Writing Tutorials

CHANGELOG.rst

@@ -5,8 +5,8 @@ Release Notes
 .. current developments
 
 v0.0.1
-====================
+------
 
-**Changed:**
+**Added:**
 
-* Fixed rever GH address
+* INSERT SYNOPSIS

diffpy/pdfmorph/__init__.py

@@ -17,7 +17,7 @@
 """
 
 # obtain version information
-__version__ = '0.0.1'
+from diffpy.pdfmorph.version import __version__
 
 # top-level import
 from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph

diffpy/pdfmorph/log.py

@@ -29,9 +29,9 @@
 def set_verbosity(vb):
     '''Set verbosity of the pdfmorph logger.
 
-    vb   -- integer or one of ('debug', 'info', 'warning', 'error') strings
+    :param vb: integer or one of ('debug', 'info', 'warning', 'error') strings.
 
-    No return value.
+    :return: No return value.
     '''
     try:
         if type(vb) is str:

diffpy/pdfmorph/morph_helpers/transformpdftordf.py

@@ -14,28 +14,23 @@
 ##############################################################################
 
 
-"""class TransformXtalPDFtoRDF -- Transform crystal PDFs to RDFs.
-"""
+"""Transform crystal PDFs to RDFs."""
 
 
 from diffpy.pdfmorph.morphs.morph import *
 
 
 class TransformXtalPDFtoRDF(Morph):
-    '''Transform crystal PDFs to RDFs.
-
-    Converts both morph data and target data PDFs to RDFs.
+    """Converts both morph data and target data PDFs to RDFs.
 
     Configuration variables:
 
-    baselineslope   --  The slope of the PDF baseline.  With the perfect scale,
-                        the baseline slope is equal to -4*pi*rho0, where rho0
-                        is the density of the crystalline sample.
+    :param baselineslope: The slope of the PDF baseline. With the perfect scale, the baseline slope is equal to
+        :math:`-4\\pi\\rho_0`, where :math:`\\rho_0` is the density of the crystalline sample.
 
-    With s = baselineslope,
-    R(r) = r * (G(r) - r * s)
+    With :math:`s` being the baselineslope, :math:`R(r) = r * (G(r) - rs)`.
 
-    '''
+    """
 
     # Define input output types
     summary = 'Turn the PDF into the RDF for both the morph and target'

diffpy/pdfmorph/morph_helpers/transformrdftopdf.py

@@ -14,31 +14,28 @@
 ##############################################################################
 
 
-"""class TransformXtalRDFtoPDF -- Transform crystal RDFs to PDFs.
+"""Transform crystal RDFs to PDFs.
 """
 
 
 from diffpy.pdfmorph.morphs.morph import *
+import numpy
 
 
 class TransformXtalRDFtoPDF(Morph):
-    '''Transform crystal RDFs to PDFs.
-
-    Converts both morph data and target data RDFs to PDFs.
+    """Converts both morph data and target data RDFs to PDFs.
 
     Configuration variables:
 
-    baselineslope   --  The slope of the PDF baseline.  With the perfect scale,
-                        the baseline slope is equal to -4*pi*rho0, where rho0
-                        is the density of the crystalline sample.
+    :param baselineslope: The slope of the PDF baseline. With the perfect scale, the baseline slope is equal to
+        :math:`-4\\pi\\rho_0`, where :math:`\\rho_0` is the density of the crystalline sample.
 
-    With s = baselineslope,
-    G(r) = R(r) / r + r * s
+    With :math:`s` as the baselineslope, :math:`G(r) = R(r) / r + rs`.
 
-    '''
+    """
 
     # Define input output types
-    summary = 'Turn the PDF into the RDF for both the morph and target'
+    summary = 'Turn the PDF into the RDF for both the morph and target.'
     xinlabel = LABEL_RA
     yinlabel = LABEL_RR
     xoutlabel = LABEL_RA
@@ -50,10 +47,12 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         Morph.morph(self, x_morph, y_morph, x_target, y_target)
         morph_baseline = self.baselineslope * self.x_morph_in
         target_baseline = self.baselineslope * self.x_target_in
-        self.y_target_out = self.y_target_in / self.x_target_in + target_baseline
+        with numpy.errstate(divide='ignore', invalid='ignore'):
+            self.y_target_out = self.y_target_in / self.x_target_in + target_baseline
         if self.x_target_in[0] == 0:
             self.y_target_out[0] = 0
-        self.y_morph_out = self.y_morph_in / self.x_morph_in + morph_baseline
+        with numpy.errstate(divide='ignore', invalid='ignore'):
+            self.y_morph_out = self.y_morph_in / self.x_morph_in + morph_baseline
         if self.x_morph_in[0] == 0:
             self.y_morph_out[0] = 0
         return self.xyallout

diffpy/pdfmorph/pdfmorph_api.py

@@ -55,7 +55,9 @@ def morph_default_config(**kwargs):
 
     Examples
     --------
-    morph_cfg = morph_default_config(scale=1.01)
+    .. code-block:: python
+
+        morph_cfg = morph_default_config(scale=1.01)
     """
     rv = dict(_default_config)
     # protect against foreign keys
@@ -107,7 +109,7 @@ def pdfmorph(
         A value to specify rstep of morph operations.
     pearson: Bool, optional
         Option to include Pearson coefficient as a minimizing target
-         during morphing. Default to False.
+        during morphing. Default to False.
     add_pearson: Bool, optional
         Option to include **both** Pearson coefficient and Rw as
         minimizing targets during morphing. Default to False.
@@ -146,24 +148,32 @@ def pdfmorph(
               The agreement factor between morphed data and reference
               data
         - pcc : float
-              The pearson correlation coefficient between morphed
-               data and referenced data
+              The pearson correlation coefficient between morphed data and
+              referenced data
 
     Examples
     --------
-    # morphing (x_morph, y_morph) pair to (x_target, y_target) pair with scaling
-    from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
+    morphing (x_morph, y_morph) pair to (x_target, y_target) pair with scaling
+        .. code-block:: python
+
+            from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
+            morph_cfg = morph_default_config(scale=1.01)
+            morph_rv_dict = pdfmorph(x_morph, y_morph, x_target, y_target, **morph_cfg)
+
+
+    plot morphing result
+        .. code-block:: python
+
+            plot_morph(morph_rv_dict['morph_chain'])
+
 
-    morph_cfg = morph_default_config(scale=1.01)
-    morph_rv_dict = pdfmorph(x_morph, y_morph, x_target, y_target, **morph_cfg)
+    print morphing parameters, pearson correlation coefficient, Rw
+        .. code-block:: python
 
-    # plot morhing result
-    plot_morph(morph_rv_dict['morph_chain'])
+            print(morph_rv_dict['morphed_cfg'])
+            print(morph_rv_dict['pcc'])
+            print(morph_rv_dict['rw'])
 
-    # print morphing parameters, pearson correlation coefficient, Rw
-    print(morph_rv_dict['morphed_cfg'])
-    print(morph_rv_dict['pcc'])
-    print(morph_rv_dict['rw'])
     """
     operation_dict = {}
     refpars = []
@@ -253,16 +263,16 @@ def plot_morph(chain, ax=None, **kwargs):
     ax: matplotlib.axes.Axes, optinal
         An instance of Axes class to plot the morphing result.
         If ax is None, instances of new Figure and Axes will
-         be created. Default to None.
+        be created. Default to None.
     kwargs:
         Additional keyword arguements will be passed
-         to ``ax.plot(...**kwargs)``
+        to ``ax.plot(...**kwargs)``
 
     Returns
     -------
     l_list: list
         A list of ``matplotlib.lines.Line2D`` objects representing
-         the plotted data.
+        the plotted data.
     """
     if ax is None:
         fig, ax = plt.subplots()