Update MANIFEST.in file, and updates to hopefully get coverage/coveralls

working.

MANIFEST.in

 graft examples
 graft src
-graft test
+graft parmed

devtools/travis-ci/runtest.sh

 #!/bin/sh
 set -e
 
+do_coverage() {
+    coverage combine .
+    coverage report -m
+}
+
 echo "Checking parmed source with pyflakes linter"
 if [ "$PYTHON_VERSION" = "pypy" ]; then
     export PYENV_ROOT="${HOME}/.pyenv"
@@ -12,14 +17,16 @@ cd test
 echo "Using nosetests...:"
 ./run_scripts.sh
 if [ "$PYTHON_VERSION" = "pypy" ]; then
-    # Disable coverage with pyflakes, since it multiplies the time taken by 6 or
+    # Disable coverage with pypy, since it multiplies the time taken by 6 or
     # something ridiculous like that
     nosetests -vs --with-timer --timer-ok=5s --timer-warning=12s \
               --timer-filter=warning,error .
 else
-    nosetests -vs --with-timer --timer-ok=5s --timer-warning=12s \
-              --timer-filter=warning,error --with-coverage \
-              --cover-package=parmed .
+    # Run nose under coverage, since that allows getting the full flexibility of
+    # the coverage package without sacrificing nose functionality
+    coverage run --source=parmed --parallel-mode -m \
+        nose -vs --with-timer --timer-ok=5s --timer-warning=12s \
+             --timer-filter=warning,error .
 fi
-test -z `which coverage 2>/dev/null` || coverage report -m
+test -z `which coverage 2>/dev/null` || do_coverage
 test -z `which coveralls` || coveralls

test/.coveragerc

@@ -8,7 +8,3 @@ omit =
     */parmed/utils/netcdf.py
     */parmed/tinker/*
     */parmed/rosetta/*
-
-[report]
-    show_missing = True
-    skip_covered = True

test/run_scripts.sh

@@ -47,11 +47,6 @@ $run_cmd -m parmed.gromacs._cpp -i - < files/pptest1/pptest1.h \
 evaluate_test $? cpptest1
 ###### END TESTS ######
 
-if [ "$has_coverage" = "yes" ]; then
-    coverage combine .coverage*
-    echo "Coverage data combined. Run 'coverage report' to get the report"
-fi
-
 # Clean up if everything passed
 if [ $failures -eq 0 ]; then
     /bin/rm -fr files/writes