Merge pull request #71 from phobson/minor-cleanup

Minor cleanup of easily removed deprecated items

.travis_coveragerc

@@ -16,11 +16,11 @@ omit =
 
 # Regexes for lines to exclude from consideration
 exclude_lines =
-    # Have to re-enable the standard pragma
     pragma: no cover
-
-    # Don't complain if tests don't hit defensive assertion code:
+    def __repr__
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
     raise NotImplementedError
-    except NotImplementedError
-    # Ignore pass
-    pass
+    if 0:
+    if __name__ == .__main__.:

wqio/algo/ros.py

@@ -15,7 +15,7 @@
 
 
 @np.deprecate(message="algo.ros is deprectated. use algo.robustros instead.")
-def rosSort(dataframe, rescol='res', qualcol='qual', ndsymbol='ND'):
+def rosSort(dataframe, rescol='res', qualcol='qual', ndsymbol='ND'): # pragma: no cover
     """ Prepare a dataframe for ROS. It sorts ascending with non-detects
     on top. So something like this:
         [2, 4, 4, 10, 3, 5, 6, 10, 12, 40, 78, 120]
@@ -53,7 +53,7 @@ def rosSort(dataframe, rescol='res', qualcol='qual', ndsymbol='ND'):
     return ros_data #.reset_index(drop=True)
 
 @np.deprecate(message="algo.ros is deprectated. use algo.robustros instead.")
-class MR(object):
+class MR(object): # pragma: no cover
     """ Censored data analysis via regression on order statistics (ROS)
 
     This class implements the MR method outlined Hirsch and Stedinger
@@ -111,7 +111,7 @@ class MR(object):
     """
 
     def __init__(self, data, rescol='res', qualcol='qual', finalcol='final_data',
-                 ndsymbol='ND', fitlogs=True, dist='norm'):
+                 ndsymbol='ND', fitlogs=True, dist='norm'): # pragma: no cover
 
         self.rescol = rescol
         self.qualcol = qualcol
@@ -184,7 +184,7 @@ def _ros_DL_index(row):
         # select out only the necessary columns for data
         self.data = self.data[[self.finalcol, self.rescol, self.qualcol]]
 
-    def cohn(self):
+    def cohn(self): # pragma: no cover
         """ Creates a DataFrame of the unique detection limits in the
         dataset and the other Cohn numbers (A, B, C).
         """
@@ -269,7 +269,7 @@ def _C(row):
 
         return DLs
 
-    def _ros_ranks(self):
+    def _ros_ranks(self): # pragma: no cover
         """ Determine the ranks of the data according to the following
         logic:
         1) rank[n] = rank[n-1] + 1 when:
@@ -315,7 +315,7 @@ def avgrank(r):
 
         self.data['Avg Ranks'] = self.data.apply(avgrank, axis=1)
 
-    def estimator(self):
+    def estimator(self): # pragma: no cover
         """ Estimates the values of the censored data """
 
         def _ros_plotting_pos(row):
@@ -407,7 +407,7 @@ def _select_half_DLs(row):
 
         return self.data
 
-    def plot(self, filename):
+    def plot(self, filename): # pragma: no cover
         """ Makes a simple plot showing the original and modeled data
 
         Parameters

wqio/core/features.py

@@ -34,14 +34,6 @@
 }
 
 
-def sanitizeTexParam(x):
-    return x
-
-
-def sanitizeTexUnit(x):
-    return x
-
-
 class Parameter(object):
     def __init__(self, name, units, usingTex=False):
         """ Class representing a single analytical parameter (pollutant).
@@ -102,10 +94,6 @@ def paramunit(self, usecomma=False):
         else:
             paramunit = '{0} ({1})'
 
-        #if self.usingTex:
-        #    n = sanitizeTexParam(self.name)
-        #    u = sanitizeTexUnit(self.units)
-        #else:
         n = self.name
         u = self.units
 
@@ -282,11 +270,6 @@ def dataframe(self):
                     self._dataframe = df[[self.rescol, self.cencol]]
         return self._dataframe
 
-    @property
-    @np.deprecate
-    def filtered_data(self):
-        return self.dataframe
-
     @property
     @np.deprecate
     def full_data(self):
@@ -883,44 +866,6 @@ def verticalScatter(self, ax=None, pos=1, jitter=0.4, alpha=0.75,
 
         return fig
 
-    # other methods
-    @np.deprecate
-    def applyFilter(self, filterfxn, **fxnkwargs):
-        """ Filter the dataset and set the `include`/`exclude`
-        properties based on a user-defined function.
-
-        Warning
-        -------
-        This is very advanced functionality. Proceed with caution and
-        ask for help.
-
-        Parameters
-        ----------
-        filterfxn : callable
-            A user defined function that filters the data and determines
-            if the `include` attribute should be True or False. It *must*
-            return a pandas.DataFrame and a bool (in that order), or an
-            error will be raised. The `filterfxn` must accept the
-            `Location.data` attribute as its first argument.
-
-        **fxnkwargs : keyword arguments
-            Optional named arguments pass to `filterfxn`.
-
-        Returns
-        -------
-        None
-
-        """
-
-        newdata, include = filterfxn(self.full_data, **fxnkwargs)
-        if not isinstance(newdata, pandas.DataFrame):
-            raise ValueError ('first item returned by filterfxn must be a pandas.DataFrame')
-
-        if not isinstance(include, bool):
-            raise ValueError ('second item returned by filterfxn must be a bool')
-
-        self.include = include
-
 
 class Dataset(object):
     """ Dataset: object for comparings two Location objects

wqio/testing/testutils.py

@@ -44,25 +44,11 @@ def assert_timestamp_equal(x, y):
     nptest.assert_equal(x.strftime('%x %X'), y.strftime('%x %X'))
 
 
-def setup_prefix(folder):
-    for imgdir in ['baseline_images', 'result_images']:
-        subdir = os.path.join('.', imgdir)
-        subsubdir = os.path.join(subdir, folder)
-
-        if not os.path.exists(subdir):
-            os.mkdir(subdir)
-
-        if not os.path.exists(subsubdir):
-            os.mkdir(subsubdir)
-
-    return subsubdir
-
-
-def fail(message):
+def fail(message): # pragma: no cover
     raise AssertionError(message)
 
 
-def wip(f):
+def wip(f):  # pragma: no cover
     @wraps(f)
     def run_test(*args, **kwargs):
         try:
@@ -74,7 +60,7 @@ def run_test(*args, **kwargs):
     return attr('wip')(run_test)
 
 
-def compare_versions(utility='latex'):
+def compare_versions(utility='latex'):  # pragma: no cover
     "return True if a is greater than or equal to b"
     requirements = {
     	'latex': '3.1415'
@@ -97,12 +83,12 @@ def compare_versions(utility='latex'):
     	return False
 
 
-def _show_package_info(package, name):
+def _show_package_info(package, name):  # pragma: no cover
     packagedir = os.path.dirname(package.__file__)
     print("%s version %s is installed in %s" % (name, package.__version__, packagedir))
 
 
-def _show_system_info():
+def _show_system_info():  # pragma: no cover
     import nose
 
     pyversion = sys.version.replace('\n','')
@@ -125,7 +111,7 @@ def _show_system_info():
     _show_package_info(pandas, 'pandas')
 
 
-class NoseWrapper(nptest.Tester):
+class NoseWrapper(nptest.Tester):  # pragma: no cover
     '''
     This is simply a monkey patch for numpy.testing.Tester.
 
@@ -188,13 +174,13 @@ def ascii(s): return bytes(s, 'ascii')
 
     def byte2str(b): return b.decode('ascii')
 
-else:
+else:  # pragma: no cover
     ascii = str
 
     def byte2str(b): return b
 
 
-def checkdep_tex():
+def checkdep_tex():  # pragma: no cover
     try:
         s = subprocess.Popen(['tex','-version'], stdout=subprocess.PIPE,
                              stderr=subprocess.PIPE)
@@ -207,7 +193,7 @@ def checkdep_tex():
         return None
 
 
-def assert_bigstring_equal(input_string, known_string, input_out, known_out):
+def assert_bigstring_equal(input_string, known_string, input_out, known_out):  # pragma: no cover
     try:
         nt.assert_equal(input_string, known_string)
     except:

wqio/tests/core_tests/features_tests.py

@@ -5,7 +5,6 @@
 import numpy.testing as nptest
 
 from wqio import testing
-from wqio.testing.testutils import setup_prefix
 usetex = testing.compare_versions(utility='latex')
 
 import matplotlib

wqio/tests/core_tests/hydro_tests.py

@@ -11,7 +11,7 @@
 import pandas.util.testing as pdtest
 
 from wqio import testing
-from wqio.testing.testutils import assert_timestamp_equal, setup_prefix
+from wqio.testing.testutils import assert_timestamp_equal
 usetex = testing.compare_versions(utility='latex')
 
 import matplotlib

wqio/tests/core_tests/samples_tests.py

@@ -11,7 +11,7 @@
 import pandas.util.testing as pdtest
 
 from wqio import testing
-from wqio.testing.testutils import assert_timestamp_equal, setup_prefix
+from wqio.testing.testutils import assert_timestamp_equal
 usetex = testing.compare_versions(utility='latex')
 
 import matplotlib

wqio/tests/utils_tests/misc_tests.py

@@ -97,30 +97,31 @@ def test_stringify_None(self):
 
 
 class test_uniqueIndex(object):
-    def setup():
+    def setup(self):
         dates = range(5)
         params = list('ABCDE')
         locations = ['Inflow', 'Outflow']
+        dual = []
         for d in dates:
             for p in params:
                 for loc in locations:
                     dual.append([d,p,loc])
-
+        dual_array = np.array(dual)
         index = pandas.MultiIndex.from_arrays([dual_array[:,0],
-                                                    dual_array[:,1],
-                                                    dual_array[:,2]])
+                                               dual_array[:,1],
+                                               dual_array[:,2]])
         index.names = ['date', 'param', 'loc']
 
-        self.data = pandas.DataFrame(np.range.normal(size=len(index)), index=index)
+        self.data = pandas.DataFrame(np.random.normal(size=len(index)), index=index)
 
-        def test_getUniqueDataframeIndexVal():
-            test = misc.getUniqueDataframeIndexVal(self.data.select(lambda x: x[0]=='0'), 'date')
-            known = '0'
-            nt.assert_equal(test, known)
+    def test_getUniqueDataframeIndexVal(self):
+        test = misc.getUniqueDataframeIndexVal(self.data.select(lambda x: x[0]=='0'), 'date')
+        known = '0'
+        nt.assert_equal(test, known)
 
-        @nptest.raises(ValueError)
-        def test_getUniqueDataframeIndexVal_error():
-            misc.getUniqueDataframeIndexVal(self.data, 'date')
+    @nptest.raises(ValueError)
+    def test_getUniqueDataframeIndexVal_error(self):
+        misc.getUniqueDataframeIndexVal(self.data, 'date')
 
 
 class test_redefineIndexLevel(object):

wqio/utils/misc.py

@@ -201,8 +201,7 @@ def stringify(value, fmt, attribute=None):
         return fmt % quantity
 
 
-
-class ProgressBar:
+class ProgressBar: # pragma: no cover
     def __init__(self, sequence, width=50, labels=None, labelfxn=None):
         '''Progress bar for notebookes: