Merge pull request #17 in INF/allensdk from import_check_improvements…

… to dev * commit '6782dc5fb432ce3dbd27619c52d0887f19066f4b': IT-14563; better import checking, remove leftover extra imports.
AllenInstitute · Feb 28, 2017 · 3c2656e · 3c2656e
2 parents 8ca828f + 6782dc5
commit 3c2656e
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Showing 19 changed files with 39 additions and 46 deletions.
diff --git a/Makefile b/Makefile
@@ -35,21 +35,21 @@ pypi_deploy:
 	python setup.py sdist upload --repository https://testpypi.python.org/pypi
 
 pytest:
-	find -L . -name "test_*.py" -exec py.test --boxed --pep8 --cov-config coveragerc --cov=allensdk --cov-report html --junitxml=test-reports/test.xml {} \+
+	find -L . -name "test_*.py" -exec py.test --boxed --pep8 --cov-config coveragerc --cov=allensdk --cov-report html --assert=reinterp --junitxml=test-reports/test.xml {} \+
 
 pytest_lax:
-	find -L . -name "test_*.py" -exec py.test --boxed --cov-config coveragerc --cov=allensdk --cov-report html --junitxml=test-reports/test.xml {} \+
+	find -L . -name "test_*.py" -exec py.test --boxed --cov-config coveragerc --cov=allensdk --cov-report html --assert=reinterp --junitxml=test-reports/test.xml {} \+
 
 pytest_lite:
-	find -L . -name "test_*.py" -exec py.test --boxed --assert=rewrite --junitxml=test-reports/test.xml {} \+
+	find -L . -name "test_*.py" -exec py.test --boxed --assert=reinterp --junitxml=test-reports/test.xml {} \+
 
 pylint:
 	pylint --disable=C allensdk > htmlcov/pylint.txt || exit 0
-	egrep '(import-error)|(Unable to import)|(Undefined variable)' htmlcov/pylint.txt > htmlcov/pylint_imports.txt
+	grep import-error htmlcov/pylint.txt > htmlcov/pylint_imports.txt
 
 flake8:
-	flake8 --ignore=E201,E202,E226 --max-line-length=200 allensdk | grep -v "local variable '_' is assigned to but never used" > htmlcov/flake8.txt
-	grep "imported but unused" htmlcov/flake8.txt > htmlcov/imports.txt
+	flake8 --ignore=E201,E202,E226 --max-line-length=200 --filename 'allensdk/**/*.py' allensdk | grep -v "local variable '_' is assigned to but never used" > htmlcov/flake8.txt
+	grep -i "import" htmlcov/flake8.txt > htmlcov/imports.txt || exit 0
 
 EXAMPLES=doc/_static/examples
 

diff --git a/allensdk/api/api.py b/allensdk/api/api.py
@@ -22,7 +22,6 @@
 import os
 import errno
 import warnings
-from allensdk.deprecated import deprecated
 
 
 class Api(object):

diff --git a/allensdk/api/queries/glif_api.py b/allensdk/api/queries/glif_api.py
@@ -15,10 +15,9 @@
 
 import json
 import logging
-
 from ...deprecated import deprecated
 from .rma_template import RmaTemplate
-from ..cache import cacheable
+
 
 class GlifApi(RmaTemplate):
 

diff --git a/allensdk/brain_observatory/circle_plots.py b/allensdk/brain_observatory/circle_plots.py
@@ -2,12 +2,10 @@
 
 import pandas as pd
 import math
-import h5py
 
-from matplotlib.colors import LinearSegmentedColormap, rgb2hex
+from matplotlib.colors import LinearSegmentedColormap
 import matplotlib.pyplot as plt
 import matplotlib.patches as mpatches
-from matplotlib.path import Path
 from matplotlib.collections import PatchCollection, LineCollection
 import matplotlib.transforms as mxfms
 import matplotlib.colors as mcolors
@@ -125,7 +123,7 @@ def build_hex_pack(n):
     while len(pos) < n:
         layer_pos = [  ] 
 
-        for i,v in enumerate(vs):            
+        for i,v in enumerate(vs):
             x = - N * v[1] * sq32
             y = N * v[0] * sq32
 
@@ -134,7 +132,7 @@ def build_hex_pack(n):
                 y -= 0.5 * v[1]
 
             layer_pos.append([])
-            layer_pos[i].append([x,y])                                    
+            layer_pos[i].append([x,y])
             mag = 1
             sign = 1
 
@@ -143,7 +141,7 @@ def build_hex_pack(n):
                 y += v[1] * mag * sign
                 mag += 1
                 sign = -sign
-                layer_pos[i].append([x,y])            
+                layer_pos[i].append([x,y])
 
         for j in range(N):
             for i in range(len(vs)):

diff --git a/allensdk/brain_observatory/observatory_plots.py b/allensdk/brain_observatory/observatory_plots.py
@@ -1,18 +1,13 @@
-import matplotlib
-
 import matplotlib.pyplot as plt
 from matplotlib.colors import LinearSegmentedColormap
-from matplotlib.collections import PatchCollection, LineCollection
+from matplotlib.collections import PatchCollection
 import matplotlib.patches as mpatches
 import scipy.interpolate as si
 from scipy.stats.mstats import zscore
 
 import allensdk.brain_observatory.circle_plots as cplots
 from contextlib import contextmanager
 
-import h5py
-import pandas as pd
-import logging
 import numpy as np
 
 SI_RANGE = [ 0, 1.5 ]

diff --git a/allensdk/core/brain_observatory_nwb_data_set.py b/allensdk/core/brain_observatory_nwb_data_set.py
@@ -457,8 +457,8 @@ def get_roi_mask_array(self, cell_specimen_ids=None):
         roi_arr = np.zeros((len(roi_list), roi_list[0].shape[
                            0], roi_list[0].shape[1]), dtype=np.uint8)
 
-        for i, roi in enumerate(roi_list):
-            roi_arr[i, :, :] = roi
+        for i, an_roi in enumerate(roi_list):
+            roi_arr[i, :, :] = an_roi
 
         return roi_arr
 

diff --git a/allensdk/model/glif/glif_neuron_methods.py b/allensdk/model/glif/glif_neuron_methods.py
@@ -1,14 +1,14 @@
 """ The methods in this module are used for configuring dynamics and reset rules for the GlifNeuron.  
 For more details on how to use these methods, see :doc:`glif_models`.
 """
-import logging
 import functools
 import numpy as np
-from numpy.distutils.npy_pkg_config import VariableSet
+
 
 #fast_threshold=[]
 #slow_threshold=[]
 
+
 class GlifNeuronMethod( object ):
     """ A simple class to keep track of the name and parameters associated with a neuron method.
     This class is initialized with a name, function, and parameters to pass to the function.  The

diff --git a/allensdk/test/brain_observatory/test_drifting_gratings.py b/allensdk/test/brain_observatory/test_drifting_gratings.py
@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 from allensdk.brain_observatory.drifting_gratings import DriftingGratings
 from allensdk.brain_observatory.stimulus_analysis import StimulusAnalysis
 

diff --git a/allensdk/test/brain_observatory/test_locally_sparse_noise.py b/allensdk/test/brain_observatory/test_locally_sparse_noise.py
@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 from allensdk.brain_observatory.locally_sparse_noise import LocallySparseNoise
 from allensdk.brain_observatory.stimulus_analysis import StimulusAnalysis
 import pytest

diff --git a/allensdk/test/brain_observatory/test_natural_movie.py b/allensdk/test/brain_observatory/test_natural_movie.py
@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 from allensdk.brain_observatory.natural_movie import NaturalMovie
 from allensdk.brain_observatory.stimulus_analysis import StimulusAnalysis
 import pytest

diff --git a/allensdk/test/brain_observatory/test_natural_scenes.py b/allensdk/test/brain_observatory/test_natural_scenes.py
@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 from allensdk.brain_observatory.natural_scenes import NaturalScenes
 from allensdk.brain_observatory.stimulus_analysis import StimulusAnalysis
 import pytest

diff --git a/allensdk/test/brain_observatory/test_observatory_plots.py b/allensdk/test/brain_observatory/test_observatory_plots.py
@@ -1,7 +1,5 @@
 import pytest
-import matplotlib
 import os
-import matplotlib.pyplot as plt
 import matplotlib.image as mpimg
 import numpy as np
 from allensdk.core.brain_observatory_nwb_data_set import BrainObservatoryNwbDataSet

diff --git a/allensdk/test/brain_observatory/test_session_analysis.py b/allensdk/test/brain_observatory/test_session_analysis.py
@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 import pytest
 from mock import patch
 from allensdk.core.brain_observatory_nwb_data_set import BrainObservatoryNwbDataSet

diff --git a/allensdk/test/brain_observatory/test_static_gratings.py b/allensdk/test/brain_observatory/test_static_gratings.py
@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 from allensdk.brain_observatory.static_gratings import StaticGratings
 from allensdk.brain_observatory.stimulus_analysis import StimulusAnalysis
 import pytest

diff --git a/allensdk/test/brain_observatory/test_stimulus_analysis.py b/allensdk/test/brain_observatory/test_stimulus_analysis.py
@@ -13,11 +13,10 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import matplotlib
+
 from allensdk.brain_observatory.stimulus_analysis import StimulusAnalysis
 import pytest
 from mock import patch, MagicMock
-import itertools as it
 
 
 @pytest.fixture

diff --git a/allensdk/test/core/test_brain_observatory_nwb_data_set.py b/allensdk/test/core/test_brain_observatory_nwb_data_set.py
@@ -13,14 +13,17 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
+
 import numpy as np
 from pkg_resources import resource_filename  # @UnresolvedImport
 from allensdk.core.brain_observatory_nwb_data_set import BrainObservatoryNwbDataSet
 import pytest
 import os
 
+
 NWB_FLAVORS = []
 
+
 if 'TEST_NWB_FILES' in os.environ:
     nwb_list_file = os.environ['TEST_NWB_FILES']
 else:

diff --git a/allensdk/test/core/test_mouse_connectivity_manifest.py b/allensdk/test/core/test_mouse_connectivity_manifest.py
@@ -1,14 +1,14 @@
 import pytest
 from mock import Mock, MagicMock, patch
 import numpy as np
-import nrrd
+import nrrd  # noqa: F401
 from allensdk.core import mouse_connectivity_cache
 from allensdk.api.queries import mouse_connectivity_api
 
 
 @pytest.fixture(scope='module', autouse=True)
 def mock_imports():
-    import nrrd
+    import nrrd  # noqa: F401
     nrrd.read = MagicMock(name='nrrd_read_file_mcm',
                           return_value=('mock_annotation_data',
                                         'mock_annotation_image'))

diff --git a/allensdk/test/glif_tests.py b/allensdk/test/glif_tests.py
@@ -16,14 +16,14 @@
 
 import matplotlib
 matplotlib.use('agg')
-import matplotlib.pyplot as plt
-from allensdk.api.queries.glif_api import GlifApi
-import allensdk.core.json_utilities as json_utilities
-from allensdk.model.glif.glif_neuron import GlifNeuron
-from allensdk.model.glif.simulate_neuron import simulate_neuron
-import os
-import shutil
-import logging
+import matplotlib.pyplot as plt # noqa: #402
+from allensdk.api.queries.glif_api import GlifApi  # noqa: #402
+import allensdk.core.json_utilities as json_utilities  # noqa: #402
+from allensdk.model.glif.glif_neuron import GlifNeuron  # noqa: #402
+from allensdk.model.glif.simulate_neuron import simulate_neuron  # noqa: #402
+import os         # noqa: #402
+import shutil     # noqa: #402
+import logging    # noqa: #402
 
 
 # NEURONAL_MODEL_ID = 491547163 # level 1 LIF

diff --git a/allensdk/test/model/test_biophysical_perisomatic.py b/allensdk/test/model/test_biophysical_perisomatic.py
@@ -13,7 +13,9 @@
 # You should have received a copy of the GNU General Public License
 # along with Allen SDK.  If not, see <http://www.gnu.org/licenses/>.
 
-import pytest, os, numpy
+import pytest
+import os
+import numpy
 from allensdk.model.biophys_sim.config import Config
 from allensdk.model.biophysical.utils import Utils
 from allensdk.core.dat_utilities import DatUtilities