Merge pull request #37 from broadinstitute/ew-code-coverage

Report code coverage metrics (SCP-1809)

Author: eweitz

.circleci/config.yml

@@ -4,6 +4,9 @@
 #
 version: 2.1
 
+orbs:
+  codecov: codecov/[email protected]
+
 jobs:
   build:
     docker:
@@ -61,9 +64,7 @@ jobs:
             export FIRESTORE_EMULATOR_HOST=localhost:8081
             . venv/bin/activate
             cd tests
-            coverage run -m pytest
-            coverage report --include *scp-ingest-pipeline/ingest*
-            coverage html --include *scp-ingest-pipeline/ingest*
+            pytest --cov-report=xml --cov=../ingest/
 
-      - store_artifacts:
-          path: tests/htmlcov
+      - codecov/upload:
+          file: tests/coverage.xml

README.md

@@ -2,6 +2,7 @@
 File Ingest Pipeline for Single Cell Portal
 
 [![Build status](https://img.shields.io/circleci/build/github/broadinstitute/scp-ingest-pipeline.svg)](https://circleci.com/gh/broadinstitute/scp-ingest-pipeline)
+[![Code coverage](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline/branch/master/graph/badge.svg)](https://codecov.io/gh/broadinstitute/scp-ingest-pipeline)
 
 The SCP Ingest Pipeline is an ETL pipeline for single-cell RNA-seq data.