Merge pull request #160 from scikit-learn-contrib/release_prep

Release prep

Author: jcrudy

appveyor.yml

@@ -46,15 +46,10 @@ install:
   # Install the build and runtime dependencies of the project.
   - "conda install --quiet --yes six numpy pandas sympy scipy cython nose scikit-learn wheel conda-build"
   - "pip install sphinx-gallery"
-  - "python setup.py build_ext --inplace --cythonize"
   - "python setup.py bdist_wheel bdist_wininst"
+  - "python setup.py build_ext --inplace --cythonize"
+  
   - ps: "ls"
-  # build the conda package
-  - "conda build conda-recipe"
-  # Move the conda package into the dist directory, to register it
-  # as an "artifact" for Appveyor. cmd.exe does't have good globbing, so
-  # we'll use a simple python script.
-  - "python conda-recipe/move-conda-package.py conda-recipe"
 
   # Install the generated wheel package to test it
   - "pip install --pre --no-index --find-links dist/ py-earth"

description.md

@@ -0,0 +1 @@
+The py-earth package implements Multivariate Adaptive Regression Splines and provides an interface that is compatible with scikit-learn's Estimator, Predictor, Transformer, and Model interfaces.

pyearth/earth.py

@@ -463,13 +463,13 @@ def _scrub(self, X, y, sample_weight, output_weight, missing, **kwargs):
         if sample_weight is None:
             sample_weight = np.ones((y.shape[0], 1), dtype=y.dtype)
         else:
-            sample_weight = np.asarray(sample_weight)
+            sample_weight = np.asarray(sample_weight, dtype=np.float64)
             assert_all_finite(sample_weight)
             if len(sample_weight.shape) == 1:
                 sample_weight = sample_weight[:, np.newaxis]
         # Deal with output_weight
         if output_weight is not None:
-            output_weight = np.asarray(output_weight)
+            output_weight = np.asarray(output_weight, dtype=np.float64)
             assert_all_finite(output_weight)
 
         # Make sure dimensions match

pyearth/test/earth_linvars_regress.txt

@@ -1,47 +1 @@
-Forward Pass
----------------------------------------------------------------
-iter  parent  var  knot  mse       terms  gcv    rsq    grsq   
----------------------------------------------------------------
-0     -       -    -     1.373069  1      1.401  0.000  0.000  
-1     0       1    -1    0.861043  2      0.906  0.373  0.353  
-2     0       2    -1    0.774582  3      0.840  0.436  0.400  
-3     0       3    -1    0.764313  4      0.856  0.443  0.389  
-4     0       6    -1    0.753043  5      0.871  0.452  0.379  
-5     0       5    -1    0.740056  6      0.884  0.461  0.369  
-6     0       7    -1    0.734362  7      0.907  0.465  0.353  
-7     0       8    -1    0.732358  8      0.935  0.467  0.333  
-8     0       4    -1    0.731261  9      0.966  0.467  0.310  
----------------------------------------------------------------
-Stopping Condition 2: Improvement below threshold
-
-Pruning Pass
---------------------------------------------
-iter  bf  terms  mse   gcv    rsq    grsq   
---------------------------------------------
-0     -   9      0.73  0.966  0.467  0.310  
-1     8   8      0.73  0.935  0.467  0.333  
-2     7   7      0.73  0.907  0.465  0.353  
-3     6   6      0.74  0.884  0.461  0.369  
-4     5   5      0.75  0.871  0.452  0.379  
-5     4   4      0.76  0.856  0.443  0.389  
-6     3   3      0.77  0.840  0.436  0.400  
-7     2   2      0.86  0.906  0.373  0.353  
-8     1   1      1.37  1.401  0.000  0.000  
---------------------------------------------
-Selected iteration: 6
-
-Earth Model
--------------------------------------
-Basis Function  Pruned  Coefficient  
--------------------------------------
-(Intercept)     No      0.657403     
-x1              No      0.757872     
-x2              No      0.325515     
-x3              Yes     None         
-x6              Yes     None         
-x5              Yes     None         
-x7              Yes     None         
-x8              Yes     None         
-x4              Yes     None         
--------------------------------------
-MSE: 0.7746, GCV: 0.8405, RSQ: 0.4359, GRSQ: 0.4001
+0.151785846961

pyearth/test/earth_regress.txt

@@ -1 +1 @@
-0.513434373667
+0.219175992389

pyearth/test/earth_regress_missing_data.txt

@@ -1 +1 @@
-0.471040262964
+0.178314473548

pyearth/test/earth_regress_smooth.txt

@@ -1 +1 @@
-0.493873566832
+0.209074299412

pyearth/test/test_earth.py

@@ -9,7 +9,8 @@
 from .testing_utils import (if_statsmodels, if_pandas, if_patsy,
                             if_environ_has, assert_list_almost_equal_value,
                             assert_list_almost_equal,
-                            if_sklearn_version_greater_than_or_equal_to)
+                            if_sklearn_version_greater_than_or_equal_to,
+                            if_platform_not_win_32)
 from nose.tools import (assert_equal, assert_true, assert_almost_equal,
                         assert_list_equal, assert_raises, assert_not_equal)
 import numpy
@@ -19,9 +20,11 @@
                             HingeBasisFunction, LinearBasisFunction)
 from pyearth import Earth
 import pyearth
+from numpy.testing.utils import assert_array_almost_equal
 
-numpy.random.seed(0)
+regenerate_target_files = False
 
+numpy.random.seed(1)
 basis = Basis(10)
 constant = ConstantBasisFunction()
 basis.append(constant)
@@ -31,18 +34,19 @@
 basis.append(bf1)
 basis.append(bf2)
 basis.append(bf3)
-X = numpy.random.normal(size=(100, 10))
+X = numpy.random.normal(size=(1000, 10))
 missing = numpy.zeros_like(X, dtype=BOOL)
-B = numpy.empty(shape=(100, 4), dtype=numpy.float64)
+B = numpy.empty(shape=(1000, 4), dtype=numpy.float64)
 basis.transform(X, missing, B)
 beta = numpy.random.normal(size=4)
-y = numpy.empty(shape=100, dtype=numpy.float64)
-y[:] = numpy.dot(B, beta) + numpy.random.normal(size=100)
+y = numpy.empty(shape=1000, dtype=numpy.float64)
+y[:] = numpy.dot(B, beta) + numpy.random.normal(size=1000)
 default_params = {"penalty": 1}
 
-
+@if_platform_not_win_32
 @if_sklearn_version_greater_than_or_equal_to('0.17.2')
 def test_check_estimator():
+    numpy.random.seed(0)
     import sklearn.utils.estimator_checks
     sklearn.utils.estimator_checks.MULTI_OUTPUT.append('Earth')
     sklearn.utils.estimator_checks.check_estimator(Earth)
@@ -149,6 +153,7 @@ def test_output_weight():
 
 
 def test_missing_data():
+    numpy.random.seed(0)
     earth = Earth(allow_missing=True, **default_params)
     missing_ = numpy.random.binomial(1, .05, X.shape).astype(bool)
     X_ = X.copy()
@@ -157,34 +162,42 @@ def test_missing_data():
     res = str(earth.score(X_, y))
     filename = os.path.join(os.path.dirname(__file__),
                             'earth_regress_missing_data.txt')
-#     with open(filename, 'w') as fl:
-#         fl.write(res)
+    if regenerate_target_files:
+        with open(filename, 'w') as fl:
+            fl.write(res)
     with open(filename, 'r') as fl:
         prev = fl.read()
-    assert_true(abs(float(res) - float(prev)) < .03)
-
+    try:
+        assert_true(abs(float(res) - float(prev)) < .03)
+    except AssertionError:
+        print('Got %f, %f' % (float(res), float(prev)))
+        raise
 
 def test_fit():
+    numpy.random.seed(0)
     earth = Earth(**default_params)
     earth.fit(X, y)
     res = str(earth.rsq_)
     filename = os.path.join(os.path.dirname(__file__),
                             'earth_regress.txt')
-#     with open(filename, 'w') as fl:
-#         fl.write(res)
+    if regenerate_target_files:
+        with open(filename, 'w') as fl:
+            fl.write(res)
     with open(filename, 'r') as fl:
         prev = fl.read()
     assert_true(abs(float(res) - float(prev)) < .05)
 
 
 def test_smooth():
+    numpy.random.seed(0)
     model = Earth(penalty=1, smooth=True)
     model.fit(X, y)
     res = str(model.rsq_)
     filename = os.path.join(os.path.dirname(__file__),
                             'earth_regress_smooth.txt')
-#     with open(filename, 'w') as fl:
-#         fl.write(res)
+    if regenerate_target_files:
+        with open(filename, 'w') as fl:
+            fl.write(res)
     with open(filename, 'r') as fl:
         prev = fl.read()
     assert_true(abs(float(res) - float(prev)) < .05)
@@ -193,11 +206,12 @@ def test_smooth():
 def test_linvars():
     earth = Earth(**default_params)
     earth.fit(X, y, linvars=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
-    res = str(earth.trace()) + '\n' + earth.summary()
+    res = str(earth.rsq_)
     filename = os.path.join(os.path.dirname(__file__),
                             'earth_linvars_regress.txt')
-#     with open(filename, 'w') as fl:
-#         fl.write(res)
+    if regenerate_target_files:
+        with open(filename, 'w') as fl:
+            fl.write(res)
     with open(filename, 'r') as fl:
         prev = fl.read()
 
@@ -301,8 +315,7 @@ def test_pickle_compatibility():
     model = earth.fit(X, y)
     model_copy = pickle.loads(pickle.dumps(model))
     assert_true(model_copy == model)
-    assert_true(
-        numpy.all(model.predict(X) == model_copy.predict(X)))
+    assert_array_almost_equal(model.predict(X), model_copy.predict(X))
     assert_true(model.basis_[0] is model.basis_[1]._get_root())
     assert_true(model_copy.basis_[0] is model_copy.basis_[1]._get_root())
 
@@ -318,11 +331,11 @@ def test_pickle_version_storage():
 
 
 def test_copy_compatibility():
+    numpy.random.seed(0)
     model = Earth(**default_params).fit(X, y)
     model_copy = copy.copy(model)
     assert_true(model_copy == model)
-    assert_true(
-        numpy.all(model.predict(X) == model_copy.predict(X)))
+    assert_array_almost_equal(model.predict(X), model_copy.predict(X))
     assert_true(model.basis_[0] is model.basis_[1]._get_root())
     assert_true(model_copy.basis_[0] is model_copy.basis_[1]._get_root())
 

pyearth/test/testing_utils.py

@@ -3,7 +3,7 @@
 from nose import SkipTest
 from nose.tools import assert_almost_equal
 from distutils.version import LooseVersion
-
+import sys
 
 def if_environ_has(var_name):
     # Test decorator that skips test if environment variable is not defined
@@ -18,7 +18,15 @@ def run_test(*args, **kwargs):
         return run_test
     return if_environ
 
-
+def if_platform_not_win_32(func):
+    @wraps(func)
+    def run_test(*args, **kwargs):
+        if sys.platform == 'win32':
+            raise SkipTest('Skip for 32 bit Windows platforms.')
+        else:
+            return func(*args, **kwargs)
+    return run_test
+            
 def if_sklearn_version_greater_than_or_equal_to(min_version):
     '''
     Test decorator that skips test unless sklearn version is greater than or

setup.cfg

@@ -4,4 +4,8 @@ style = pep440
 versionfile_source = pyearth/_version.py
 versionfile_build = pyearth/_version.py
 tag_prefix=
-parentdir_prefix = py-earth
+parentdir_prefix = py-earth
+
+[metadata]
+description-file = description.md
+license_file = LICENSE.txt