Merge pull request #2771 from galenlynch/fix/remove-six

Remove Python 2 compatibility shims

Author: dyf

allensdk/api/queries/brain_observatory_api.py

@@ -38,7 +38,6 @@
 from pathlib import Path
 
 import pandas as pd
-from six import string_types
 
 import allensdk.brain_observatory.stimulus_info as stimulus_info
 
@@ -785,7 +784,7 @@ def dataframe_query_string(self, filters):
         """
 
         def _quote_string(v):
-            if isinstance(v, string_types):
+            if isinstance(v, str):
                 return "'%s'" % (v)
             else:
                 return str(v)

allensdk/api/queries/image_download_api.py

@@ -35,8 +35,6 @@
 #
 from .rma_template import RmaTemplate
 from allensdk.api.warehouse_cache.cache import cacheable
-from six import string_types
-
 
 class ImageDownloadApi(RmaTemplate):
     '''HTTP Client to download whole or partial two-dimensional images from the Allen Institute
@@ -384,7 +382,7 @@ def download_image(self,
         colormap_filter = kwargs.get('colormap', None)
 
         if colormap_filter is not None:
-            if isinstance(colormap_filter, string_types):
+            if isinstance(colormap_filter, str):
                 params.append('colormap=%s' % (colormap_filter))
             else:
                 lower_threshold = colormap_filter[0]

allensdk/api/queries/mouse_connectivity_api.py

@@ -38,8 +38,6 @@
 from allensdk.api.warehouse_cache.cache import cacheable, Cache
 import numpy as np
 import nrrd
-import six
-
 
 class MouseConnectivityApi(ReferenceSpaceApi, GridDataApi):
     '''
@@ -282,7 +280,7 @@ def experiment_source_search(self, **kwargs):
         `service::mouse_connectivity_injection_structure <http://help.brain-map.org/display/api/Connected+Services+and+Pipes#ConnectedServicesandPipes-service%3A%3Amouseconnectivityinjectionstructure>`_.
 
         '''
-        tuples = [(k, v) for k, v in six.iteritems(kwargs)]
+        tuples = [(k, v) for k, v in kwargs.items()]
         return self.service_query('mouse_connectivity_injection_structure', parameters=tuples)
 
     def experiment_spatial_search(self, **kwargs):
@@ -318,7 +316,7 @@ def experiment_spatial_search(self, **kwargs):
 
         '''
 
-        tuples = [(k, v) for k, v in six.iteritems(kwargs)]
+        tuples = [(k, v) for k, v in kwargs.items()]
         return self.service_query('mouse_connectivity_target_spatial', parameters=tuples)
 
     def experiment_injection_coordinate_search(self, **kwargs):
@@ -349,7 +347,7 @@ def experiment_injection_coordinate_search(self, **kwargs):
         `service::mouse_connectivity_injection_coordinate <http://help.brain-map.org/display/api/Connected+Services+and+Pipes#ConnectedServicesandPipes-service%3A%3Amouseconnectivityinjectioncoordinate>`_.
 
         '''
-        tuples = [(k, v) for k, v in six.iteritems(kwargs)]
+        tuples = [(k, v) for k, v in kwargs.items()]
         return self.service_query('mouse_connectivity_injection_coordinate', parameters=tuples)
 
     def experiment_correlation_search(self, **kwargs):
@@ -384,7 +382,7 @@ def experiment_correlation_search(self, **kwargs):
         `service::mouse_connectivity_correlation <http://help.brain-map.org/display/api/Connected+Services+and+Pipes#ConnectedServicesandPipes-service%3A%3Amouseconnectivitycorrelation>`_.
 
         '''
-        tuples = sorted(six.iteritems(kwargs))
+        tuples = sorted(kwargs.items())
         return self.service_query('mouse_connectivity_correlation',
                                   parameters=tuples)
 

allensdk/api/queries/reference_space_api.py

@@ -39,8 +39,6 @@
 import allensdk.core.sitk_utilities as sitk_utilities
 import numpy as np
 import nrrd
-import six
-
 
 class ReferenceSpaceApi(RmaApi):
 

allensdk/brain_observatory/circle_plots.py

@@ -36,10 +36,6 @@
 
 import math
 
-try:
-    xrange
-except:
-    from past.builtins import xrange
 
 import numpy as np
 import pandas as pd
@@ -50,7 +46,6 @@
 import matplotlib.transforms as mxfms
 import matplotlib.colors as mcolors
 import skimage.transform
-from six import iteritems
 
 
 DEFAULT_COLOR_MAP = LinearSegmentedColormap.from_list('default', [[.7,0,.7,0.0],[.7,0,0,1]])
@@ -178,7 +173,7 @@ def build_hex_pack(n):
             mag = 1
             sign = 1
 
-            for j in xrange(N-1):
+            for j in range(N-1):
                 x += v[0] * mag * sign
                 y += v[1] * mag * sign
                 mag += 1
@@ -277,7 +272,7 @@ def make_pincushion_plot(data, trials, on, nrows, ncols, clim=None, color_map=No
         color_map = LSN_ON_COLOR_MAP if on else LSN_OFF_COLOR_MAP
 
     ax = plt.gca()
-    for (col,row,on_state), sweeps in iteritems(trials):
+    for (col,row,on_state), sweeps in trials.items():
         if on_state != on:
             continue
 
@@ -477,7 +472,7 @@ def plot(self, category_data,
         df = pd.DataFrame({ 'category': category_data })
         gb = df.groupby(['category'])
 
-        for category, trials in iteritems(gb.groups):
+        for category, trials in gb.groups.items():
             idx = self.cat_idx_map[category]
             order = np.argsort(data[trials])[::-1]
             trial_order = np.array(trials)[order]
@@ -714,7 +709,7 @@ def plot(self,
 
         gb = df.groupby(['group', 'angle', 'r'])
 
-        for (group, angle, r), trials in iteritems(gb.groups):
+        for (group, angle, r), trials in gb.groups.items():
             responses = np.sort(data[trials])[::-1]
 
             circles = spiral_trials_polar(self.r_radius_map[r],

allensdk/brain_observatory/ecephys/stimulus_analysis/drifting_gratings.py

@@ -1,6 +1,5 @@
 import numpy as np
 import pandas as pd
-from six import string_types
 import scipy.ndimage as ndi
 import scipy.stats as st
 from scipy.signal import welch

allensdk/brain_observatory/ecephys/stimulus_analysis/flashes.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pandas as pd
-from six import string_types
+
 import scipy.ndimage as ndi
 import scipy.stats as st
 from scipy.optimize import curve_fit

allensdk/brain_observatory/ecephys/stimulus_analysis/natural_movies.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pandas as pd
-from six import string_types
+
 import scipy.ndimage as ndi
 import scipy.stats as st
 from scipy.optimize import curve_fit

allensdk/brain_observatory/ecephys/stimulus_analysis/static_gratings.py

@@ -1,4 +1,3 @@
-from six import string_types
 import numpy as np
 import pandas as pd
 from scipy.optimize import curve_fit

allensdk/brain_observatory/ecephys/stimulus_analysis/stimulus_analysis.py

@@ -1,4 +1,3 @@
-from six import string_types
 import numpy as np
 import pandas as pd
 import scipy.stats as st
@@ -25,7 +24,7 @@ def __init__(self, ecephys_session, trial_duration=None, **kwargs):
         # TODO: Create a set of a class methods.
         if isinstance(ecephys_session, EcephysSession):
             self._ecephys_session = ecephys_session
-        elif isinstance(ecephys_session, string_types):
+        elif isinstance(ecephys_session, str):
             nwb_version = kwargs.get('nwb_version', 2)
             self._ecephys_session = EcephysSession.from_nwb_path(
                 path=ecephys_session, nwb_version=nwb_version)
@@ -172,7 +171,7 @@ def stim_table(self):
 
             self._stim_table = self.ecephys_session.get_stimulus_table(
                 [self._stimulus_key] if isinstance(self._stimulus_key,
-                                                   string_types) else
+                                                   str) else
                 self._stimulus_key
             )