Add coverage tests

.coveralls.yml

@@ -0,0 +1,2 @@
+service_name: codeship
+

deployment/codeship_runtests.sh

@@ -1,40 +1,64 @@
 #!/usr/bin/env bash
 
+# this script expects to run from the moldesign/_tests directory
+
+function check_if_tests_should_run(){
+	echo "Should I run the tests in this environment?"
 
-function shouldruntests(){
    if [ "${TESTENV}" == "complete" ]; then
-       echo true
+       runthem=true
+       echo "YES: always run in 'complete' environment"
    fi
 
    case "${CI_BRANCH}" in
        master|deploy|dev)
-       echo true
+       runthem=true
+       echo "YES: always run in branch \"${CI_BRANCH}\""
        ;;
    esac
 
-   if [[ "${CI_COMMIT_MESSAGE}" == *" --testall "* ]];  then
-       echo true
+   if [[ "${CI_COMMIT_MESSAGE}" == *"--testall"* ]];  then
+       runthem=true
+       echo "YES: found \"--testall\" flag in commit message"
    fi
 
-   echo false
+   if [ "${runthem}" != "true" ]; then
+     echo "SKIPPING tests in this environment."
+     echo "To run these tests, add \"--testall\" to your commit message"
+     echo "(or work in the dev or deploy branches)"
+     python ../../deployment/send_test_status.py 0 "Skipped (dev/deploy branches only)"
+     exit 0
+   fi
 }
 
-if [ $(shouldruntests) == false ]; then
-    echo "SKIPPING minimal environment tests for this commit."
-    echo "To run these tests, add \"--testall\" to your commit message"
-    echo "(or work in the dev or deploy branches)"
-    python ../../deployment/send_test_status.py 0 "Skipped (dev/deploy branches only)"
-    exit 0
-else
-    py.test -n 4 --junit-xml=/opt/reports/junit.${TESTENV}.xml | tee /opt/reports/pytest.${TESTENV}.log
-    exitstat=${PIPESTATUS[0]}
 
-    statline="$(tail -n1 /opt/reports/pytest.${TESTENV}.log)"
+function run_tests(){
+	if [ "${TESTENV}" == "complete" ]; then
+	   coverageflags="--cov .. --cov-report=term-missing:/opt/reports/coverage --cov-report="
+	fi
+
+	py.test -n 4 --junit-xml=/opt/reports/junit.${TESTENV}.xml $coverageflags | tee /opt/reports/pytest.${TESTENV}.log
+	exitstat=${PIPESTATUS[0]}
+
+	statline="$(tail -n1 /opt/reports/pytest.${TESTENV}.log)"
 
-    echo 'Test status:'
-    echo ${statline}
+	echo 'Test status:'
+	echo ${statline}
+
+	python ../../deployment/send_test_status.py ${exitstat} "${statline}"
+
+	if [ "${TESTENV}" == "complete" ]; then
+       if [ ${exitstat} -eq 0 ]; then
+          coveralls || echo "Failed to upload code coverage stats"
+       else
+       	  echo "Skipping coveralls upload: tests not passing."
+       	  coverage report
+       fi
+    fi
+
+	exit ${exitstat}
+}
 
-    python ../../deployment/send_test_status.py ${exitstat} "${statline}"
 
-    exit ${exitstat}
-fi
+check_if_tests_should_run
+run_tests

moldesign/_tests/.coveragerc

@@ -0,0 +1,5 @@
+[run]
+omit =
+   ../_notebooks/
+   ../_static_data/
+   ../_tests/