Build cython extension module when the source distribution is created…

…, not on the fly. This means that zounds users don't need cython installed

.travis.yml

@@ -21,7 +21,7 @@ install:
   - conda update -q conda
   # Useful for debugging any issues with conda
   - conda info -a
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy=1.12 scipy=0.18
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy=1.12 scipy=0.18 cython
   - source activate test-environment
   - python setup.py install
   - pip install coveralls

setup.py

@@ -1,5 +1,8 @@
 from setuptools import setup
 import re
+import numpy as np
+from distutils.extension import Extension
+
 
 try:
     import pypandoc
@@ -16,6 +19,21 @@
 download_url = 'https://github.com/jvinyard/zounds/tarball/{version}'\
     .format(**locals())
 
+
+countbits = Extension(
+    name='countbits',
+    sources=['zounds/nputil/countbits.pyx'],
+    include_dirs=[np.get_include()],
+    extra_compile_args=[
+        '-shared',
+        '-pthread',
+        '-fPIC',
+        '-fwrapv',
+        '-O2',
+        '-Wall',
+        '-fno-strict-aliasing'
+    ])
+
 setup(
         name='zounds',
         version=version,
@@ -24,6 +42,7 @@
         author_email='john.vinyard@gmail.com',
         long_description=long_description,
         download_url=download_url,
+        ext_modules=[countbits],
         packages=[
             'zounds',
             'zounds.basic',
@@ -49,7 +68,6 @@
             'requests',
             'tornado',
             'pysoundfile',
-            'cython',
             'matplotlib',
             'argparse'
         ],

zounds/learn/preprocess.py

@@ -329,7 +329,10 @@ def _forward_func(self):
         def x(d):
             import numpy as np
             axes = tuple(range(1, len(d.shape)))
-            return d / np.max(np.abs(d), axis=axes, keepdims=True)
+            m = np.max(np.abs(d), axis=axes, keepdims=True)
+            output = d / m
+            output[np.isnan(output)] = 0
+            return output
 
         return x
 

zounds/learn/test_instancescaling.py

@@ -47,3 +47,11 @@ def test_backward_transform_reconstructs_data_3d(self):
         transformed = model.pipeline.transform(inp)
         inverted = transformed.inverse_transform()
         np.testing.assert_allclose(inverted, inp)
+
+    def test_correctly_handles_max_of_zero(self):
+        model = self.get_model()
+        inp = np.random.random_sample((100, 30, 3)) - 0.5
+        inp[0, ...] = 0
+        transformed = model.pipeline.transform(inp)
+        inverted = transformed.inverse_transform()
+        np.testing.assert_allclose(inverted, inp)

zounds/nputil/npx.py

@@ -2,9 +2,6 @@
 
 import numpy as np
 from numpy.lib.stride_tricks import as_strided as ast
-
-import pyximport
-pyximport.install()
 from countbits import *