidual)
-    assert "\nVariables" in out
-    assert "c = " in out
-    return
-
-
-def test_add_and_remove_ParameterSet():
-    # add a parset
-    recipe = FitRecipe("recipe")
-    parameter_to_add = Parameter("added_param", 1)
-    recipe.addParameterSet(parameter_to_add)
-    # check that the parameter is added
-    assert recipe.added_param == parameter_to_add
-    assert recipe.added_param.value == 1
-    # remove the added parameter
-    recipe.removeParameterSet(parameter_to_add)
-    # check that the parameter is removed
-    assert not hasattr(recipe, "added_param")
-
-
 def test_add_and_remove_parameter_set():
     recipe = FitRecipe("recipe")
     parameter_to_add = Parameter("added_param", 1)
@@ -411,12 +355,12 @@ def test_add_and_remove_parameter_set():
 
 
 def test_add_contribution(capturestdout):
-    """Duplicated test of PrintFitHooks except addContribution method
-    has changed to the new add_contribution method. This is because
-    addContribution is deprecated.
+    """Check output from default PrintFitHook using add_contribution.
 
-    Remove this test after addContribution is removed and update
-    testPrintFitHook to use add_contribution instead of addContribution.
+    Covers the same behavior as test_print_fit_hook_deprecated (see the
+    deprecated-API section at the bottom of this file), which uses the
+    deprecated addContribution instead. Once addContribution is removed
+    in 4.0.0, delete that test and keep this one.
     """
     recipe = FitRecipe("recipe")
     recipe.fithooks[0].verbose = 0
@@ -668,27 +612,6 @@ def build_recipe_from_datafile(datafile):
     return recipe
 
 
-def build_recipe_from_datafile_deprecated(datafile):
-    """Duplicate of build_recipe_from_datafile to use deprecated
-    loadParsedData method.
-
-    Remove in version 4.0.0.
-    """
-    profile = Profile()
-    parser = PDFParser()
-    parser.parseFile(str(datafile))
-    profile.loadParsedData(parser)
-
-    contribution = FitContribution("c")
-    contribution.set_profile(profile)
-    contribution.set_equation("m*x + b")
-    recipe = FitRecipe()
-    recipe.add_contribution(contribution)
-    recipe.add_variable(contribution.m, 1)
-    recipe.add_variable(contribution.b, 0)
-    return recipe
-
-
 def test_plot_recipe_bad_display(build_recipes_one_contribution):
     recipe, _ = build_recipes_one_contribution
     # Case: All plots are disabled
@@ -1043,23 +966,6 @@ def test_plot_recipe_labels_from_gr_file_overwrite(temp_data_files):
     assert actual_ylabel == expected_ylabel
 
 
-def test_plot_recipe_labels_from_gr_file_overwrite_deprecated(temp_data_files):
-    "Remove this test with version 4.0.0."
-    gr_file = temp_data_files / "gr_file.gr"
-    recipe = build_recipe_from_datafile_deprecated(gr_file)
-    optimize_recipe(recipe)
-    plt.close("all")
-    fig, ax = recipe.plot_recipe(
-        return_fig=True, show=False, xlabel="My X", ylabel="My Y"
-    )
-    actual_xlabel = ax.get_xlabel()
-    actual_ylabel = ax.get_ylabel()
-    expected_xlabel = "My X"
-    expected_ylabel = "My Y"
-    assert actual_xlabel == expected_xlabel
-    assert actual_ylabel == expected_ylabel
-
-
 def test_plot_recipe_reset_all_defaults(build_recipes_one_contribution):
     expected_defaults = {
         "show_observed": True,
@@ -1229,5 +1135,114 @@ def test_residual_is_weighted_by_uncertainty(
     assert actual_residual == pytest.approx(expected_residual)
 
 
+# ----------------------------------------------------------------------------
+# addContribution, addParameterSet/removeParameterSet, and
+# PDFParser.parseFile/Profile.loadParsedData are deprecated in favor of
+# add_contribution, add_parameter_set/remove_parameter_set, and
+# PDFParser.parse_file/Profile.load_parsed_data. The old names must still
+# work and forward to the new implementation.
+
+
+def test_print_fit_hook_deprecated(capturestdout):
+    """Check output from default PrintFitHook using the deprecated
+    addContribution, getFitHooks, and scalarResidual methods.
+
+    Remove this test after addContribution is removed in 4.0.0; see
+    test_add_contribution for the permanent replacement.
+    """
+    recipe = FitRecipe("recipe")
+    recipe.fithooks[0].verbose = 0
+
+    # Set up the Profile
+    profile = Profile()
+    x = linspace(0, pi, 10)
+    y = sin(x)
+    profile.set_observed_profile(x, y)
+
+    # Set up the FitContribution
+    fitcontribution = FitContribution("cont")
+    fitcontribution.set_profile(profile)
+    fitcontribution.set_equation("A*sin(k*x + c)")
+    fitcontribution.A.set_value(1)
+    fitcontribution.k.set_value(1)
+    fitcontribution.c.set_value(0)
+
+    recipe.addContribution(fitcontribution)
+
+    recipe.add_variable(fitcontribution.c)
+    recipe.add_soft_bounds("c", lower_bound=5)
+    (pfh,) = recipe.getFitHooks()
+    out = capturestdout(recipe.scalar_residual)
+    assert "" == out
+    pfh.verbose = 1
+    out = capturestdout(recipe.scalar_residual)
+    assert out.strip().isdigit()
+    assert "\nRestraints:" not in out
+    pfh.verbose = 2
+    out = capturestdout(recipe.scalar_residual)
+    assert "\nResidual:" in out
+    assert "\nRestraints:" in out
+    assert "\nVariables" not in out
+    pfh.verbose = 3
+    out = capturestdout(recipe.scalarResidual)
+    assert "\nVariables" in out
+    assert "c = " in out
+    return
+
+
+def test_add_and_remove_parameter_set_deprecated():
+    """Test the deprecated addParameterSet and removeParameterSet
+    methods."""
+    recipe = FitRecipe("recipe")
+    parameter_to_add = Parameter("added_param", 1)
+    # add a parset
+    recipe.addParameterSet(parameter_to_add)
+    # check that the parameter is added
+    assert recipe.added_param == parameter_to_add
+    assert recipe.added_param.value == 1
+    # remove the added parameter
+    recipe.removeParameterSet(parameter_to_add)
+    # check that the parameter is removed
+    assert not hasattr(recipe, "added_param")
+
+
+def build_recipe_from_datafile_deprecated(datafile):
+    """Duplicate of build_recipe_from_datafile to use the deprecated
+    PDFParser.parseFile and Profile.loadParsedData methods.
+
+    Remove in version 4.0.0.
+    """
+    profile = Profile()
+    parser = PDFParser()
+    parser.parseFile(str(datafile))
+    profile.loadParsedData(parser)
+
+    contribution = FitContribution("c")
+    contribution.set_profile(profile)
+    contribution.set_equation("m*x + b")
+    recipe = FitRecipe()
+    recipe.add_contribution(contribution)
+    recipe.add_variable(contribution.m, 1)
+    recipe.add_variable(contribution.b, 0)
+    return recipe
+
+
+def test_plot_recipe_labels_from_gr_file_overwrite_deprecated(temp_data_files):
+    "Remove this test with version 4.0.0."
+    gr_file = temp_data_files / "gr_file.gr"
+    recipe = build_recipe_from_datafile_deprecated(gr_file)
+    optimize_recipe(recipe)
+    plt.close("all")
+    fig, ax = recipe.plot_recipe(
+        return_fig=True, show=False, xlabel="My X", ylabel="My Y"
+    )
+    actual_xlabel = ax.get_xlabel()
+    actual_ylabel = ax.get_ylabel()
+    expected_xlabel = "My X"
+    expected_ylabel = "My Y"
+    assert actual_xlabel == expected_xlabel
+    assert actual_ylabel == expected_ylabel
+
+
 if __name__ == "__main__":
     unittest.main()

{diffpy_srfit-3.3.0rc2 → diffpy_srfit-3.3.1rc0}/tests/test_parameterset.py

@@ -26,16 +26,12 @@ class TestParameterSet(unittest.TestCase):
         self.parset = ParameterSet("test")
         return
 
-    def testAddParameterSet(self):
-        """Test the deprecated addParameterSet method.
-
-        Remove this test after the addParameterSet is removed in version
-        4.0.0.
-        """
+    def test_add_parameter_set(self):
+        """Test the add_parameter_set method."""
         parset2 = ParameterSet("parset2")
         p1 = Parameter("parset2", 1)
 
-        self.parset.addParameterSet(parset2)
+        self.parset.add_parameter_set(parset2)
         self.assertTrue(self.parset.parset2 is parset2)
 
         self.assertRaises(ValueError, self.parset.add_parameter_set, p1)
@@ -47,12 +43,28 @@ class TestParameterSet(unittest.TestCase):
 
         return
 
-    def test_add_parameter_set(self):
-        """Test the add_parameter_set method."""
+
+# ----------------------------------------------------------------------------
+# addParameterSet is deprecated in favor of add_parameter_set. The old name
+# must still work and forward to the new implementation.
+
+
+class TestParameterSetDeprecated(unittest.TestCase):
+
+    def setUp(self):
+        self.parset = ParameterSet("test")
+        return
+
+    def test_add_parameter_set_deprecated(self):
+        """Test the deprecated addParameterSet method.
+
+        Remove this test after the addParameterSet is removed in version
+        4.0.0.
+        """
         parset2 = ParameterSet("parset2")
         p1 = Parameter("parset2", 1)
 
-        self.parset.add_parameter_set(parset2)
+        self.parset.addParameterSet(parset2)
         self.assertTrue(self.parset.parset2 is parset2)
 
         self.assertRaises(ValueError, self.parset.add_parameter_set, p1)