Squashing more code style issues

.travis.yml

@@ -45,11 +45,10 @@ install:
   # - conda install --yes scikit-image
   # Hyperspy is now an optional dependency for 3.6 onwards
   - if [[ "$TRAVIS_PYTHON_VERSION" == "3.7" ]] || [[ "$TRAVIS_PYTHON_VERSION" == "3.6" ]] ; then
-        conda install --yes -c conda-forge hyperspy; 
+        conda install --yes -c conda-forge hyperspy;
     fi
   # Now we unistall the stable stoner - use force to stop downgrading packages!
   - conda remove --yes --force stoner
-  - pip install opencv_python
   - pip install coveralls
   - pip install .
 

Stoner/Core.py

@@ -1610,17 +1610,17 @@ def __search_index(self, xcol, value, accuracy):
         if isinstance(value, (int_types, float)):
             ix = _np_.less_equal(_np_.abs(self.data[:, x] - value), accuracy)
         elif isinstance(value, tuple) and len(value) == 2:
-            (l, u) = (min(value), max(value))
-            l -= accuracy
+            (low, u) = (min(value), max(value))
+            low -= accuracy
             u += accuracy
             v = self.data[:, x]
-            l = _np_.ones_like(v) * l
+            low = _np_.ones_like(v) * low
             u = _np_.ones_like(v) * u
-            ix = _np_.logical_and(v > l, v <= u)
+            ix = _np_.logical_and(v > low, v <= u)
         elif isinstance(value, (list, _np_.ndarray)):
             ix = _np_.zeros(len(self), dtype=bool)
             for v in value:
-                ix = _np_.logical_or(ix, self.__search_index(xcol, v), accuracy)
+                ix = _np_.logical_or(ix, self.__search_index(xcol, v, accuracy))
         elif callable(value):
             ix = _np_.array([value(r[x], r) for r in self], dtype=bool)
         else:
@@ -2168,7 +2168,7 @@ def find_col(self, col, force_list=False):
         """
         return self.data._setas.find_col(col, force_list)
 
-    def get(self, item, default=None):
+    def get(self, item, default=None):  # pylint: disalbe=arguments-differ
         """A wrapper around __get_item__ that handles missing keys by returning None.
 
         This is useful for the :py:class:`Stoner.Folder.DataFolder` class.

Stoner/Fit.py

@@ -237,6 +237,7 @@ def guesser(cls, func):
 
             @wraps(func)
             def guess_proxy(self, *args, **kargs):
+                """A magic proxy call around a function to guess initial prameters."""
                 guesses = func(*args, **kargs)
                 pars = {x: y for x, y in zip(self.param_names, guesses)}
                 pars = self.make_params(**pars)

Stoner/Image/core.py

@@ -264,6 +264,7 @@ def __array_finalize__(self, obj):
         super(ImageArray, self).__array_finalize__(obj)
 
     def __array_prepare__(self, arr, context=None):
+        """Support the numpy machinery for subclassing ndarray."""
         return super(ImageArray, self).__array_prepare__(arr, context)
 
     def __array_wrap__(self, out_arr, context=None):
@@ -346,6 +347,7 @@ def _load_npy(cls, filename, **kargs):
 
     @classmethod
     def _load_png(cls, filename, **kargs):
+        """Create a new ImageArray from a png file."""
         with Image.open(filename, "r") as img:
             image = np.asarray(img).view(cls)
             # Since skimage.img_as_float() looks at the dtype of the array when mapping ranges, it's important to make
@@ -369,6 +371,7 @@ def _load_png(cls, filename, **kargs):
 
     @classmethod
     def _load_tiff(cls, filename, **kargs):
+        """Create a new ImageArray from a tiff file."""
         metadict = typeHintedDict({})
         with Image.open(filename, "r") as img:
             image = np.asarray(img)
@@ -475,6 +478,7 @@ def aspect(self):
 
     @property
     def centre(self):
+        """Return the coordinates of the centre of the image."""
         return tuple(np.array(self.shape) / 2.0)
 
     @property
@@ -649,6 +653,7 @@ def _func_generator(self, workingfunc):
 
         @wraps(workingfunc)
         def gen_func(*args, **kwargs):
+            """Wrapped magic proxy function call."""
             transpose = getattr(workingfunc, "transpose", False)
             if transpose:
                 change = self.clone.T
@@ -1543,6 +1548,9 @@ def square(self, r, c, w, angle=0.0, shape=None, value=1.0):
 
 
 class MaskProxy(object):
+
+    """Provides a wrapper to support manipulating the image mask easily."""
+
     @property
     def _IA(self):
         """Get the underliying image data."""

Stoner/analysis/fitting/__init__.py

@@ -1,2 +1,3 @@
+"""Provides additional functionality for doing curve fitting to data."""
 __all__ = ["odr_Model", "FittingMixin"]
 from .mixins import odr_Model, FittingMixin

Stoner/analysis/fitting/mixins.py

@@ -1030,7 +1030,16 @@ def _func(x, *beta):
                     pguess = func.guess
                 else:
                     pguess = None
-            except:
+            except (
+                ArithmeticError,
+                AttributeError,
+                LookupError,
+                RuntimeError,
+                NameError,
+                OSError,
+                TypeError,
+                ValueError,
+            ):
                 pguess = None
             p0 = kargs.pop("p0", pguess)
         elif callable(func):

Stoner/compat.py

@@ -63,6 +63,7 @@
     from os import getcwd, path, mkdir
 
     def get_func_params(func):
+        """Get Function parameter names from signature."""
         ret = []
         for arg in getargspec(func)[0][1:]:
             ret.append(arg)
@@ -197,12 +198,12 @@ def _access_check(fn, mode):
             files = [cmd]
 
         seen = set()
-        for dir in path:
-            normdir = os.path.normcase(dir)
+        for _dir in path:
+            normdir = os.path.normcase(_dir)
             if not normdir in seen:
                 seen.add(normdir)
                 for thefile in files:
-                    name = os.path.join(dir, thefile)
+                    name = os.path.join(_dir, thefile)
                     if _access_check(name, mode):
                         return name
         return None

Stoner/core/setas.py

@@ -10,6 +10,7 @@
 
 from ..compat import string_types, int_types, index_types, _pattern_type
 from ..tools import _attribute_store, isiterable, typedList, islike_list
+from .utils import decode_string
 
 from collections import MutableMapping, Mapping
 
@@ -117,18 +118,6 @@ def __init__(self, row=False, bless=None):
             },
         }  # xyzuvw
 
-    def _decode_string(self, value):
-        """Expands a string of column assignments, replacing numbers with repeated characters."""
-        pattern = re.compile("(([0-9]+)(x|y|z|d|e|f|u|v|w|\.|\-))")
-        while True:
-            res = pattern.search(value)
-            if res is None:
-                break
-            (total, count, code) = res.groups()
-            count = int(count)
-            value = value.replace(total, code * count, 1)
-        return value
-
     def _prepare_call(self, args, kargs):
         """Extract a value to be used to evaluate the setas attribute during a call."""
         reset = kargs.pop("reset", True)
@@ -140,7 +129,7 @@ def _prepare_call(self, args, kargs):
             if isinstance(value, string_types):  # expand the number-code combos in value
                 if reset:
                     self.setas = []
-                value = self._decode_string(value)
+                value = decode_string(value)
             elif isinstance(value, setas):
                 if value is not self:
                     value = value.setas
@@ -358,7 +347,7 @@ def __eq__(self, other):
         """Checks to see if this is the same object, or has the same headers and the same setas values."""
         ret = False
         if isinstance(other, string_types):  # Expand strings and convert to list
-            other = [c for c in self._decode_string(other)]
+            other = [c for c in decode_string(other)]
         if not isinstance(other, setas):  # Ok, need to check whether items match
             if isiterable(other) and len(other) <= self._size:
                 for m in self.setas[len(other) :]:  # Check that if other is short we don't have assignments there
@@ -367,8 +356,7 @@ def __eq__(self, other):
                 for o, m in zip(other, self.setas):
                     if o != m:  # Look for mis-matched assignments
                         return False
-                else:
-                    return True
+                return True
             else:  # If other is longer then we can't matchj
                 return False
         elif id(self) == id(other):
@@ -644,7 +632,7 @@ def clear(self):
         """
         self.unset()
 
-    def get(self, name, default=None):
+    def get(self, name, default=None):  # pylint: disalbe=arguments-differ
         """Implement a get method."""
         try:
             return self[name]
@@ -669,7 +657,7 @@ def items(self):
         for k, v in zip(self._unique_headers, self.setas):
             yield k, v
 
-    def pop(self, name, default=None):
+    def pop(self, name, default=None):  # pylint: disalbe=arguments-differ
         """Implement a get method."""
         try:
             ret = self[name]
@@ -689,7 +677,7 @@ def popitem(self):
                 return (c, v)
         raise KeyError("No columns set in setas!")
 
-    def setdefault(self, name, default=None):
+    def setdefault(self, name, default=None):  # pylint: disalbe=arguments-differ
         """Implement a setdefault method."""
         try:
             return self[name]
@@ -717,12 +705,17 @@ def unset(self, what=None):
         else:
             self -= what
 
-    def update(self, other):
+    def update(self, other=(), **kwds):
         """Replace any assignments in self with assignments from other."""
         if isinstance(other, setas):
             other = other.to_dict()
-        elif not isinstance(other, dict):
-            raise TypeError("setas.update requires a dictionary not a {}".format(type(other)))
+        elif isinstance(other, tuple) and len(other) == 0:
+            other = kwds
+        else:
+            try:
+                other = dict(other)
+            except (ValueError, TypeError):
+                raise TypeError("setas.update requires a dictionary not a {}".format(type(other)))
         vals = list(other.values())
         keys = list(other.keys())
         for k in "xyzuvwdef":

Stoner/core/utils.py

@@ -2,10 +2,11 @@
 # -*- coding: utf-8 -*-
 """Utility functions to support :py:mod:`Stoner.Core`."""
 
-__all__ = ["copy_into", "itersubclasses", "tab_delimited"]
+__all__ = ["copy_into", "itersubclasses", "tab_delimited", "decode_string"]
 
 import copy
 import csv
+import re
 
 
 def copy_into(source, dest):
@@ -80,3 +81,16 @@ def itersubclasses(cls, _seen=None):
             yield sub
             for sub in itersubclasses(sub, _seen):
                 yield sub
+
+
+def decode_string(value):
+    """Expands a string of column assignments, replacing numbers with repeated characters."""
+    pattern = re.compile(r"(([0-9]+)(x|y|z|d|e|f|u|v|w|\.|\-))")
+    while True:
+        res = pattern.search(value)
+        if res is None:
+            break
+        (total, count, code) = res.groups()
+        count = int(count)
+        value = value.replace(total, code * count, 1)
+    return value