diff --git a/.coveragerc b/.coveragerc
index 14a1acac..5d00ff08 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,6 +1,8 @@
 [run]
+data_file = .coverage2
 
 omit =
+    setup.py
     /usr/*
     tests/*
 
@@ -8,3 +10,6 @@ omit =
 exclude_lines =
     pragma: no cover
     no cover: 2.x
+
+[html]
+directory = htmlcov/py2
diff --git a/.coveragerc3 b/.coveragerc3
index 7d4bec13..e7f85d37 100644
--- a/.coveragerc3
+++ b/.coveragerc3
@@ -1,8 +1,10 @@
 [run]
+data_file = .coverage3
 
 ; extra omissions for py3 for now
 
 omit =
+    setup.py
     /usr/*
     tests/*
 
@@ -11,3 +13,6 @@ exclude_lines =
     pragma: no cover
     no cover 3.x
     if six.PY2
+
+[html]
+directory = htmlcov/py3
diff --git a/.gitignore b/.gitignore
index dbcbef60..59b5da0f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@ util/koji-shadowc
 #
 # coverage artifacts
 .coverage
+.coverage[23]
 htmlcov/
 *,cover
 #
diff --git a/Makefile b/Makefile
index 83787694..4cfac743 100644
--- a/Makefile
+++ b/Makefile
@@ -61,29 +61,39 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~ koji*.bz2 koji*.src.rpm
+	rm -rf __pycache__
+	rm -rf devtools/fakehubc devtools/fakewebc devtools/__pycache__
 	rm -rf koji-$(VERSION)
 	for d in $(SUBDIRS); do make -s -C $$d clean; done
-	coverage erase ||:
+	find ./tests -name "__pycache__" -exec rm -rf {} \; ||:
+	find ./tests -name "*.pyc" -exec rm -f {} \;
+	rm -rf docs/source/__pycache__ docs/source/*.pyc
+	coverage2 erase ||:
+	coverage3 erase --rcfile .coveragerc3 ||:
+	rm -rf htmlcov
 
 git-clean:
 	@git clean -d -q -x
 
-test:
+test: test2 test3
+	@echo "All tests are finished for python 2&3"
+
+test2:
 	coverage2 erase
 	PYTHONPATH=hub/.:plugins/hub/.:plugins/builder/.:plugins/cli/.:cli/.:www/lib coverage2 run \
 	    --source . /usr/bin/nosetests
 	coverage2 report
 	coverage2 html
-	@echo Full coverage report at file://$(CURDIR)/htmlcov/index.html
+	@echo Full coverage report at file://${CURDIR}/htmlcov/py2/index.html
 
 test3:
-	coverage3 erase
+	coverage3 erase --rcfile .coveragerc3
 	PYTHONPATH=hub/.:plugins/hub/.:plugins/builder/.:plugins/cli/.:cli/.:www/lib coverage3 run \
 	    --rcfile .coveragerc3 --source . \
 	    /usr/bin/nosetests-3
-	coverage3 report --rcfile .coveragerc3
-	coverage3 html --rcfile .coveragerc3
-	@echo Full coverage report at file://$(CURDIR)/htmlcov/index.html
+	coverage report --rcfile .coveragerc3
+	coverage html --rcfile .coveragerc3
+	@echo Full coverage report at file://${CURDIR}/htmlcov/py3/index.html
 
 test-tarball:
 	@rm -rf .koji-$(VERSION)
diff --git a/builder/Makefile b/builder/Makefile
index da56c47f..9d16298f 100644
--- a/builder/Makefile
+++ b/builder/Makefile
@@ -8,6 +8,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~ kojidc
+	rm -rf __pycache__
 
 
 _install:
diff --git a/cli/Makefile b/cli/Makefile
index 605c9eac..d5cca841 100644
--- a/cli/Makefile
+++ b/cli/Makefile
@@ -13,6 +13,8 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~ kojic
+	rm -rf __pycache__
+	for d in $(SUBDIRS); do make -s -C $$d clean; done
 
 install:
 	@if [ "$(DESTDIR)" = "" ]; then \
diff --git a/cli/koji_cli/Makefile b/cli/koji_cli/Makefile
index baf78d37..c7c460a9 100644
--- a/cli/koji_cli/Makefile
+++ b/cli/koji_cli/Makefile
@@ -11,6 +11,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~
+	rm -rf __pycache__
 
 install:
 	@if [ "$(DESTDIR)" = "" ]; then \
diff --git a/hub/Makefile b/hub/Makefile
index 59e0f9f6..e8fe6517 100644
--- a/hub/Makefile
+++ b/hub/Makefile
@@ -13,6 +13,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~
+	rm -rf __pycache__
 
 install:
 	@if [ "$(DESTDIR)" = "" ]; then \
diff --git a/koji/Makefile b/koji/Makefile
index 7a3925a7..df2991c7 100644
--- a/koji/Makefile
+++ b/koji/Makefile
@@ -12,7 +12,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~
-	for d in $(SUBDIRS); do make -s -C $$d clean; done
+	rm -rf __pycache__
 
 install:
 	mkdir -p $(DESTDIR)/$(PKGDIR)
diff --git a/plugins/Makefile b/plugins/Makefile
index 500d944f..690e5c36 100644
--- a/plugins/Makefile
+++ b/plugins/Makefile
@@ -21,7 +21,8 @@ _default:
 	@echo "nothing to make.  try make install"
 
 clean:
-	rm -f *.o *.so *.pyc *.pyo *~
+	find . -name "__pycache__" -exec rm -rf {} \; ||:
+	find . -name "*.pyc" -exec rm -f {} \;
 
 install:
 	@if [ "$(DESTDIR)" = "" ]; then \
diff --git a/util/Makefile b/util/Makefile
index 3310b513..bcaddc90 100644
--- a/util/Makefile
+++ b/util/Makefile
@@ -7,6 +7,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~
+	rm -rf __pycache__
 	for b in $(BINFILES); do rm -f $${b}c; done
 
 _install:
diff --git a/www/kojiweb/Makefile b/www/kojiweb/Makefile
index 4feda333..214a88a5 100644
--- a/www/kojiweb/Makefile
+++ b/www/kojiweb/Makefile
@@ -8,6 +8,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~
+	rm -rf __pycache__
 	for d in $(SUBDIRS); do make -s -C $$d clean; done
 
 install:
diff --git a/www/lib/kojiweb/Makefile b/www/lib/kojiweb/Makefile
index 84e8b033..e23fb4db 100644
--- a/www/lib/kojiweb/Makefile
+++ b/www/lib/kojiweb/Makefile
@@ -13,6 +13,7 @@ _default:
 
 clean:
 	rm -f *.o *.so *.pyc *~
+	rm -rf __pycache__
 	for d in $(SUBDIRS); do make -s -C $$d clean; done
 
 install: