add python module unittest code

Author: bingmann

.gitignore

@@ -5,3 +5,6 @@ build/
 cmake-build-release
 python/docs/_build
 python/docs/_generate
+*.cobs_cache
+*.cobs_classic
+*.cobs_compact

python/tests/__init__.py

@@ -0,0 +1 @@
+

python/tests/cobs_index_test.py

@@ -0,0 +1,46 @@
+import unittest
+import os
+
+import cobs_index as cobs
+
+mydir = os.path.dirname(os.path.realpath(__file__))
+datadir = os.path.realpath(mydir + "/../../tests/data")
+
+class MainTest(unittest.TestCase):
+    # read a directory containing FastA files
+    def test_doc_list(self):
+        l = cobs.doc_list(datadir + "/fasta")
+        self.assertEqual(l.size(), 7)
+
+    # construct classic index and run queries
+    def test_classic_construct_query(self):
+        index_file = datadir + "/python_test.cobs_classic"
+
+        # construct classic index
+        p = cobs.ClassicIndexParameters()
+        p.clobber = True
+        cobs.classic_construct(
+            input=datadir + "/fasta",
+            out_file=index_file,
+            index_params=p)
+        self.assertTrue(os.path.isfile(index_file))
+
+        # TODO: run queries
+
+    # construct compact index and run queries
+    def test_compact_construct_query(self):
+        index_file = datadir + "/python_test.cobs_compact"
+
+        # construct compact index
+        p = cobs.CompactIndexParameters()
+        p.clobber = True
+        cobs.compact_construct(
+            input=datadir + "/fasta",
+            out_file=index_file,
+            index_params=p)
+        self.assertTrue(os.path.isfile(index_file))
+
+        # TODO: run queries
+
+if __name__ == '__main__':
+    unittest.main()

setup.py

@@ -3,18 +3,17 @@
 import sys
 import platform
 import subprocess
+import unittest
 
 from setuptools import setup, Extension
 from setuptools.command.build_ext import build_ext
 from distutils.version import LooseVersion
 
-
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=''):
         Extension.__init__(self, name, sources=[])
         self.sourcedir = os.path.abspath(sourcedir)
 
-
 class CMakeBuild(build_ext):
     def run(self):
         try:
@@ -56,15 +55,22 @@ def build_extension(self, ext):
         subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
         subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)
 
-setup(
-    name='cobs_index',
-    version='0.1',
-    author='Timo Bingmann',
-    author_email='tbdev@panthema.net',
-    description='Compact Bit-Sliced Signature Index (COBS)',
-    long_description='',
-    url="https://github.com/bingmann/cobs",
-    ext_modules=[CMakeExtension('cobs_index')],
-    cmdclass=dict(build_ext=CMakeBuild),
-    zip_safe=False,
-)
+def test_suite():
+    test_loader = unittest.TestLoader()
+    test_suite = test_loader.discover('python/tests', pattern='*_test.py')
+    return test_suite
+
+if __name__ == '__main__':
+    setup(
+        name='cobs_index',
+        version='0.1',
+        author='Timo Bingmann',
+        author_email='tbdev@panthema.net',
+        description='Compact Bit-Sliced Signature Index (COBS)',
+        long_description='',
+        url="https://github.com/bingmann/cobs",
+        ext_modules=[CMakeExtension('cobs_index')],
+        cmdclass=dict(build_ext=CMakeBuild),
+        zip_safe=False,
+        test_suite='setup.test_suite',
+    )