Merge 7a09f92 into b5c75c7

neurodata · Dec 13, 2018 · f53ff37 · f53ff37
2 parents b5c75c7 + 7a09f92
commit f53ff37
Show file tree

Hide file tree

Showing 11 changed files with 1,566 additions and 136 deletions.
diff --git a/demos/mgc.ipynb b/demos/mgc.ipynb
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = 'v0.0.5'
+release = 'v0.1.0'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/mgcpy/benchmarks/mgc_vs_fast_mgc.ipynb b/mgcpy/benchmarks/mgc_vs_fast_mgc.ipynb
diff --git a/mgcpy/benchmarks/power.py b/mgcpy/benchmarks/power.py
@@ -1,9 +1,10 @@
-import numpy as np
 import math
-from mgcpy.independence_tests.dcorr import DCorr
-import scipy.io
 import os
 
+import numpy as np
+import scipy.io
+from mgcpy.independence_tests.dcorr import DCorr
+
 
 def power(independence_test, sample_generator, num_samples=100, num_dimensions=1, noise=0.0, repeats=1000, alpha=.05, simulation_type=''):
     '''

diff --git a/mgcpy/benchmarks/unit_tests/power_test.py b/mgcpy/benchmarks/unit_tests/power_test.py
@@ -1,12 +1,16 @@
-import pytest
+import pickle
+
+import h5py
 import numpy as np
-from scipy.spatial.distance import pdist, squareform
-from mgcpy.independence_tests.dcorr import DCorr
-from mgcpy.benchmarks.simulations import w_sim, ubern_sim, sin_sim, multi_noise_sim, multi_indep_sim, circle_sim, square_sim, joint_sim
+import pytest
 from mgcpy.benchmarks.power import power, power_given_data
+from mgcpy.benchmarks.simulations import (circle_sim, joint_sim,
+                                          multi_indep_sim, multi_noise_sim,
+                                          sin_sim, square_sim, ubern_sim,
+                                          w_sim)
+from mgcpy.independence_tests.dcorr import DCorr
 from mgcpy.independence_tests.rv_corr import RVCorr
-import pickle
-import h5py
+from scipy.spatial.distance import pdist, squareform
 
 
 def test_power():

diff --git a/mgcpy/independence_tests/dcorr.py b/mgcpy/independence_tests/dcorr.py
@@ -1,7 +1,8 @@
 import numpy as np
 from mgcpy.independence_tests.abstract_class import IndependenceTest
+from mgcpy.independence_tests.mgc.distance_transform import \
+    transform_distance_matrix
 from scipy.stats import t
-from mgcpy.independence_tests.mgc.distance_transform import transform_distance_matrix
 
 
 class DCorr(IndependenceTest):

diff --git a/mgcpy/independence_tests/mdmr/__init__.py b/mgcpy/independence_tests/mdmr/__init__.py
@@ -1 +1 @@
-from .mdmr import MDMR
+from .mdmr import MDMR
diff --git a/mgcpy/independence_tests/mgc/mgc.py b/mgcpy/independence_tests/mgc/mgc.py
@@ -164,8 +164,8 @@ def _fast_mgc_test_statistic(self, matrix_X, matrix_Y, sub_samples=100, null_onl
         test_statistic_sub_sampling = np.zeros(num_samples)
 
         # add trivial noise to break any ties
-        matrix_X += 1e-10 * np.random.uniform(size=matrix_X.shape)
-        matrix_Y += 1e-10 * np.random.uniform(size=matrix_Y.shape)
+        matrix_X = matrix_X + 1e-10 * np.random.uniform(size=matrix_X.shape)
+        matrix_Y = matrix_Y + 1e-10 * np.random.uniform(size=matrix_Y.shape)
 
         # the local correlations by subsampling
         local_correlation_matrix_sub_sampling = np.zeros((sub_samples, sub_samples, num_samples))

diff --git a/mgcpy/independence_tests/unit_tests/dcorr/dcorr_test.py b/mgcpy/independence_tests/unit_tests/dcorr/dcorr_test.py
@@ -1,5 +1,5 @@
-import pytest
 import numpy as np
+import pytest
 from mgcpy.independence_tests.dcorr import DCorr
 
 

diff --git a/mgcpy/independence_tests/unit_tests/mgc/distance_transform_test.py b/mgcpy/independence_tests/unit_tests/mgc/distance_transform_test.py
@@ -1,9 +1,10 @@
-import pytest
 import numpy as np
+import pytest
+from mgcpy.independence_tests.mgc.distance_transform import (center_distance_matrix,
+                                                             rank_distance_matrix,
+                                                             transform_distance_matrix)
 from scipy.spatial import distance_matrix
 
-from mgcpy.independence_tests.mgc.distance_transform import rank_distance_matrix, center_distance_matrix, transform_distance_matrix
-
 
 def test_rank_distance_matrix():
     a = np.array([[1, 4, 6],

diff --git a/setup.py b/setup.py
@@ -9,7 +9,6 @@
 from sys import platform
 import numpy
 
-
 PACKAGE_NAME = 'mgcpy'
 DESCRIPTION = 'A set of tools in Python for multiscale graph correlation and other statistical tests'
 with open('README.md', encoding='utf-8') as f:
@@ -21,7 +20,7 @@
 
 REQUIRED_PACKAGES = ["numpy>=1.14.5", "scipy>=1.1.0", "pytest>=3.8.0", "pycodestyle>=2.3.1", "h5py>=2.7.1",
                      "Cython==0.29", "flake8>=3.5.0", "pytest-cov>=2.6.0", "coveralls>=1.5.1", "Sphinx>=1.8.2"]
-VERSION = '0.0.5'
+VERSION = '0.1.0'
 
 
 def check_python_version():