From d7e619b72a20acec686305593227597e3e4a7b0f Mon Sep 17 00:00:00 2001
From: Aaron Virshup <avirshup@gmail.com>
Date: Tue, 28 Nov 2017 23:22:11 -0800
Subject: [PATCH] Combine coverage from all environments

---
 .coveragerc                     |  2 +-
 codeship-services.yml           |  8 ++++++++
 codeship-steps.yml              | 22 ++++++++--------------
 deployment/build-env.dockerfile |  5 +++--
 deployment/push-coverage.sh     | 11 +++++++++++
 deployment/run-ci-tests.sh      | 23 +++++++++--------------
 6 files changed, 40 insertions(+), 31 deletions(-)
 create mode 100755 deployment/push-coverage.sh

diff --git a/.coveragerc b/.coveragerc
index 2d586d5..f5572e2 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,7 +1,7 @@
 [paths]
 source =
   moldesign
-
+  */moldesign
 
 [run]
 source = moldesign
diff --git a/codeship-services.yml b/codeship-services.yml
index 719f777..dc731cd 100644
--- a/codeship-services.yml
+++ b/codeship-services.yml
@@ -9,6 +9,14 @@ image_builder: &build-base
     REPO: "docker.io/autodesk/moldesign:"
 
 
+coverage_pusher:
+   <<: *build-base
+   cached: false
+   encrypted_env_file: ./deployment/test-tokens.crypt
+   volumes:
+    - ./tmp/reports:/opt/reports
+
+
 publisher:
    <<: *build-base
    cached: false
diff --git a/codeship-steps.yml b/codeship-steps.yml
index 7eec4b4..7bac42a 100644
--- a/codeship-steps.yml
+++ b/codeship-steps.yml
@@ -66,19 +66,7 @@
           command: deployment/push-and-tag.sh moldesign_notebook
 
 
-# Prints out internal information about the test environments
-- name: print-environments
-  type: parallel
-  services:
-    - test_moldesign_complete
-    - test_moldesign_complete_py2
-    - test_moldesign_minimal
-    - test_moldesign_minimal_py2
-  steps:
-   - command: deployment/print-environment.sh
-     name: env-report
-
-# Run the tests in each environment.
+# Run the tests in each environment
 - name: run-tests
   type: serial
   services:
@@ -87,10 +75,16 @@
    - test_moldesign_minimal_py2
    - test_moldesign_minimal
   steps:
+   - command: deployment/print-environment.sh
+     name: environment
    - command: deployment/run-ci-tests.sh
-     name: testrunner
+     name: tests
 
 
+# Upload coverage results
+- name: push-coverage
+  service: coverage_pusher
+  command: deployment/push-coverage.sh
 
 
 # If this build is tagged with a PEP440-compliant version number AND the tests have passed,
diff --git a/deployment/build-env.dockerfile b/deployment/build-env.dockerfile
index 9f0a20f..467efb0 100644
--- a/deployment/build-env.dockerfile
+++ b/deployment/build-env.dockerfile
@@ -10,6 +10,7 @@ RUN curl -fsSLO https://get.docker.com/builds/Linux/x86_64/docker-17.04.0-ce.tgz
   && mv docker/docker /usr/local/bin \
   && rm -r docker docker-17.04.0-ce.tgz
 
-ADD . /opt/molecular-design-toolkit
-RUN pip install -r /opt/molecular-design-toolkit/DockerMakefiles/requirements.txt
+ADD ./DockerMakefiles/requirements.txt /tmp/reqs.txt
+RUN pip install -r /tmp/reqs.txt && pip install coveralls
 
+ADD . /opt/molecular-design-toolkit
diff --git a/deployment/push-coverage.sh b/deployment/push-coverage.sh
new file mode 100755
index 0000000..05de8e8
--- /dev/null
+++ b/deployment/push-coverage.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+# combines coverage from all test environments and pushes it to coveralls.io
+
+set -e
+
+mkdir -p /opt/reports/env-coverage
+cp /opt/reports/env-coverage/coverage.* /opt/reports/
+
+coverage combine /opt/reports/coverage.*              \
+  && coveralls                                        \
+  || echo "Failed to upload coverage to coveralls.io"
\ No newline at end of file
diff --git a/deployment/run-ci-tests.sh b/deployment/run-ci-tests.sh
index e0c8cb3..33f7fd4 100755
--- a/deployment/run-ci-tests.sh
+++ b/deployment/run-ci-tests.sh
@@ -19,10 +19,9 @@ install_location=$(python -c "import moldesign, os; print(moldesign.__path__[0])
 test_location=$(dirname "${install_location}")
 
 VERSION="${TESTENV}.py${PYVERSION}"
-PYTESTFLAGS="moldesign/_tests/ -n 2 --spec  --durations=20 --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=3600 --tb=short"
-if [ "${VERSION}" == "complete.py3" ]; then
-       PYTESTFLAGS="${PYTESTFLAGS} --cov moldesign --cov-config /opt/molecular-design-toolkit/.coveragerc"
-fi
+PYTESTFLAGS="moldesign/_tests/ -n 2 --spec  --durations=20
+        --junit-xml=/opt/reports/junit.${VERSION}.xml --timeout=3600 --tb=short
+        --cov moldesign --cov-config /opt/molecular-design-toolkit/.coveragerc"
 
 
 function send_status_update(){
@@ -78,29 +77,25 @@ function run_tests(){
     send_status_update "na" "Starting tests for ${VERSION}"
     cd ${test_location}
 
+
     echo
     echo "Test command running in working dir '$(pwd)':"
     echo "py.test ${PYTESTFLAGS}"
     echo
 
-    py.test ${PYTESTFLAGS} | tee /opt/reports/pytest.${VERSION}.log
+    py.test ${PYTESTFLAGS} -k test_bond_alignment_on_axis | tee /opt/reports/pytest.${VERSION}.log
     exitstat=${PIPESTATUS[0]}
-
     statline="$(tail -n1 /opt/reports/pytest.${VERSION}.log)"
 
+    # Make a copy of the coverage report
+    mkdir -p /opt/reports/env-coverage/
+    cp .coverage /opt/reports/env-coverage/coverage.${VERSION}
+
     echo 'Test status:'
     echo ${statline}
 
     send_status_update "${exitstat}" "${statline}"
 
-    if [ "${VERSION}" == "complete.py3" ]; then
-       if [[ ${exitstat} == 0 && "$CI_BRANCH" != "" ]]; then
-          coveralls || echo "Failed to upload code coverage stats"
-       else
-          echo "Skipping coveralls upload: tests not passing or \$CI_COMMIT not set."
-       fi
-    fi
-
     exit ${exitstat}
 }