Merge pull request #10 from chiahaoliu/CLN_history_v2

CLN: test and repo structure

Author: CJ-Wright

.travis.yml

@@ -0,0 +1,51 @@
+language: python
+sudo: false
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+    - $HOME/.cache/matplotlib
+
+python:
+  - 2.7
+  - 3.5
+  - 3.6
+
+before_install:
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b -p ~/mc
+  - export PATH=~/mc/bin:$PATH
+  - conda config --add channels conda-forge
+  - conda config --set always_yes yes --set changeps1 no --set quiet true
+  - conda update conda --yes
+
+install:
+  - export GIT_FULL_HASH=`git rev-parse HEAD`
+  - conda create --yes -n testenv python=$TRAVIS_PYTHON_VERSION
+  - source activate testenv
+  - conda install --yes --file requirements/build.txt
+  - conda install pip
+  - pip install -r requirements/pip.txt
+  - python setup.py install
+  - git clean -xfd
+
+script:
+  - set -e
+  - conda install --yes --file requirements/run.txt
+  - conda install --yes --file requirements/test.txt
+  - coverage run run_tests.py
+  - coverage report -m
+  - codecov
+#  - |
+#    if [ $TRAVIS_PYTHON_VERSION = "3.6" ]; then
+#      conda install --yes --file requirements/docs.txt
+#      cd doc
+#      make html
+#      cd ..
+#      doctr deploy . --built-docs ./docs/_build/html;
+#    fi
+
+after_script:
+  - set +e
+  - flake8 diffpy

CHANGELOG.rst

@@ -0,0 +1,6 @@
+==========================
+diffpy.pdfmorph Change Log
+==========================
+
+.. current developments
+

diffpy/pdfmorph/__init__.py

@@ -19,6 +19,6 @@
 __id__ = "$Id$"
 
 # obtain version information
-from diffpy.pdfmorph.version import __version__
+__version__ = '1.0'
 
 # End of file

diffpy/pdfmorph/morphs/__init__.py

@@ -38,6 +38,6 @@
         MorphISpheroid, MorphResolutionDamping, MorphShift]
 
 # obtain version information
-from diffpy.pdfmorph.version import __version__
+from diffpy.pdfmorph import __version__
 
 # End of file

diffpy/pdfmorph/morphs/morph.py

@@ -89,12 +89,14 @@ class Morph(object):
             (self.xobjout, self.yobjout, self.xrefout, self.yrefout), 
             doc='Return a tuple of all output arrays')
 
-    def __init__(self, config = {}):
+    def __init__(self, config=None):
         '''Create a default Morph instance.
 
         config  -- dictionary that contains all configuration variables
         '''
         # declare empty attributes
+        if config is None:
+            config = {}
         self.xobjin = None
         self.yobjin = None
         self.xobjout = None
@@ -205,7 +207,6 @@ def __getattr__(self, name):
         else:
             emsg = 'Object has no attribute %r' % name
             raise AttributeError(emsg)
-        return
 
 
     def __setattr__(self, name, val):

diffpy/pdfmorph/morphs/morphchain.py

@@ -134,7 +134,6 @@ def __getattr__(self, name):
         else:
             emsg = 'Object has no attribute %r' % name
             raise AttributeError(emsg)
-        return
 
 
     def __setattr__(self, name, val):

diffpy/pdfmorph/morphs/morphsmear.py

@@ -55,7 +55,7 @@ def morph(self, xobj, yobj, xref, yref):
         # later.
         r = self.xobjin
         rr = self.yobjin
-        r0 = r[len(r) / 2]
+        r0 = r[len(r) // 2]
         gaussian = numpy.exp(-0.5 * ((r - r0)/self.smear)**2 ) 
 
         # Get the full convolution

diffpy/pdfmorph/pdfmorphapp.py

@@ -17,7 +17,7 @@
 import os
 import os.path
 
-
+import numpy
 from diffpy.pdfmorph import __version__
 import diffpy.pdfmorph.tools as tools
 import diffpy.pdfmorph.pdfplot as pdfplot
@@ -214,12 +214,12 @@ def main():
                     rptemp.append("scale")
                 refiner.refine(*rptemp)
             refiner.refine(*refpars)
-        except ValueError, e:
+        except ValueError as e:
             parser.error(str(e))
     elif "smear" in refpars and opts.baselineslope is None:
         try:
             refiner.refine("baselineslope", baselineslope = -0.5)
-        except ValueError, e:
+        except ValueError as e:
             parser.error(str(e))
     else:
         chain(xobj, yobj, xref, yref)
@@ -231,12 +231,12 @@ def main():
     chain[0] = morphs.Morph()
     chain(xobj, yobj, xref, yref)
 
-    items = config.items()
+    items = list(config.items())
     items.sort()
     output = "\n".join("# %s = %f"%i for i in items)
     output += "\n# Rw = %f" % rw
     output += "\n# Pearson = %f" % pcc
-    print output
+    print(output)
     if opts.savefile is not None:
         header = "# PDF created by pdfmorph\n"
         header += "# from %s\n" % os.path.abspath(pargs[0])
@@ -245,10 +245,10 @@ def main():
         if opts.savefile == "-":
             outfile = sys.stdout
         else:
-            outfile = file(opts.savefile, 'w')
-        print >> outfile, header
-        import numpy
-        numpy.savetxt(outfile, zip(chain.xobjout, chain.yobjout))
+            outfile = open(opts.savefile, 'w')
+        print(header, file=outfile)
+        numpy.savetxt(outfile, numpy.transpose([chain.xobjout,
+                                                chain.yobjout]))
         outfile.close()
 
     if opts.plot:
@@ -269,11 +269,11 @@ def getPDFFromFile(fn):
     from diffpy.pdfmorph.tools import readPDF
     try:
         r, gr = readPDF(fn)
-    except IOError, (errno, errmsg):
-        print >> sys.stderr, "%s: %s" % (fn, errmsg)
+    except IOError as (errno, errmsg):
+        print("%s: %s" % (fn, errmsg), file=sys.stderr)
         sys.exit(1)
-    except ValueError, errmsg:
-        print >> sys.stderr, "Cannot read %s" % fn
+    except ValueError as errmsg:
+        print("Cannot read %s" % fn, file=sys.stderr)
         sys.exit(1)
 
     return r, gr

diffpy/pdfmorph/pdfplot.py

@@ -19,7 +19,7 @@
 
 # FIXME - make this return the figure object in the future, so several views
 # can be composed.
-def plotPDFs(pairlist, labels = [], offset = 'auto', rmin = None, rmax = None):
+def plotPDFs(pairlist, labels=None, offset ='auto', rmin = None, rmax = None):
     """Plots several PDFs on top of one another.
 
     pairlist    --  iterable of (r, gr) pairs to plot
@@ -36,6 +36,8 @@ def plotPDFs(pairlist, labels = [], offset = 'auto', rmin = None, rmax = None):
                     upper bound of the PDF is not altered.
 
     """
+    if labels is None:
+        labels = []
     if offset is 'auto':
         offset = _findOffset(pairlist)
 
@@ -59,8 +61,8 @@ def plotPDFs(pairlist, labels = [], offset = 'auto', rmin = None, rmax = None):
     pylab.show()
     return
 
-def comparePDFs(pairlist, labels = [], rmin = None, rmax = None, show = True,
-        maglim = None, mag = 5, rw = None, legend = True):
+def comparePDFs(pairlist, labels=None, rmin = None, rmax = None, show = True,
+                maglim = None, mag = 5, rw = None, legend = True):
     """Plot two PDFs on top of each other and difference curve.
 
     pairlist    --  iterable of (r, gr) pairs to plot
@@ -82,6 +84,8 @@ def comparePDFs(pairlist, labels = [], rmin = None, rmax = None, show = True,
     line.  The difference curve will be in green and offset for clarity.
     
     """
+    if labels is None:
+        labels = []
     rfit, grfit = pairlist[0]
     rdat, grdat = pairlist[1]
     labeldata = labels[1]

news/TEMPLATE.rst

@@ -0,0 +1,11 @@
+**Added:** None
+
+**Changed:** None
+
+**Deprecated:** None
+
+**Removed:** None
+
+**Fixed:** None
+
+**Security:** None