nailed down automated testing and deployment, and fixed test_generic_search_cython

.travis.yml

@@ -5,8 +5,6 @@ install:
 env:
   - TOX_ENV=py26
   - TOX_ENV=py27
-  # Travis no longer supports Python 3.1
-  #  - TOX_ENV=py31
   - TOX_ENV=py32
   - TOX_ENV=py33
 script:

Makefile

@@ -1,27 +1,35 @@
-.PHONY: clean-pyc clean-build docs
+.PHONY: clean clean-pyc clean-build clean-cython lint test test-all coverage docs cython release sdist
 
 help:
 	@echo "clean-build - remove build artifacts"
 	@echo "clean-pyc - remove Python file artifacts"
+	@echo "clean-cython - remove compiled cython files (*.c, *.a, *.o, *.so)"
+	@echo "clean - run all of the above clean commands
 	@echo "lint - check style with flake8"
 	@echo "test - run tests quickly with the default Python"
 	@echo "testall - run tests on every Python version with tox"
 	@echo "coverage - check code coverage quickly with the default Python"
 	@echo "docs - generate Sphinx HTML documentation, including API docs"
+	@echo "cython - compile *.pyx to *.c with cython
 	@echo "release - package and upload a release"
 	@echo "sdist - package"
 
-clean: clean-build clean-pyc
+clean: clean-build clean-pyc clean-cython
 
 clean-build:
 	rm -fr build/
 	rm -fr dist/
 	rm -fr *.egg-info
+	find fuzzysearch -name '*.so' -exec rm -f {} +
 
 clean-pyc:
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
+	find . -type d -name __pycache__ -exec rm -rf {} +
+
+clean-cython:
+	find fuzzysearch -name '*.pyx' | sed -n 's/\(.*\/\)*\([^\/]*\)\.pyx$$/\2/p' | xargs -I {} find . -name {}.a -o -name {}.o -o -name {}.c -o -name {}.so | grep -v '^\./build/' | xargs rm -vf
 
 lint:
 	flake8 fuzzysearch tests
@@ -46,9 +54,14 @@ docs:
 	$(MAKE) -C docs html
 	open docs/_build/html/index.html
 
+fuzzysearch/_generic_search.c: fuzzysearch/_generic_search.pyx
+	cython fuzzysearch/_generic_search.pyx
+
+cython: fuzzysearch/_generic_search.c
+
 release: clean
 	python setup.py sdist upload
 
-sdist: clean
+sdist: clean cython
 	python setup.py sdist
 	ls -l dist

requirements.txt

@@ -1 +0,0 @@
-cython

setup.py

@@ -3,20 +3,27 @@
 
 import os
 import sys
-from Cython.Build import cythonize
 
-try:
+from distutils.core import setup, Extension
-    from setuptools import setup
+
-except ImportError:
-    from distutils.core import setup
 
 if sys.argv[-1] == 'publish':
     os.system('python setup.py sdist upload')
     sys.exit()
 
+os.chdir(os.path.dirname(os.path.abspath(__file__)))
 readme = open('README.rst').read()
 history = open('HISTORY.rst').read().replace('.. :changelog:', '')
 
+_substitutions_only_module = Extension(
+    'fuzzysearch._substitutions_only',
+    sources=['fuzzysearch/_substitutions_only.c'],
+)
+_generic_search_module = Extension(
+    'fuzzysearch._generic_search',
+    sources=['fuzzysearch/_generic_search.c'],
+)
+
 setup(
     name='fuzzysearch',
     version='0.2.2',
@@ -29,7 +36,7 @@ setup(
         'fuzzysearch',
     ],
     package_dir={'fuzzysearch': 'fuzzysearch'},
-    ext_modules=cythonize("fuzzysearch/_generic_search.pyx"),
+    ext_modules=[_substitutions_only_module, _generic_search_module],
     include_package_data=True,
     install_requires=[],
     use_2to3=True,

tests/test_generic_search_cython.py

@@ -3,11 +3,8 @@ from tests.test_levenshtein import TestFindNearMatchesLevenshteinBase
 from fuzzysearch.common import Match, get_best_match_in_group, group_matches
 from tests.test_substitutions_only import TestSubstitionsOnlyBase
 
-import pyximport
-pyimporter, pyximporter = pyximport.install()
 from fuzzysearch._generic_search import \
     find_near_matches_generic_linear_programming as fnm_generic_lp
-pyximport.uninstall(pyimporter, pyximporter)
 
 
 class TestGenericSearchAsLevenshtein(TestFindNearMatchesLevenshteinBase,
@@ -16,8 +13,9 @@ class TestGenericSearchAsLevenshtein(TestFindNearMatchesLevenshteinBase,
         return [
             get_best_match_in_group(group)
             for group in group_matches(
-                fnm_generic_lp(subsequence, sequence, max_l_dist,
+                fnm_generic_lp(subsequence.encode('ascii'),
-                               max_l_dist, max_l_dist, max_l_dist)
+                               sequence.encode('ascii'),
+                               max_l_dist, max_l_dist, max_l_dist, max_l_dist)
             )
         ]
 
@@ -26,15 +24,20 @@ class TestGenericSearchAsSubstitutionsOnly(TestSubstitionsOnlyBase,
                                            unittest.TestCase):
     def search(self, subsequence, sequence, max_subs):
         return list(
-            fnm_generic_lp(subsequence, sequence, max_subs, 0, 0, max_subs)
+            fnm_generic_lp(subsequence.encode('ascii'),
+                           sequence.encode('ascii'),
+                           max_subs, 0, 0, max_subs)
         )
 
 
 class TestGenericSearch(unittest.TestCase):
     def search(self, pattern, sequence, max_subs, max_ins, max_dels,
                max_l_dist=None):
-        return list(fnm_generic_lp(pattern, sequence, max_subs,
+        return list(
-                                   max_ins, max_dels, max_l_dist))
+            fnm_generic_lp(pattern.encode('ascii'),
+                           sequence.encode('ascii'),
+                           max_subs, max_ins, max_dels, max_l_dist)
+        )
 
     def test_empty_sequence(self):
         self.assertEqual([], self.search('PATTERN', '', 0, 0, 0))

tox.ini

@@ -1,42 +1,51 @@
 [tox]
-envlist = py26, py27, py31, py32, py33
+envlist = py26, py27, py32, py33
 
 [testenv]
-commands = python setup.py test
+setenv =
+    CFLAGS=-Qunused-arguments
+    CPPFLAGS=-Qunused-arguments
+changedir = {toxworkdir}
 deps =
     -r{toxinidir}/requirements.txt
     -r{toxinidir}/test_requirements.txt
 whitelist_externals =
     rm
+    cp
     2to3
 
 [testenv:py26]
+setenv =
+    PYTHONPATH = {envtmpdir}
+    {[testenv]setenv}
+commands =
+    cp -r {toxinidir}/tests/ {envtmpdir}/tests/
+    unit2 discover {envtmpdir}/tests -t {envtmpdir}
+    rm -rf {envtmpdir}/tests
 deps =
     unittest2
     mock
     {[testenv]deps}
 
 [testenv:py27]
+setenv =
+    PYTHONPATH = {envtmpdir}
+    {[testenv]setenv}
+commands =
+    cp -r {toxinidir}/tests/ {envtmpdir}/tests/
+    python -m unittest discover {envtmpdir}/tests -t {envtmpdir}
+    rm -rf {envtmpdir}/tests
 deps =
     mock
     {[testenv]deps}
     biopython
 
-[testenv:py31]
-changedir = {toxworkdir}
-commands =
-    2to3 -n -W --output-dir {envtmpdir}/tests3 {toxinidir}/tests
-    {envpython} -m unittest2 discover {envtmpdir}/tests3
-    rm -rf {envtmpdir}/tests3
-deps =
-    unittest2py3k
-    mock
-    {[testenv]deps}
-
 [testenv:py32]
-changedir = {toxworkdir}
+setenv =
+    PYTHONPATH = {envtmpdir}/tests3
+    {[testenv]setenv}
 commands =
-    2to3 -n -W --output-dir {envtmpdir}/tests3 {toxinidir}/tests
+    2to3 -n -W --output-dir {envtmpdir}/tests3/tests {toxinidir}/tests
     {envpython} -m unittest discover {envtmpdir}/tests3
     rm -rf {envtmpdir}/tests3
 deps =
@@ -44,9 +53,11 @@ deps =
     {[testenv]deps}
 
 [testenv:py33]
-changedir = {toxworkdir}
+setenv =
+    PYTHONPATH = {envtmpdir}/tests3
+    {[testenv]setenv}
 commands =
-    2to3 -n -W --output-dir {envtmpdir}/tests3 {toxinidir}/tests
+    2to3 -n -W --output-dir {envtmpdir}/tests3/tests {toxinidir}/tests
     {envpython} -m unittest discover {envtmpdir}/tests3
     rm -rf {envtmpdir}/tests3
 deps =