Added testsuite

.gitignore

@@ -3,4 +3,5 @@ dist/
 spectrophore/__pycache__/
 uamc_spectrophore.egg-info/
 spectrophore/spectrophore_notebook.ipynb
-spectrophore/.ipynb_checkpoints/
+spectrophore/.ipynb_checkpoints/
+__pycache__/

run_tests.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+python -m unittest -v tests

setup.py

@@ -1,21 +1,43 @@
 #!/usr/bin/env python
 
 from setuptools import setup, find_packages
+import codecs
+import os.path
+
+
+
+def read(rel_path):
+    here = os.path.abspath(os.path.dirname(__file__))
+    with codecs.open(os.path.join(here, rel_path), 'r') as fp:
+        return fp.read()
+
+
+def get_version(rel_path):
+    for line in read(rel_path).splitlines():
+        if line.startswith('__version__'):
+            delim = '"' if '"' in line else "'"
+            return line.split(delim)[1]
+    else:
+        raise RuntimeError("Unable to find version string.")
+
 
 with open("README.md", "r") as fh:
 	long_description = fh.read()
 
+
 setup(
     name = "uamc-spectrophore",
-    version = "1.1.0",
+    version = get_version("spectrophore/__init__.py"),
     author = "Hans De Winter",
     author_email = "hans.dewinter@uantwerpen.be",
     description = ("Python implementation of the spectrophore descriptor"),
     long_description = long_description,
 	long_description_content_type="text/markdown",
     url = "https://github.com/UAMCAntwerpen/spectrophore",
-	download_url = "https://github.com/UAMCAntwerpen/spectrophore/releases/tag/1.0.1",
-    packages = find_packages(include=['spectrophore']),
+	download_url = "https://github.com/UAMCAntwerpen/spectrophore/releases/tag/1.1.0",
+    packages = ['spectrophore'],
+    package_dir = {'spectrophore': 'spectrophore'},
+    package_data = {'spectrophore': ['images/*']},
 	keywords = ['uamc', 'spectrophore', 'rdkit', 'cheminformatics'],
     classifiers = [
         "Development Status :: 5 - Production/Stable",

spectrophore/__init__.py

@@ -1 +1,2 @@
 __all__ = ["spectrophore"]
+__version__ = "1.1.0"

spectrophore/spectrophore.py

@@ -5,7 +5,6 @@
 # of Antwerp
 
 __all__ = ['SpectrophoreCalculator']
-__version__ = "1.1.0"
 
 # Numba support
 from numba import njit
@@ -234,11 +233,11 @@ class SpectrophoreCalculator:
     # self.BOX[i][2]      z-coordinate of the i'th box point (1-12)
 
     ####################################################
-    def __init__(self, resolution=3.0, accuracy=20, stereo='none', normalization='none'):
+    def __init__(self, resolution=3.0, accuracy=20, stereo='none', normalization='all'):
 
         # Initiate PARMS
         self.PARMS = np.array([
-            0,      #  0 Normalisation
+            3,      #  0 Normalisation
             20,     #  1 Accuracy
             0,      #  2 Stereo
             0,      #  3 BeginProbe
@@ -743,7 +742,7 @@ def __processCommandline():
     parser.add_argument('-n', '--norm', 
                         dest = 'norm', 
                         help = 'normalization setting', 
-                        default = 'none', 
+                        default = 'all', 
                         choices = ['none','mean','all','std'])
     parser.add_argument('-s', '--stereo', 
                         dest = 'stereo', 
@@ -813,4 +812,3 @@ def __processCommandline():
 		    if spec is not None: of.write("%s\n" % (spec))
 
     of.close()
-