Merge pull request #70 from Sparks29032/update_tests

Fixed some pytest compatibility issues

Author: sbillinge

diffpy/pdfmorph/log.py

@@ -26,7 +26,7 @@
 plog = logging.getLogger('diffpy.pdfmorph')
 
 
-def setVerbosity(vb):
+def set_verbosity(vb):
     '''Set verbosity of the pdfmorph logger.
 
     vb   -- integer or one of ('debug', 'info', 'warning', 'error') strings

diffpy/pdfmorph/pdfmorph_api.py

@@ -152,7 +152,7 @@ def pdfmorph(
     Examples
     --------
     # morphing (xobj, yobj) pair to (xref, yref) pair with scaling
-    from diffpy.pdfmorph import pdfmorph, morph_default_config, plot_morph
+    from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
 
     morph_cfg = morph_default_config(scale=1.01)
     morph_rv_dict = pdfmorph(xobj, yobj, xref, yref, **morph_cfg)
@@ -203,7 +203,7 @@ def pdfmorph(
     if pearson:
         refiner.residual = refiner._pearson
     if add_pearson:
-        refiner.residual = refiner._addpearson
+        refiner.residual = refiner._add_pearson
     # execute morphing
     if refpars and refine:
         # This works better when we adjust scale and smear first.
@@ -220,7 +220,7 @@ def pdfmorph(
 
     # summary
     rw = tools.getRw(chain)
-    pcc = tools.getPearson(chain)
+    pcc = tools.get_pearson(chain)
     # restore rgrid
     chain[0] = morphs.Morph()
     chain(xobj, yobj, xref, yref)

diffpy/pdfmorph/pdfmorphapp.py

@@ -28,7 +28,7 @@
 import diffpy.pdfmorph.refine as refine
 
 
-def createOptionParser():
+def create_option_parser():
     import optparse
 
     class CustomParser(optparse.OptionParser):
@@ -48,6 +48,7 @@ def custom_error(self, msg):
             [
                 "%prog [options] FILE1 FILE2",
                 "Manipulate and compare PDFs.",
+                "Use --help for help.",
             ]
         ),
         epilog="Please report bugs to diffpy-dev@googlegroups.com.",
@@ -189,19 +190,23 @@ def custom_error(self, msg):
     group.add_option(
         '--mag', type="float", help="Magnify plot curves beyond MAGLIM by MAG."
     )
+    group.add_option(
+        '--lwidth', type="float", help="Line thickness of plotted curves."
+    )
 
     # Defaults
     parser.set_defaults(plot=True)
     parser.set_defaults(refine=True)
     parser.set_defaults(pearson=False)
     parser.set_defaults(addpearson=False)
     parser.set_defaults(mag=5)
+    parser.set_defaults(lwidth=1.5)
 
     return parser
 
 
 def main():
-    parser = createOptionParser()
+    parser = create_option_parser()
     (opts, pargs) = parser.parse_args()
 
     if len(pargs) != 2:
@@ -253,31 +258,39 @@ def main():
         if opts.baselineslope is None:
             refpars.append("baselineslope")
             config["baselineslope"] = -0.5
+
+    def nn_value(val, name):
+        if val < 0:
+            negative_value_warning = f"\n# Negative value for {name} given. Using absolute value instead."
+            print(negative_value_warning)
+            return -val
+        return val
+
     ## Size
     radii = [opts.radius, opts.pradius]
     nrad = 2 - radii.count(None)
     if nrad == 1:
         radii.remove(None)
-        config["radius"] = radii[0]
+        config["radius"] = nn_value(radii[0], "radius or pradius")
         chain.append(morphs.MorphSphere())
         refpars.append("radius")
     elif nrad == 2:
-        config["radius"] = radii[0]
+        config["radius"] = nn_value(radii[0], "radius")
         refpars.append("radius")
-        config["pradius"] = radii[1]
+        config["pradius"] = nn_value(radii[1], "pradius")
         refpars.append("pradius")
         chain.append(morphs.MorphSpheroid())
     iradii = [opts.iradius, opts.ipradius]
     inrad = 2 - iradii.count(None)
     if inrad == 1:
         iradii.remove(None)
-        config["iradius"] = iradii[0]
+        config["iradius"] = nn_value(iradii[0], "iradius or ipradius")
         chain.append(morphs.MorphISphere())
         refpars.append("iradius")
     elif inrad == 2:
-        config["iradius"] = iradii[0]
+        config["iradius"] = nn_value(iradii[0], "iradius")
         refpars.append("iradius")
-        config["ipradius"] = iradii[1]
+        config["ipradius"] = nn_value(iradii[1], "ipradius")
         refpars.append("ipradius")
         chain.append(morphs.MorphISpheroid())
 
@@ -297,7 +310,7 @@ def main():
     if opts.pearson:
         refiner.residual = refiner._pearson
     if opts.addpearson:
-        refiner.residual = refiner._addpearson
+        refiner.residual = refiner._add_pearson
     if opts.refine and refpars:
         try:
             # This works better when we adjust scale and smear first.
@@ -319,7 +332,7 @@ def main():
 
     # Get Rw for the morph range
     rw = tools.getRw(chain)
-    pcc = tools.getPearson(chain)
+    pcc = tools.get_pearson(chain)
     # Replace the MorphRGrid with Morph identity
     chain[0] = morphs.Morph()
     chain(xobj, yobj, xref, yref)
@@ -376,8 +389,9 @@ def main():
         pmax = opts.pmax if opts.pmax is not None else opts.rmax
         maglim = opts.maglim
         mag = opts.mag
+        l_width = opts.lwidth
         pdfplot.comparePDFs(
-            pairlist, labels, rmin=pmin, rmax=pmax, maglim=maglim, mag=mag, rw=rw
+            pairlist, labels, rmin=pmin, rmax=pmax, maglim=maglim, mag=mag, rw=rw, l_width=l_width
         )
 
     return

diffpy/pdfmorph/pdfplot.py

@@ -43,7 +43,7 @@ def plotPDFs(pairlist, labels=None, offset='auto', rmin=None, rmax=None):
     if labels is None:
         labels = []
     if offset == 'auto':
-        offset = _findOffset(pairlist)
+        offset = _find_offset(pairlist)
 
     gap = len(pairlist) - len(labels)
     labels = list(labels)
@@ -74,6 +74,7 @@ def comparePDFs(
     mag=5,
     rw=None,
     legend=True,
+    l_width=1.5,
 ):
     """Plot two PDFs on top of each other and difference curve.
 
@@ -96,7 +97,6 @@ def comparePDFs(
     line.  The difference curve will be in green and offset for clarity.
 
     """
-
     if labels is None:
         labels = [2]
         labeldata = None
@@ -111,7 +111,7 @@ def comparePDFs(
     rvmin = max(rfit[0], rdat[0])
     rvmin = rmin or rvmin
     rvmax = min(rfit[-1], rdat[-1])
-    rvmax = rmax or rfit[-1]
+    rvmax = rmax or rvmax
 
     gap = 2 - len(labels)
     labels = list(labels)
@@ -162,12 +162,12 @@ def comparePDFs(
     fig.add_axes(axes)
     plt.minorticks_on()
 
-    plt.plot(rdat, grdat, label=labeldata)
-    plt.plot(rfit, grfit, label=labelfit)
-    plt.plot(rdat, offset * numpy.ones_like(diff), color='black')
+    plt.plot(rdat, grdat, linewidth=l_width, label=labeldata)
+    plt.plot(rfit, grfit, linewidth=l_width, label=labelfit)
+    plt.plot(rdat, offset * numpy.ones_like(diff), linewidth=3, color='black')
 
     diff += offset
-    plt.plot(rdat, diff, label=labeldiff)
+    plt.plot(rdat, diff, linewidth=l_width, label=labeldiff)
 
     if maglim is not None:
         # Add a line for the magnification cutoff
@@ -232,7 +232,7 @@ def truncatePDFs(r, gr, rmin=None, rmax=None):
     return r, gr
 
 
-def _findOffset(pairlist):
+def _find_offset(pairlist):
     """Find an optimal offset between PDFs."""
     maxlist = [max(p[1]) for p in pairlist]
     minlist = [min(p[1]) for p in pairlist]

diffpy/pdfmorph/refine.py

@@ -56,15 +56,15 @@ def __init__(self, chain, xobj, yobj, xref, yref):
         self.residual = self._residual
         return
 
-    def _updateChain(self, pvals):
+    def _update_chain(self, pvals):
         """Update the parameters in the chain."""
         pairs = zip(self.pars, pvals)
         self.chain.config.update(pairs)
         return
 
     def _residual(self, pvals):
         """Standard vector residual."""
-        self._updateChain(pvals)
+        self._update_chain(pvals)
         _xobj, _yobj, _xref, _yref = self.chain(
             self.xobj, self.yobj, self.xref, self.yref
         )
@@ -78,14 +78,14 @@ def _pearson(self, pvals):
         We seek to minimize this, which occurrs when the correlation is the
         largest.
         """
-        self._updateChain(pvals)
+        self._update_chain(pvals)
         _xobj, _yobj, _xref, _yref = self.chain(
             self.xobj, self.yobj, self.xref, self.yref
         )
         pcc, pval = pearsonr(_yobj, _yref)
         return ones_like(_xobj) * exp(-pcc)
 
-    def _addpearson(self, pvals):
+    def _add_pearson(self, pvals):
         """Refine both the pearson and residual."""
         res1 = self._residual(pvals)
         res2 = self._pearson(pvals)

diffpy/pdfmorph/tests/__init__.py

@@ -14,7 +14,7 @@
 ##############################################################################
 
 """Convenience module for executing all unit tests with
-python -m diffpy.structure.tests.run
+python -m diffpy.morphs.tests.run
 """
 
 

diffpy/pdfmorph/tests/run.py

@@ -1,6 +1,8 @@
-import pytest
+#!/usr/bin/env python
+
+
 import numpy as np
-from diffpy.pdfmorph import pdfmorph, morph_default_config
+from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config
 from diffpy.pdfmorph.tests.test_morphstretch import heaviside
 
 

diffpy/pdfmorph/tests/test_morph_func.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+
+
+import unittest
+from diffpy.pdfmorph.pdfmorphapp import create_option_parser
+
+
+class TestCreateOptionParser(unittest.TestCase):
+    def setUp(self):
+        self.parser = create_option_parser()
+        return
+
+    # Check numerical inputs parsed correctly into parser
+    def test_parser_numerical(self):
+        renamed_dests = {"slope": "baselineslope"}
+
+        # Check values parsed correctly
+        n_names = ["--rmin", "--rmax", "--scale", "--smear", "--stretch", "--slope", "--qdamp"]
+        n_values = ["2.5", "40", "2.1", "-0.8", "0.0000005", "-0.0000005", ".00000003"]
+        n_names.extend(["--radius", "--pradius", "--iradius", "--ipradius", "--pmin", "--pmax"])
+        n_values.extend(["+0.5", "-0.2", "+.3", "-.1", "2.5", "40"])
+        n_names.extend(["--lwidth", "--maglim", "--mag"])
+        n_values.extend(["1.6", "50", "5"])
+        n_total = len(n_names)
+        n_input = []
+        for idx in range(n_total):
+            n_input.append(n_names[idx])
+            n_input.append(n_values[idx])
+        n_input.append("leftover")  # One leftover
+        n_opts, n_args = self.parser.parse_args(n_input)
+        n_opts_dict = vars(n_opts)
+        for idx in range(n_total):
+            n_parsed_name = n_names[idx][2:]
+            n_parsed_val = n_opts_dict.get(n_parsed_name)
+            if n_parsed_val is None:
+                assert n_parsed_name in renamed_dests  # Ensure .get() failed due to destination renaming
+                n_parsed_name = renamed_dests.get(n_parsed_name)
+                n_parsed_val = n_opts_dict.get(n_parsed_name)
+            assert isinstance(n_parsed_val, float)  # Check if is float
+            assert n_parsed_val == float(n_values[idx])  # Check correct value parsed
+        assert len(n_args) == 1  # Check one leftover

diffpy/pdfmorph/tests/test_parser.py

@@ -1,7 +1,10 @@
+#!/usr/bin/env python
+
+
 import numpy as np
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-from diffpy.pdfmorph import pdfmorph, morph_default_config, plot_morph
+from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
 from diffpy.pdfmorph.tests.test_morphstretch import heaviside
 
 

diffpy/pdfmorph/tests/test_plot_morph.py

@@ -88,7 +88,7 @@ def getRw(chain):
     return rw
 
 
-def getPearson(chain):
+def get_pearson(chain):
     from scipy.stats import pearsonr
 
     xobj, yobj, xref, yref = chain.xyallout